tag:blogger.com,1999:blog-33781999950755093982024-03-05T00:04:44.733-05:00Molecular Evolution ForumIntroduction of notable papers and booksIMEGhttp://www.blogger.com/profile/03091807894936657414noreply@blogger.comBlogger31125tag:blogger.com,1999:blog-3378199995075509398.post-83539619755112150662014-03-14T15:30:00.000-04:002014-03-14T16:57:15.058-04:00Horizontal Gene Transfer Takes a Turn: Expansins from Plants to their Bacterial and Eukaryotic Parasites<b><span style="font-family: Times, "Times New Roman", serif; font-size:12pt;">Contributed by: </span><a href="mailto:chalkiad@email.chop.edu" target="_blank"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Dimitra Chalkia</span></a></b><br />
<b><br /><span style="font-family: Times, "Times New Roman", serif;"></span></b>
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;"></span><br />
<div style="line-height: 200%; margin: 0in 0in 0pt; mso-add-space: auto; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Genetic material is inherited from parents
to offspring and this process is known as vertical transmission. However
genetic material can be transferred form one organism to another in a non-genealogical
fashion. Such type of transmission is defined as horizontal transmission or gene
transfer (HGT) <a href="#t1">(1)</a>. Although mechanisms for the transfer of genetic material
between organisms were known from the early years of molecular biology and
genetics research, and the theoretical potential of cross-species gene transfer
in evolution was proposed in the 1980s, the concept of HGT emerged in the 1990s
<a href="#t2">(2)</a>. It was invoked as an alternative explanation for rarely observed incongruent
phylogenetic relationships between species <a href="#t2">(2)</a>. However, the recent
availability of genome sequence information and the thorough study of multiple pro-
and eukaryotic genomes has revealed that HGT is pervasive and powerful among
microbes (<a href="#t1">1</a>,<a href="#t2">2</a>,<a href="#t3">3</a>). Additionally, more recent studies have shown that HGT is also
evident between animals and bacteria, with the bacteria being the donor species
(<a href="#t4">4</a>,<a href="#t5">5</a>). In plants, HGT has been relatively well documented, and in most cases
involves the transfer of genetic material from a parasite to its host plant. Yet,
HGTs with the plant species being the donor have rarely been documented. </span></div>
<br />
<div style="line-height: 200%; margin: 0in 0in 0pt; mso-add-space: auto; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Recently Nikolaidis et al <a href="#t6">(6)</a> reported a
rare case of HGT from plants to multiple plant parasites or free living microorganisms.
Specifically, they found that members of the plant expansin gene family, which
code for plant cell-wall loosening proteins and are comprised of two distinct
protein domains D1 and D2, were transferred from plants to bacteria, fungi, and
unicellular eukaryotes (amoebozoa).</span></div>
<br />
<div style="line-height: 200%; margin: 0in 0in 10pt; mso-add-space: auto; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Having previously established that the
bacterial protein EXLX1 from <i style="mso-bidi-font-style: normal;">Bacillus subtilis</i>
is structurally and functionally very similar to plant expansins (<a href="#t7">7</a>,<a href="#t8">8</a>,<a href="#t9">9</a>),
Nikolaidis et al investigated the evolution of the expansin family in-depth. To
do so they used the bacterial EXLX1 sequence as their primary-sequence database
interrogator. <span style="mso-spacerun: yes;"> </span>Like expansins, EXLX1
protein contains two domains, D1 and D2, which are tightly packed structurally
with a conserved open surface spanning both of them (Figure 1a,b). To ensure
that the resulted raw sequence alignments of their exhaustive similarity
searches are not random hits, the authors employed a set of established strict search
criteria. <span style="mso-spacerun: yes;"> </span>Remarkably, they identified numerous
sequences from bacteria, fungi, and amoebozoa that align to both EXLX1 domains
and therefore may share ancestry with it. If so, the identified sequences are EXLX1
homologs. By employing proven phylogenetic tools and methods, as well as
protein domain and fold recognition programs, the authors confirmed that all
identified proteins contain both expansin domains, and showed that the
predicted protein structures are very similar to both <i style="mso-bidi-font-style: normal;">B. subtilis</i> EXLX1 and plant expansins, further supporting the homology
inference (Figures 1 and 2).</span></div>
<br />
<span id="goog_240169772"></span><span id="goog_240169773"><br /></span>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuSc6bR9svQR4g-zOk7q8Nh9sUf-NLhFfIoG3orMMvMQ4WmO3LxmRvnrNQY7pJA35dAyoLSMeSPvvZetfiTObKaQ8WPApAX7adSSDesVhh-ItcZ7lSB0mpmZtOy9aWD6hS8KLvK5J0jJY/s1600/Fig2+Chalkia.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuSc6bR9svQR4g-zOk7q8Nh9sUf-NLhFfIoG3orMMvMQ4WmO3LxmRvnrNQY7pJA35dAyoLSMeSPvvZetfiTObKaQ8WPApAX7adSSDesVhh-ItcZ7lSB0mpmZtOy9aWD6hS8KLvK5J0jJY/s1600/Fig2+Chalkia.jpg" height="640" width="484" /></a></td></tr>
<tr align="left"><td class="tr-caption"><b>Figure 1</b>. The EXLX1 homologs
are predicted to contain two domains, fold similarly to the <i style="mso-bidi-font-style: normal;">Zea mays</i> EXPB1 (a) and the <i style="mso-bidi-font-style: normal;">B. subtilis</i> EXLX1 (b), and contain a
conserved long hydrophobic surface. (c, d) structural alignments of the
three-dimensional models of the EXLX1 homologs from <i style="mso-bidi-font-style: normal;">Ralstonia</i> and <i style="mso-bidi-font-style: normal;">Erwinia</i>
with the EXLX1structure. Surface (e) and ribbon (f) representations of the
EXLX1 structure are colored according to conservation in 70 EXP domain
sequences from bacteria and fungi (blue to red with increasing
conservation). From Nikolaidis et al. (2014) <a href="#t6">(6)</a>.</td></tr>
</tbody></table>
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-nFulTAK3vI9eY17kCl0-kbDwUKudd0UtQKR0xkw1INNkIrCGOX7XDDTYsQaU_0JPN4YXSX_PVWZFWh75Q6NgSfu8fyzWbafoXJVA85RWwdVCiBMqxW0mhAFYbiijqDnApgtKcASgdGg/s1600/Fig1+Chalkia.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-nFulTAK3vI9eY17kCl0-kbDwUKudd0UtQKR0xkw1INNkIrCGOX7XDDTYsQaU_0JPN4YXSX_PVWZFWh75Q6NgSfu8fyzWbafoXJVA85RWwdVCiBMqxW0mhAFYbiijqDnApgtKcASgdGg/s1600/Fig1+Chalkia.jpg" height="640" width="496" /></a></td></tr>
<tr align="left"><td class="tr-caption"><b style="mso-bidi-font-weight: normal;">Figure 2.</b> The <i>Bacillus subtilis </i>EXLX1protein has many
homologs in bacteria, fungi, and amoebozoa. (<i>a</i>) Phylogenetic
relationships of representative <i>B. subtilis</i>EXLX1 homologs. Two
different phylogenetic methods (NJ and ML) were used with gamma-distributed
distances from the WAG substitution model with <i>α</i> = 1.72.
Alignment gaps were excluded and the total number of sites used to construct
the trees was 176. The numbers at the nodes are bootstrap values (NJ/ML). The
biology of each species is shown with different symbols next to the species
name. Species names abbreviations are given in supplementary table S1, Supplementary
Material online. Only sequences producing BLAST hits with E-values lower
than 10<sup>−4</sup> and query coverage higher than 80% were used for the
construction of these trees (<i>b</i>). Many EXLX1homologs contain additional
domains. The domain organization of the EXLX1 homologs was identified using the
Conserved Domains Database (CDD) database from NCBI coupled to fold recognition
analysis. We define as expansin the domain that contains both D1 and D2 domains
according to the EXLX1structure (Kerff et al. 2008; Georgelis et al. 2013).
From Nikolaidis et al. (2014) <a href="#t6">(6)</a>.</td></tr>
</tbody></table>
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<span style="font-family: Times, "Times New Roman", serif;"></span><br /></div>
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<br />
<div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">However, sequence similarity is not sufficient for
showing the genetic-material-transmission type—vertical or horizontal. Five significant
observations led the authors to support the HGT type: a) the sporadic
distribution of organisms harboring expansin homologs, b) the biological
features of these organisms –plant pathogens, soil inhabitants, or cellulose
producers, c) the incongruence between the phylogenetic tree derived from EXLX1
and its homologs and the established bacterial or fungal species tree, d) the
fusion of additional and shared protein domains (cellulase GH5 or
carbohydrate-binding modules) in several EXLX1 homologs, and e) the functional
similarities between microbial and plant expansins, especially the lack of
catalytic activity. The latter observation argues against convergence (independent
fusion of D1 and D2 domains) because such a scenario would require the biochemically
and evolutionarily improbable independent loss and gain of the same amino acid
residues in multiple distant phyla. </span></div>
<span style="font-family: Calibri;"><span style="font-family: Times, "Times New Roman", serif;">
</span></span>
<br />
<div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Calibri;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Relaxing the criteria of their sequence similarity
searches, the authors also examined whether sequences similar to each one of
the two expansin domains exist. Their results were positive for both domains. Applying
their phylogenetic/protein fold recognition methodology to the sequences
similar only to the second expansin domain (D2), the authors showed that the
fungal swollenin protein family is homologous to expansins. Swollenin proteins
are composed of two domains, too. Interestingly, although their N-terminal D1
domain contains many conserved insertions and therefore bears very low similarity
with the expansin D1 domain, the folding patterns are very similar.</span></span></div>
<span style="font-family: Calibri;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">
</span></span><br />
<div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Calibri;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Regarding the timing of the expansin HGT, the lack of
any differences in parametric measures such as GC-content, amino acid or
nucleotide usage, etc., in the EXLX1 homologs allowed the authors to conclude
it was not recent. Two additional observations augmented this conclusion.
First, the phylogenetic patterns revealed that the HGT of expansins was
followed by vertical transfers during certain fungal or amoebozoan species
evolution. Second, several bacterial and fungal distant species contain
expansin genes fused with cellulose GH5 and carbohydrate-binding domains,
respectively. According to the authors’ phylogenetic analysis these extra
domains were most likely acquired independently by convergence. Therefore the
HGT of expansins from plants to other organisms preceded the long-lasting and
slow events of convergence and speciation. Hence it must be ancient.</span></span></div>
<span style="font-family: Calibri;">
<span style="font-family: Times, "Times New Roman", serif;">
</span></span><br />
<div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Calibri;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Regarding the origin of the expansin gene family, the
authors, following a <i style="mso-bidi-font-style: normal;">reductio ad absurdum</i>
argumentation, favor the scenario of a single origin in the common ancestor of
plants and subsequent horizontal transmission to non-plant species. The patchy distribution
of EXLX1 homologs in a small percentage of the tested bacterial (128/4,281 or
3%) and fungal (28 /543 or 5.2%) genomes argues against a single origin in
bacteria and subsequent vertical transmission, since such a scenario demands
the absurd assumption of multiple independent gene losses.<span style="mso-spacerun: yes;"> </span>Additionally, the authors’ previously
reported functional similarities between plant and microbial expansins (<a href="#t8">8</a>,<a href="#t9">9</a>) argues
against convergence, and therefore augments the single origin scenario. </span></span></div>
<span style="font-family: Calibri;">
<span style="font-family: Times, "Times New Roman", serif;">
</span><br /><div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Nikolaidis et al., offer a long list of logical and
tightly woven arguments for the HGT scenario of non-plant expansins. However <span style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">they do admit
the difficulty of proving it b</span><span style="line-height: 200%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">eyond
reasonable doubt. Another task—yet harder in the case of expansins—is to </span>determine
precisely the donor and recipient species, as well as its mechanism and timing.
As more genomes are being sequenced we will probably be able to define at least
a plant lineage that contributed its expansins to its intimately associated parasites.
If so, then investigation for the potential mechanisms of HGT will be somehow
eased.<span style="mso-spacerun: yes;"> </span>A current plausible such
mechanism includes a plasmid-mediated transfer <a href="#t10">(10)</a>. </span></div>
<span style="font-family: Times, "Times New Roman", serif;">
</span><br /><div style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">Besides the mechanism and timing of expansins’ HGT,
their adaptive significance for the recipient species is of essence. Experimental
studies on the physiological role of non-plant expansins have started to shed
light on this topic. The authors report several such studies and propose that the
HGT of expansin proteins in plant-interacting microbes contributed new or
alternative tools for colonization or infection. The latter hypothesis implies
an adaptive advantage for the plant-infecting organisms and together with the
results of other reports on the role of HGT to the emergence of new diseases
suggests that the observed rarity of HGT is not indicative of its importance in
organismal evolution. </span><br />
<span style="font-family: Times, "Times New Roman", serif;"><br /></span>
<span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">
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<div class="MsoNormal" style="line-height: 200%; margin: 0in 0.5in 12pt;text-indent: 0in;">
<style="mso-bidi-font-weight: normal;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">
<b>Abstract of the original paper</b>
<br />
<div style="line-height: 200%;text-indent: 0in;">
Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbial–plant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.
</div>
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">References</span></b></div>
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<div id = "t10" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: Times New Roman;"><span style="font-family: Times, "Times New Roman", serif;font-size:12pt;">10.
Laine MJ, Haapalainen M, Wahlroos T, Kankare K, Nissinen R, et al. 2000. </span><a href="http://www.sciencedirect.com/science/article/pii/S0885576500903011" target="_blank"><span style="font-family: Times, "Times New Roman" serif;font-size:12pt;">Thecellulase encoded by the native plasmid of <i>Clavibacter michiganensis</i> ssp. <i>sepedonicus</i> plays a role in virulence and contains an expansin-like domain.</span></a><span style="font-family: Times, "Times New Roman"font-size:12pt;"> <i style="mso-bidi-font-style: normal; font-size:12pt;">Physiol Mol Plant
Pathol</i> 57, 221–233</span></span></div>
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<span style="font-family: Calibri;"><br /></span></div>
<br />Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-62411339632844368442014-02-21T16:19:00.000-05:002014-02-21T16:19:16.262-05:00Evolution of a Behavioral Character in a Sparrow Species<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt"> Although
the mutational study of behavioral characters was initiated by Seymour Benzer
in the 1960’s, his study was concerned primarily with laboratory mutations of fruitflies
and did not give much insight into the evolutionary mechanisms of behavioral
characters in the wild. For this reason, many authors are now investigating
this problem at the molecular level. Horton et al. (2014) recently published an
interesting result with respect to the social behavior in the white-throated
sparrow <i>Zonotrichia albicollis</i>. </span></div>
<span style="font-family: Times, Times New Roman, serif;font-size:12pt"><br /></span>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">In the
white-throated sparrow there are two polymorphic phenotypes with respect to the
color pattern of the head crown: (1) tan-striped (<i>TS</i>) and (2) white-striped (<i>WS</i>)
(Fig. 1). The male <i>WS</i> phenotype is
known to be more aggressive than the male <i>TS</i>
with respect to territoriality and mate-finding. In song-birds, these behaviors
are typically dependent on sex steroid during the breeding season. <i>WS</i> birds have higher plasma testosterone
than the same sex <i>TS</i> birds. However, morph
differences in behavior cannot be entirely explained by these hormones, because
the differences persist even when plasma levels are experimentally equalized. Therefore,
individual variation in steroid-dependent behavior may be better explained by
neural sensitivity to the hormones, for example by variation in the
distribution and abundance of steroid receptors (Horton et al., 2014).</span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0O9GN7khJDM_GBmnLiJ98rK6MoF1Y_mhDsFQxvWMDMhyAho9Fnfw67BuCunhfjZtC-RYAQoB-yBUGHeaXox1QnUDV7mR1tOTHcztE9uHbTBzqUTRnsKdC_jtTuENIem53vXSA-lLuYX4/s1600/Fig1+sparrow.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Times, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0O9GN7khJDM_GBmnLiJ98rK6MoF1Y_mhDsFQxvWMDMhyAho9Fnfw67BuCunhfjZtC-RYAQoB-yBUGHeaXox1QnUDV7mR1tOTHcztE9uHbTBzqUTRnsKdC_jtTuENIem53vXSA-lLuYX4/s1600/Fig1+sparrow.jpg" height="223" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: left;"><span style="font-family: Times, Times New Roman, serif;"> From Horton et al. (2014).</span></td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;"><br /></span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">By the way, the <i>WS</i> and <i>TS</i> are associated with two inversion haplotypes of chromosome 2
(Thomas et al. 2008). That is, the genes controlling <i>WS</i> and <i>TS</i> are apparently located
in the inverted segment of haplotypes <i>ZAL2<sup>m</sup></i>
and <i>ZAL2</i>. However, because <i>WS</i> is dominant over <i>TS</i> and the frequency of <i>ZAL2<sup>m</sup></i>
is relatively low, individuals can roughly be divided into two groups, <i>WS</i> (<i>ZAL2<sup>m</sup></i>/<i>ZAL2</i>,) and <i>TS</i> (<i>ZAL2</i>/<i>ZAL2</i>), genotype <i>ZAL2<sup>m</sup></i>/<i>ZAL2<sup>m</sup></i>,
being practically absent. It has also been inferred that <i>ZAL2<sup>m</sup> </i>was derived from <i>ZAL2 </i>about 2 million years ago by chromosomal inversion and therefore
the polymorphism has existed for a long time. Note also that there is practically
no recombination between two inverted chromosomes. </span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
</div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">Horton et al.
(2014) looked for steroid receptor genes in the inverted segment and found that
the gene (<i>ESR1</i>) encoding estrogen
receptor α (<i>ER</i><i>α</i>) is located in the
inverted segment and that the two proteins encoded by the <i>ESR1</i> genes from the <i>WS</i>
and <i>TS</i> phenotypes showed one amino
acid difference but this difference did not affect the gene expression pattern appreciably.
They then hypothesized that the phenotypic difference between <i>WS</i> and <i>TS</i> is caused by the difference in the gene regulatory region of the
gene. In fact, when the binding sites of transcription factors in the <i>cis</i>-regulatory region upstream of the <i>ESR1</i> gene were examined by a computer
program, there was considerable difference between the <i>WS</i> and <i>TS</i> haplotypes
(Fig. 2A).</span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgY-p9ywsQqFecIMUSUVyDUrpJ9ZIt6aS5O5o7wk1FcQgjyFpslt0O8ZmvZyKmcmtnWKSeRQx46cFMFXiyU9RRVlWoxS8BpuzXVQ1JgGnmgjRKDLxzNMhEVqW5AaHiwyKFcyaC1QLPxd3E/s1600/Fig2+transcription.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Times, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgY-p9ywsQqFecIMUSUVyDUrpJ9ZIt6aS5O5o7wk1FcQgjyFpslt0O8ZmvZyKmcmtnWKSeRQx46cFMFXiyU9RRVlWoxS8BpuzXVQ1JgGnmgjRKDLxzNMhEVqW5AaHiwyKFcyaC1QLPxd3E/s1600/Fig2+transcription.jpg" height="640" width="473" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: left;"><span style="font-family: Times, Times New Roman, serif;"> From Horton et al. (2014).</span></td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;"><br /></span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">However, to prove
that this difference is indeed responsible for the behavioral difference, it
was necessary to show that the expression level of the <i>ESR1</i> gene is higher in haplotype <i>ZAL2<sup>m</sup></i> than in <i>ZAL2</i>.
For this purpose, Horton et al. used several molecular techniques such as the
luciferase reporter method with HeLa cells and radioimmunoassay. Their results showed
that the expression level of the <i>ESR1</i>
gene is about 1.5 times higher in haplotype <i>ZAL2<sup>m</sup></i>
than in <i>ZAL2 </i>(Fig. 2B,C).</span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">This finding
indicates that the difference in expression level of a single major gene
generates a clear phenotypic difference, which in turn affects an important
behavioral character. At the present time, this type of data is rare, but it is
possible that many behavioral characters are controlled by similar molecular
mechanisms, and it is desirable that more studies will be conducted in the
future. In practice, behavioral characters are generally controlled by many
genes, and eventually we may be able to understand the molecular basis of the characters.
Yet, the basic principle of gene expression could be simpler than our intuition
suggests as in the case of the above example. In their “significance”
statement, Horton et al. write:</span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt"><br /></span></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: .5in; margin-top: 0in;">
<table align="center" border="0" style="height: 251px;" table="">
<tbody>
<tr>
<td bgcolor="#A9D0F5"><div align="left">
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0.5in 10pt;font-family: Times, Times New Roman, serif;font-size:12pt">
<span style="background-color: #A9D0F5; font-family: Times, Times New Roman, serif;font-size:12pt">In this series of
studies, we provide a rare illustration of how a chromosomal polymorphism has
affected overt social behavior in a vertebrate. White-throated sparrows occur
in two alternative phenotypes, or morphs, distinguished by a chromosomal
rearrangement. That the morphs differ in territorial and parental behavior has
been known for decades, but how the rearrangement affects behavior is not understood.
Here we show that genetic differentiation between the morphs affects the
transcription of a gene well known to be involved in social behavior. We then
show that in a free-living population, the neural expression of this gene
predicts both territorial and parental behavior. We hypothesize that this
mechanism has played a causal role in the evolution of alternative life-history
strategies.</span></div></td></tr>
</tbody></table></div></div>
<div class="MsoNormal" style="line-height: 200%; margin-right: .5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt"><br /></span></div>
<div class="MsoNormal" style="line-height: 200%; margin-right: .5in;">
<b><span style="font-family: Times, Times New Roman, serif;font-size:12pt">References<o:p></o:p></span></b></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: .5in; margin-top: 0in; text-indent: -.5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">1.
Thomas J.W. et al. (2008). <a href="http://www.ncbi.nlm.nih.gov/pubmed/18562641" target="_blank">The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (<i>Zonotrichia albicollis</i>) is a complex rearrangement and suppressor of recombination.</a> <i>Genetics. </i>179(3):1455–1468.</span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
</div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: .5in; margin-top: 0in; text-indent: -.5in;">
<span style="font-family: Times, Times New Roman, serif;font-size:12pt">2. Horton,
B. M., Hudson, W. H., Ortlund, E. A., Shirk, S., Thomas, J. W., Young, E. R.,
Zinzow-Kramer, W. M., & D. L. Maney. (2014). <a href="http://www.pnas.org/content/111/4/1443.abstract" target="_blank">Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes</a>. <i>Proc. Nat. Acad. Sci. USA. </i>111(4):1443-1448.</span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<br /></div>Masatoshi Neihttp://www.blogger.com/profile/15706545477678186676noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-21238285764643943522014-02-05T16:36:00.002-05:002014-02-06T15:23:56.188-05:00Symbiosis and Genome Degeneration: Micro-niche Evolution<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif;font-size: 12pt"> Symbiotic
association of bacteria with animals and plants are ubiquitous, and about 15%
of insect species have been estimated to harbor bacterial species as symbionts
(Oakeson et al. 2014). These bacterial symbionts generally have reduced genome
size compared with ancestral free-living bacteria (McCutcheon and Moran 2011). However,
these symbionts produce nutrients that are essential for survival of the host,
and therefore a mutualistic symbiosis is generated. In many of these bacteria,
the initiation of symbiosis occurred a long time ago, so that it is difficult
to know how the genome size reduction occurred. In these bacteria, the rate of
amino acid substitution is generally higher than that of ancestral free-living
bacteria (Moran 1996; Lynch 1996), and this high rate has been attributed to
advantageous mutation (Fares et al. 2002) or to Muller’s ratchet effect (Lynch
1996). However, Itoh et al. (2002) and Dale et al. (2003) suggested that the
loss of DNA repair enzymes in these bacteria is responsible for the high rate
of amino acid substitution. To resolve this controversy, however, it is important
to know how gene loss occurs in the early stage of evolution of endosymbiosis. </span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><o:p> </o:p><span style="line-height: 200%;"> </span><span style="line-height: 200%;">In
recent years a number of investigators (e.g., Dale et al 2002; Burke and Moran
2011) have identified bacterial species which started a symbiotic life very
recently so that they could study their early stage of genome reduction. In
particular, the group of Clayton et al. (2012) and Oakeson et al. (2014) discovered
a novel human-infective bacterium designated “strain </span><i style="line-height: 200%;">HS.</i><span style="line-height: 200%;">” This strain was isolated from a patient who had a hand wound
following impalement with a tree branch. Phylogenetic analysis showed that the
strain </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> is a member of the </span><i style="line-height: 200%;">Sodalis</i><span style="line-height: 200%;">-allied clade of insect
endosymbionts and that close relatives of strain </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> gave rise to symbiotic association in a range of insect species.
Using 165 rRNA genes, Clayton et al. (2012) showed that strain </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> is closely related (by 98% sequence
identity for synonymous sites) to the bacteria </span><i style="line-height: 200%;">Solidas glossinidius</i><span style="line-height: 200%;"> and </span><i style="line-height: 200%;">Sitophilus
oryzae</i><span style="line-height: 200%;"> primary endosymbiont (</span><i style="line-height: 200%;">SOPE</i><span style="line-height: 200%;">)
that are endosymbionts of grain weevils. The genome size (5.16 Mb) of </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> was only slightly greater than those
of </span><i style="line-height: 200%;">S. glossinidius</i><span style="line-height: 200%;"> and </span><i style="line-height: 200%;">SOPE</i><span style="line-height: 200%;"> (see Table 1). This result suggests
that the latter two species have become endosymbionts only recently and </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> is a free-living bacterium. (The symbiont bacterium (<i>Buchnera aphidicola</i>) of aphids has only 20% of the genome of the ancestral free bacteria.)</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg2OCMiGT1fFn8733z-h89XuvBJutTk6b6Tv-RubtaPlflwcvAQQ_ovo5q_4tgoC6hLnV5UWEOzKuaMy5vQrrNjfMhLz_7nJJiRv3a6OBU4k5ArN4j3vmbmgGzWjfB5sy_fHP7L8O8vRY/s1600/journal.pgen.1002990.t001.tif" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Times, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg2OCMiGT1fFn8733z-h89XuvBJutTk6b6Tv-RubtaPlflwcvAQQ_ovo5q_4tgoC6hLnV5UWEOzKuaMy5vQrrNjfMhLz_7nJJiRv3a6OBU4k5ArN4j3vmbmgGzWjfB5sy_fHP7L8O8vRY/s1600/journal.pgen.1002990.t001.tif" height="101" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="MsoNormal" style="line-height: 200%;">
<b><span style="line-height: 200%;"><span style="font-family: Times, Times New Roman, serif; font-size: small;">Table 1. General features of the
strain HS, SOPE, and <i>S. glossinidius</i> genome sequences<o:p></o:p></span></span></b></div>
</td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%;">
<span style="line-height: 200%;"><span style="font-family: Times, Times New Roman, serif;"><br /></span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><span style="line-height: 200%;"> Clayton
et al. (2012) and Oakeson et al. (2014) sequenced the genomes of </span><i style="line-height: 200%;">HS</i><span style="line-height: 200%;"> and </span><i style="line-height: 200%;">SOPE</i><span style="line-height: 200%;"> and compared the genomic sequences with the sequence of </span><i style="line-height: 200%;">S. glossinidius</i><span style="line-height: 200%;">, which was available
from the literature. The results indicated that the number of pseudogenes has
increased substantially in the symbiont bacteria whereas the number of intact
genes (supposedly functional genes) has been reduced (see Table 1 and Fig. 1).
Furthermore, a large number of mobile insertion sequences (IS) and a substantial
number of duplicate genes have accumulated in the symbiotic bacteria.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoLv76lakbzrVNduanlCk3wDTV0nzxvEC98fiKSglAUJ9yRUS33SDGhn2k5OtjOPXBQsyEXXg89NAvQKy8jlfjWClZlfZ6DGEw10OlRAvwJjMCEJJeApJ0LBAL9G_KTEdyClk78FifdC8/s1600/journal.pgen.1002990.g004.tif" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Times, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoLv76lakbzrVNduanlCk3wDTV0nzxvEC98fiKSglAUJ9yRUS33SDGhn2k5OtjOPXBQsyEXXg89NAvQKy8jlfjWClZlfZ6DGEw10OlRAvwJjMCEJJeApJ0LBAL9G_KTEdyClk78FifdC8/s1600/journal.pgen.1002990.g004.tif" height="245" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="MsoNormal" style="text-align: left;">
<span style="font-family: Times, Times New Roman, serif; font-size: small;"><b>Figure 1. Alignments of
three regions of the <i>S. glossinidius</i>, strain HS, and SOPE
chromosomes. </b>Alignments of three
regions of the <i>S. glossinidius</i>, strain HS, and SOPE chromosomes,
corresponding to SG0948–SG0977 (A), ps_SGL0466–SG0918 (B) and
ps_SGL0318–ps_SGL0330 (C) in the most recent <i>S. glossinidius</i> annotation
[25]. Putative ORFs and intergenic regions are drawn according to scale,
oriented according to their inferred direction of transcription and color-coded
according to COG functional categories. While all of the depicted strain <i>HS</i> genes have intact reading frames, the
status of their orthologs in <i>S. glossinidius</i> and <i>SOPE</i> are shown in the outer bars (green
= intact, purple = inactivated). Nonsense mutations (premature stop codons) are
depicted by purple diamonds, and frameshifting indels are depicted by purple
triangles. Light grey connecting bars are syntenic nucleotide alignments, while
brown bars illustrate IS-element acquisitions that occur more frequently in <i>SOPE</i>.<o:p></o:p></span></div>
</td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif;"><br /></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"> These
results suggest that when free-living bacteria entered into a host insect many
genes of the free-living bacteria was nonfunctionalized because they were not
necessary in the insect host. At the same time normally harmful IS elements
have accumulated because the destruction of many functional genes by IS elements
appear to be harmless under the condition of symbiosis. It is interesting to
note that these evolutionary changes have occurred very rapidly because in the
initial stage of symbiosis many useless genes can be pseudogenized but the
pseudogenes may be retained in the genome for some time. (In the present case
symbiosis was estimated to have occurred only about 28,000 years ago, though
this estimate seems to be too low; Concord et al. 2008.) This rapid regressive
evolution occurred apparently because a small number of free-living bacteria
colonized in the bacteriocytes of the host and the number of vertically
inherited bacteria has remained to be small. I would like to call this type of
evolution small-niche or micro-niche evolution. In micro-niche evolution, the
bacterial population was effectively homozygous, and many mutational changes
are expected to be fixed at the rate of mutation unless they are deleterious under
the symbiotic condition.</span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><o:p> </o:p><span style="line-height: 200%;"> </span><span style="line-height: 200%;">Of
course, if the evolutionary time becomes long, many pseudogenes and other
useless DNA elements would be lost by deletion and the genome size is expected
to become small as is observed in ancient endosymbionts. Furthermore, in the
long run some mutations that would enhance the mutual dependency of the
symbiont and the host are expected to occur, and eventually the symbiont
bacteria and the host organism become inseparable.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><o:p> </o:p><span style="line-height: 200%;"> </span><span style="line-height: 200%;">Note
also that because many mutations are not harmful under the symbiotic condition,
even DNA repair genes such as </span><i style="line-height: 200%;">recA </i><span style="line-height: 200%;">and
</span><i style="line-height: 200%;">recF </i><span style="line-height: 200%;">may be lost (Shigenobu et al.
2000; Itoh et al. 2002). In fact, the loss of </span><i style="line-height: 200%;">recA</i><span style="line-height: 200%;"> has been confirmed even in the symbiont bacteria </span><i style="line-height: 200%;">S. glossinidius</i><span style="line-height: 200%;"> and </span><i style="line-height: 200%;">SOPE </i><span style="line-height: 200%;">(Dale et al. 2003). This suggests that a relatively high rate
of amino acid substitution in endosymbionts has evolved in the early stage of
symbiotic life.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><o:p> </o:p><span style="line-height: 200%;"> </span><span style="line-height: 200%;">Microniche
evolution is different from the evolution by population bottlenecks proposed by
Mayr (1963), because in the latter theory population size shrinks temporarily
but increases later to the original level whereas in the former theory the
population size remains small throughout the evolutionary process. Micro-niche
evolution occurs in many different organisms, and it is often associated with
regressive evolution of various characters. For example, many organisms living
in ancient caves have lost pigmentation because in the dark cave condition
pigments are not necessary. In the case of Mexican cavefish </span><i style="line-height: 200%;">Astyanax mexicanus</i><span style="line-height: 200%;"> even the eyes are
degenerated. In this case a number of authors (e.g., Jeffrey 2009; Yoshizawa et
al. 2012) proposed that the degeneration of eyes in </span><i style="line-height: 200%;">A. mexicanus</i><span style="line-height: 200%;"> has occurred by positive Darwinian selection. Their
argument is that in the dark cave condition there is no need of having eyes and
therefore natural selection operates to reduce the eye size so that the
nutrition saved by elimination of eye formation can be used for other purposes.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><o:p> </o:p><span style="line-height: 200%;"> </span><span style="line-height: 200%;">I
have opposed this view by noting that the first step of degenerative evolution
is likely to be the reduction of eye size by destructive mutations in the small
cavefish population and therefore the degeneration of cavefish eyes can easily
be explained by micro-niche evolution (Nei 2013). Of course, positive selection
after degeneration of the eyes may have occurred in the cave condition. For
example, cavefish are known to have thin skin to cover the degenerated eyes. It
is quite possible that any mutations that cause the development of this skin
have been subjected to positive selection. However, the most important event of
eye degeneration must be caused by degenerative mutations. In fact, this view
is supported by the micro-niche evolution of symbiotic bacteria mentioned above.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<br /></div>
<div class="MsoNormal" style="line-height: 200%;">
<b><span style="font-family: Times, Times New Roman, serif; font-size: 12pt">References<o:p></o:p></span></b></div>
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Lynch M. 1996. <a href="http://mbe.oxfordjournals.org/content/13/1/209.full.pdf" target="_blank">Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes.</a> <i>Mol
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Itoh, T., Martin, W., & Nei, M. (2002). <a href="http://www.pnas.org/content/99/20/12944.full" target="_blank">Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts.</a> <i>Proc. Natl.
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Dale, C., Wang, B., Moran, N., & Ochman, H. (2003). <a href="http://www.ncbi.nlm.nih.gov/pubmed/12777518" target="_blank">Loss of DNA recombination repair enzymes in the initial stages of genome degeneration.</a> <i>Mol Biol Evol</i> 20(8)1188-1194.</span></div>
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<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">8.
Burke GR, and Moran NA. 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21266540" target="_blank">Massive genomic decay in <i>Serratia symbiotica</i>, a recently evolved symbiont of aphids</a>. <i>Genome Biol Evol</i> 3:195-208.</span></div>
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Clayton et al. (2012). <a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002990" target="_blank">A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect–bacterial symbioses</a>. <i>PLoS Genetics </i>8(11):e1002990.</span></div>
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Concord, C., Despres, L., Vallier, A., Balmand, S, Miquel C., et al. (2008). <a href="http://www.ncbi.nlm.nih.gov/pubmed/18310662" target="_blank">Long-term evolutionary stability of bacterial endosymbiosis in curculionoidea: additional evidence of symbiont replacement in the dryophthoridae family.</a> <i>Mol Biol Evol</i> 25:859-868.</span></div>
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Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., & Ishikawa, H.
(2000). <a href="http://www.ncbi.nlm.nih.gov/pubmed/10993077" target="_blank">Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS</a>. <i>Nature</i> 407(6800):81-6.</span></div>
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<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">12.
<span style="line-height: 115%; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 12.0pt;">Mayr E. 1963. Animal species and evolution. Harvard
University Press, Cambridge.<o:p></o:p></span></span></div>
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<br /></div>
<div class="MsoNormal" style="line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span style="line-height: 115%; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 12.0pt;"><span style="font-family: Times, Times New Roman, serif; font-size: 12pt">13.
Jeffery WR. 2009. <a href="http://www.ncbi.nlm.nih.gov/pubmed/19640230" target="_blank">Regressive evolution in Astyanax cavefish</a>. <i>Annu Rev Genet </i>43:25-47.<o:p></o:p></span></span></div>
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<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">14.
Yoshizawa, M., Yamamoto, Y., O’Quin, K. E., & Jeffery, W. R. (2012).
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23270452" target="_blank">Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish. </a><i>BMC Biology</i>
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</div>
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<span style="font-family: Times, Times New Roman, serif;font-size: 12pt">15.
Nei, M. (2013). <a href="http://ukcatalogue.oup.com/product/9780199661732.do" target="_blank">Mutation-driven evolution.</a> Oxford University Press, Oxford.</span></div>Masatoshi Neihttp://www.blogger.com/profile/15706545477678186676noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-81576173265613917882013-12-20T23:05:00.000-05:002014-02-06T15:18:19.392-05:00Selective Advantage of New Mutations May Depend on Mutations in Other Sites<!--[if gte mso 9]><xml>
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<b style="mso-bidi-font-weight: normal;">Contributed by</b>: <a href="mailto:zuz17@psu.edu" target="_blank"><b>Zhenguo Zhang</b></a></div>
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<span style="font-family: Times,"Times New Roman",serif;"><span style="font-size: large;"> Advantageous mutations may facilitate the adaptation of organisms to new environments. However, a single mutation which is advantageous in a given genetic background may be deleterious in another genetic background. This occurs when gene interaction or epistasis exists <a href="#s1">(1)</a>. An interesting case of epistatic interaction was recently observed in the hemoglobin of the deer mouse,<i> Peromyscus maniculatus</i> <a href="#s2">(2)</a>. </span></span></div>
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<b style="mso-bidi-font-weight: normal;"><span style="font-size: 10.0pt; line-height: 200%;">Figure 1</span></b><span style="font-size: 10.0pt; line-height: 200%;">. The 3-D structure (PDB ID: 1GZX) of
human Hemoglobin. The α-chains
and β-chains are in purple and cyan,
respectively. The heme groups are in green and the bound oxygen moleculars are
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<span style="font-family: Times,"Times New Roman",serif;">Hemoglobin is the oxygen transporter in red blood cells of all vertebrates. It can load oxygen from the respiratory organs (such as lungs and gills) and release it in other tissues (such as muscles), where oxygen is utilized for generating energy. Hemoglobin is a tetramer consisting of two α-chains and two β-chains, encoded by α- and β-globin genes, respectively (Fig. 1). It has been known that the hemoglobin of high-altitude deer mouse populations has a high hemoglobin-oxygen affinity, which enhances the physiological performance under hypoxia. However, the molecular mechanism of this high oxygen affinity was unknown. Natarajan <i>et al.</i> compared the hemoglobins of deer mice living in highland (Rocky Mountains) and lowland (Great Plains) populations and identified 12 key amino acid mutations, among which 8 mutations occurred in the α-globin and 4 in the β-globin (Fig. 2). These 12 mutations were separated into three regions of the genes based on the linkage disequilibrium information: 5 mutations in α-globin exon 2, 3 mutations in α-globin exon 3, and 4 mutations in β-globin (Fig. 2). The allelic group for each region was denoted by the letter ‘H’ or ‘L’, depending on whether it came from the highland (H) or lowland (L) population. The notation HH-H thus represents a combination of the highland allelic groups in the three regions (α-globin exon 2, α-globin exon 3, and β-globin). To test the epistasis among the mutations at these regions, Natarajan et al. constructed eight recombinant hemoglobins by permuting all (2<sup>3</sup> = 8) combinations of allelic group variants (Fig. 2), and tested the oxygen affinity of the recombinant proteins <i>in vitro</i> with or without allosteric effectors (Cl<sup>-</sup> and DPG).</span></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIillTdnSIbF_x3guKYWYiKqEkGuyrW91o3LtnFGT3T0ALHv6dWC8D37t9tVCzvKYaybO9c1zXkxYFkcm-q3snGGRMXWNs3x50do-4COfxPUCRpXNCmz7qGk84bI6DYxqC0HYo_53-Za8/s1600/Fig+2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="163" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIillTdnSIbF_x3guKYWYiKqEkGuyrW91o3LtnFGT3T0ALHv6dWC8D37t9tVCzvKYaybO9c1zXkxYFkcm-q3snGGRMXWNs3x50do-4COfxPUCRpXNCmz7qGk84bI6DYxqC0HYo_53-Za8/s400/Fig+2.jpg" width="500" /></a></td></tr>
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<b style="mso-bidi-font-weight: normal;"><span style="font-size: 10.0pt; line-height: 200%;">Figure 2</span></b><span style="font-size: 10.0pt; line-height: 200%;">. The 8 genotypes of the recombinant
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<span style="mso-tab-count: 1;"> <span style="font-size: large;"> <span style="font-family: Times,"Times New Roman",serif;"> The results of this experiment clearly showed that epistasis occurred among the allelic groups of the three regions (Table 1). For example, under the condition with the Cl<sup>-</sup> anion (the +KCl line in Table 1), changing from the L to H allelic group in any region in the LL-L background decreased oxygen affinity (corresponding to a higher <i>P<sub>50</sub></i> value), but the simultaneous changes in all three regions to the H allelic group (i.e., HH-H) increased oxygen affinity, contrary to the expectation from the additive effect model. As shown in the lower half of Table 1, the sensitivity of recombinant hemoglobins to the allosteric effectors (denoted by Δlog<i>P<sub>50</sub></i>) is also modulated by epistatic interactions of these three regions. 3-D structural analysis of different hemoglobin variants indicated no direct interactions among these mutational sites, but different sets of hydrogen bonds formed in each recombinant hemoglobin <a href="#s2">(2)</a>. This implies that the epistatic interactions of these mutations may be mediated by coordinated changes of protein topology. </span></span></span><span style="font-family: Times,"Times New Roman",serif;"><span style="font-size: small;"><br /></span></span></div>
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<span style="font-size: 10.0pt; line-height: 200%;"><span style="mso-spacerun: yes;"></span> <b>Table 1</b>(From Natarajan <i style="mso-bidi-font-style: normal;">et al.</i>, <i style="mso-bidi-font-style: normal;">Science</i>, 2013. <i style="mso-bidi-font-style: normal;">P<sub>50</sub></i> represents the oxygen pressure
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This study <a href="#s2">(2)</a> demonstrates that the effect of a mutation on the oxygen affinity depends on the genetic background. Since epistasis is prevalent in the genome <a href="#s3">(3)</a>, it is important to take into account the genetic background when one wants to know the evolution of a complex character with epistatic effect. In this case there are several possible ways of evolution from low-altitude hemoglobins to high-altitude hemoglobins or vice versa, as in the case of other proteins (<a href="#s4">4</a>, <a href="#s5">5</a>). Genetic drift and environmental changes also may have played important roles.</span></span></span></div>
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Abstract of the original paper</h3>
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<i style="mso-bidi-font-style: normal;">Epistatic
interactions between mutant sites in the same protein can exert a strong
influence on pathways of molecular evolution. We performed protein engineering
experiments that revealed pervasive epistasis among segregating amino acid variants
that contribute to adaptive functional variation in deer mouse hemoglobin (Hb).
Amino acid mutations increased or decreased Hb-O<sub>2</sub> affinity depending
on the allelic state of other sites. Structural analysis revealed that
epistasis for Hb-O<sub>2</sub> affinity and allosteric regulatory control is
attributable to indirect interactions between structurally remote sites. The
prevalence of sign epistasis for fitness-related biochemical phenotypes has
important implications for the evolutionary dynamics of protein polymorphism in
natural populations.</i></div>
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<b>References</b></div>
<div id="s1" class="MsoNormal" style="margin-left: .5in; mso-prop-change: zhangzg 20131208T1619; text-indent: -.5in;">
1.<span style="mso-tab-count: 1;"> </span>Lehner
B: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21684621" target="_blank"><b style="mso-bidi-font-weight: normal;">Molecular mechanisms of epistasis within and between genes</b></a>. <i style="mso-bidi-font-style: normal;">Trends
Genet </i>2011, <b style="mso-bidi-font-weight: normal;">27</b>(8):323-331.</div>
<div id="s2" class="MsoNormal" style="margin-left: .5in; mso-prop-change: zhangzg 20131208T1619; text-indent: -.5in;">
2.<span style="mso-tab-count: 1;"> </span>Natarajan
C, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23766324" target="_blank"><b style="mso-bidi-font-weight: normal;">Epistasis among adaptive mutations in deer mouse hemoglobin</b></a>. <i style="mso-bidi-font-style: normal;">Science </i>2013, <b style="mso-bidi-font-weight: normal;">340</b>(6138):1324-1327.</div>
<div id="s3" class="MsoNormal" style="margin-left: .5in; text-indent: -.5in;">
3.<span style="mso-tab-count: 1;"> </span>Nei M, Ebooks Corporation: <a href="http://ukcatalogue.oup.com/product/9780199661732.do" target="_blank"><b style="mso-bidi-font-weight: normal;">Mutation-driven evolution</b></a>. In<i style="mso-bidi-font-style: normal;">.</i>, 1st edn. Oxford: Oxford University
Press; 2013: 1 online resource.</div>
<div class="MsoNormal" style="margin-left: .5in; text-indent: -.5in;">
4.<span id="s4" style="mso-tab-count: 1;"> </span>Salverda ML, Dellus E, Gorter FA,
Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JA: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21408208" target="_blank"><b style="mso-bidi-font-weight: normal;">Initial mutations direct alternative pathways of protein evolution</b></a>. <i style="mso-bidi-font-style: normal;">PLoS
Genet </i>2011, <b style="mso-bidi-font-weight: normal;">7</b>(3):e1001321.</div>
<div class="MsoNormal" style="margin-left: .5in; text-indent: -.5in;">
5.<span id="s5" style="mso-tab-count: 1;"> </span>Lozovsky ER, Chookajorn T, Brown KM,
Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL: <a href="http://www.pnas.org/content/106/29/12025" target="_blank"><b style="mso-bidi-font-weight: normal;">Stepwise acquisition of pyrimethamine resistance in the malaria parasite</b></a>. <i style="mso-bidi-font-style: normal;">Proc
Natl Acad Sci U S A </i>2009, <b style="mso-bidi-font-weight: normal;">106</b>(29):12025-12030.</div>
<div class="MsoNormal">
<br /></div>
<br />
<br />
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<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;">
</span></div>
<br />
<br />
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN;"></span>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-65937886186801206142013-09-18T13:42:00.000-04:002013-09-18T13:42:54.736-04:00A Single Nucleotide Substitution in a Hox/Pax-responsive Enhancer Is Responsible for the Evolution of the Snake Body Pattern<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"><b>Contributed by: <a href="mailto:jn322@camden.rutgers.edu" target="_blank">Jongmin Nam</a></b></span></span><a href="mailto:jn322@camden.rutgers.edu" target="_blank"></a><span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><br /></span></span>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> Hox
genes control the body plan of animals along the anterior-posterior axis (<b>Figure 1</b>). Their expression patterns
and protein function determine the identity of each body segment, and changes
in their functions are often responsible for the variations in the number and
structure of body segments in vertebrates. </span></span></div>
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<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><b><span style="color: black; line-height: 200%;">Figure </span><span style="color: black; line-height: 200%;">1</span></b><span style="color: black; line-height: 200%;"><b>.</b> </span><span style="color: black; font-weight: normal; line-height: 200%;">The spatial expression
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> Among
many vertebrates, snakes are fascinating models for studying body plan
evolution: they have more vertebrae than other vertebrates and have ribs even
in the posterior parts of their trunk, where most vertebrates have rib-less
vertebrae. It has been known in mice that Hox6 is expressed in the anterior
trunk and Hox10 in the posterior trunk (<b>Figure
2</b>). The former is an activator of rib formation, and the latter a
suppressor. When mouse Hox10 was ectopically expressed in the anterior trunk,
rib development was inhibited. Interestingly in snakes, Hox6 expression is
extended to the posterior trunk and overlaps with Hox10 expression (<b>Figure 2</b>). Because <i>Hox10</i> function is dominant over <i>Hox6</i>
function in the rib development in mice, it was hypothesized that snake Hox10
lost its function to repress rib formation.</span></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> To test
this hypothesis, Guerreriro and colleagues <a href="#s1">(1)</a> examined a gene regulatory
network involving <i>Hox10</i> in a recent
PNAS paper. The authors hypothesized that loss of gene expression or protein
function of <i>Hox10</i> in snakes might be
responsible for the posterior extension of ribs. However, expression patterns
of <i>Hox10</i> between mice and snakes were
similar, and the snake Hox10 protein could still repress rib development in
transgenic mice, rejecting the hypothesis.</span></span></div>
<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><br /></span></span>
<br />
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<tr><td style="text-align: center;"><span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeEZmNjaMYvdDY9MB1fC_FtyZF3VYwU2NsrGy02NMpEa4s13GSNlyyk2jSGkLMLvOKIhZxlC0zfP359IfrLDfhkKuRduaOJT-tW2gEIVhZmU0n8opJV-gDQunKtuUxNcal2NslqT49dDs/s1600/Hox+Fig+2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeEZmNjaMYvdDY9MB1fC_FtyZF3VYwU2NsrGy02NMpEa4s13GSNlyyk2jSGkLMLvOKIhZxlC0zfP359IfrLDfhkKuRduaOJT-tW2gEIVhZmU0n8opJV-gDQunKtuUxNcal2NslqT49dDs/s1600/Hox+Fig+2.jpg" /></a></span></span></td></tr>
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<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><b><span style="color: black; line-height: 200%;">Figure </span><span style="color: black; line-height: 200%;">2</span></b><span style="color: black; line-height: 200%;"><b>.</b> </span><span style="color: black; font-weight: normal; line-height: 200%;">Loss of <i>Hox10</i>
rib-suppressing activity in the trunk of the snake. In mice suppression of <i>Myf5/6</i>
in the posterior part of the body is responsible for rib-less phenotype.
However, in snakes Hox10 cannot suppress <i>Myf5/6</i>
resulting in rib-bearing vertebrae in the trunk.</span><span style="color: black; line-height: 200%;"> </span><i><span style="color: black; font-weight: normal; line-height: 200%;">(From
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> If
it is not <i>Hox10</i>, then are the downstream
target genes of <i>Hox10</i> responsible for
the phenotypic difference? The authors examined several known downstream target
genes of <i>Hox10</i>. Interestingly, they
found a single base-pair difference in a highly conserved enhancer region of
the snake <i>Myogenic factor 5</i> (<i>Myf5</i>), a transcription factor gene that
controls skeletal muscle development. In mice, this enhancer is repressed by <i>Hox10</i> in the posterior trunk and is
activated by<a href="http://www.blogger.com/null" name="_GoBack"></a> <i>Hox6</i>
and <i>Pax3 </i>in the anterior trunk. When
the snake mutation was introduced into the mouse <i>Myf5</i> enhancer, ectopic reporter expression in the posterior trunk
was observed, which is consistent with the posterior extension of ribs in
snakes.</span></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> Is
this change specific to the snake lineage? The authors' survey of the enhancer
sequences from a variety of vertebrate species discovered independent
occurrences of the same mutation in at least two other lineages, elephant/hyrax/manatee and tenrec. Because the former
three species also have longer rib-cages than other mammals, it is possible
that the <i>Myf5</i> enhancer is a hotspot <a href="#s2">(2)</a> for morphological evolution.
Note that the title is a bit misleading, because the causal mutation is fixed
in the snake lineage, and therefore is not a polymorphism.</span></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> Although
the findings look clear-cut, it was puzzling that the single base-pair mutation
in the snake enhancer is within the binding site of both <i>Hox6</i> (activator) and <i>Hox10</i>
(repressor). How did the snake enhancer lose only repression, but not both activation
and repression? The answer was quite unexpected: although Hox6 can bind directly
on the enhancer in mice, Hox6 can also indirectly interact with the enhancer
via interaction with Pax3, whose binding is not affected by the mutation.
Because Hox10 does not interact with Pax3, Hox10's interaction with the snake
enhancer is significantly reduced resulting in ectopic expression of <i>Myf5</i>. This result explains why snake <i>Myf5</i> enhancer lost its repression by <i>Hox10</i>, yet maintained activation by <i>Hox6</i>.</span></span></div>
<br />
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<tr><td style="text-align: center;"><span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTRe7SLcFxN5YNYSLWhH3GkhE8PR2oCjhq-a8y9h_wZ4Zd-jrRoCxg97-GutgWUY-J2MeF2XEWPZZIvUi3WkJ3kx5uue4HnaTTFOM0rF4qpyudP7ufK9QgelgI0fn4IMInaikspsK5al8/s1600/Hox+Fig+3.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="86" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTRe7SLcFxN5YNYSLWhH3GkhE8PR2oCjhq-a8y9h_wZ4Zd-jrRoCxg97-GutgWUY-J2MeF2XEWPZZIvUi3WkJ3kx5uue4HnaTTFOM0rF4qpyudP7ufK9QgelgI0fn4IMInaikspsK5al8/s400/Hox+Fig+3.jpg" width="400" /></a></span></span></td></tr>
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<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><b>Figure 3.</b> Model for rib growth vs.
repression in mice and snakes. In mice, Hox6, an activator of <i>Myf5</i>, is expressed in the anterior
trunk, and Hox10, a repressor of <i>Myf5</i>,
in the posterior trunk. In snakes, Hox6 is expressed in both anterior and
posterior trunks and Hox10 only in the poster trunk. However, neither Hox6 nor
Hox10 can bind directly to the snake <i>Myf5</i>
enhancer due to a single-nucleotide change within the enhancer. Unexpectedly in
snakes, Hox6 still can activate <i>Myf5</i>
with the help of Pax3, whose binding to the enhancer is independent of the
mutation. The newly discovered mechanism of Hox6/Pax3 is also conserved in
mice. <i>(From Mansfield JH, 2013, PNAS)</i></span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> The
present study highlights the power of studying evolution in the framework of
gene regulatory networks: it not only provided genetic clues for morphological
differences, but also deepened our understanding on the underlying molecular
mechanisms. Is functional variation within conserved genes the main underlying
causes of morphological evolution? We need more of these studies to answer this
question.</span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"><br /></span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"><b>References</b></span></span></div>
<div id = "s1" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0in 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">1. Guerreiro I, et al. (2013) <a href="http://www.pnas.org/content/110/26/10682.long" target="_blank">Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine</a>. <i>Proceedings of the National Academy of
Sciences</i> 110:10682-10686.</span></span></div>
<div id = "s2" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">2. Stern DL (2011) <i>Evolution, development, & the
predictable genome</i> (Roberts and Co. Publishers).</span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"><br /></span></span></div>
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<br /></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><o:p>
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<b>Abstract of the original paper</b>
<br />
<div style="line-height: 200%;">
Patterning of the vertebrate skeleton requires the coordinated activity of Hox genes. In particular, Hox10 proteins are essential to set the transition from thoracic to lumbar vertebrae because of their rib-repressing activity. In snakes, however, the thoracic region extends well into Hox10-expressing areas of the embryo, suggesting that these proteins are unable to block rib formation. Here, we show that this is not a result of the loss of rib-repressing properties by the snake proteins, but rather to a single base pair change in a Hox/Paired box (Pax)-responsive enhancer, which prevents the binding of Hox proteins. This polymorphism is also found in Paenungulata, such as elephants and manatees, which have extended rib cages. In vivo, this modified enhancer failed to respond to Hox10 activity, supporting its role in the extension of rib cages. In contrast, the enhancer could still interact with Hoxb6 and Pax3 to promote rib formation. These results suggest that a polymorphism in the Hox/Pax-responsive enhancer may have played a role in the evolution of the vertebrate spine by differently modulating its response to rib-suppressing and rib-promoting Hox proteins.
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</o:p></span></div>
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<o:p></o:p>
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Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-23943473543863890012013-04-09T14:42:00.000-04:002013-04-09T14:42:11.939-04:00Rapid Evolution of Resistance to Toxic Chemicals in Atlantic Tomcod<div style ="font-size: 12pt;"><span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><strong>Contributed by: <a href="mailto:mem8@rice.edu" target="_blank">Mary Morales</strong></a><strong>, Rice University</strong></span><br /></div>
<br />
<br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">The melanic form of peppered moth
<i style="mso-bidi-font-style: normal;">Biston betularia</i> in England has been
widely used as an example of natural selection in action. Before the industrial
revolution in England around 1850 the melanic form of peppered moth was rarely
observed in nature and most peppered moth were the light-colored wild type, but
by the end of the 19<sup>th</sup> century it was the dominant phenotype as soot
pollution caused the environment to darken. Even though the English peppered
moth is a great example of natural selection caused by pollution, molecular
basis of this evolution is still not elucidated. Furthermore, the population is
not isolated due to constant migration. This makes it difficult to accurately
infer the effect of environmental change on survival of natural moth
populations. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">As in the case of the peppered
moth, the Atlantic tomcod</span><span style="font-size: 12pt; font-family: Cambria;"> </span><i style="font-size: 12pt;mso-bidi-font-style: normal;"><span style="font-family: "Times New Roman","serif";">Microgadus tomcod</span></i><span style="font-size: 12pt; font-family: "Times New Roman","serif";"> of the Hudson River experienced a
rapid evolutionary change caused by pollution. For the Atlantic tomcod of the
Hudson River, water pollution caused by the improper disposal of toxic
chemicals served as the cause of natural selection. Increase in the toxicity of
its environment forced the fish to adapt to an environment heavily polluted by
polychlorinated biphenyls (PCBs).<span style="font-size: 12pt; mso-spacerun: yes;">
</span>Recently, the molecular basis of the evolutionary change was clarified,
making the Atlantic tomcod the first well understood case of evolution driven
by change of environments <a href="#r1">(1)</a>.<o:p></o:p></span></div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi09owcjqn8k5xhp4A4QvDNGz6dgRVz6gIh4Dub8DQ2pjtH6Znjdy-y96KvdH55JeEywMgX1Zzd2jrP4drlFuaHOfWllDipRt1U6cDOuTLgnLE0trH0v8Sn_HxqD42wPyoSl_H1j_NUojI/s1600/Tomcod+Fig.+1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="207" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi09owcjqn8k5xhp4A4QvDNGz6dgRVz6gIh4Dub8DQ2pjtH6Znjdy-y96KvdH55JeEywMgX1Zzd2jrP4drlFuaHOfWllDipRt1U6cDOuTLgnLE0trH0v8Sn_HxqD42wPyoSl_H1j_NUojI/s320/Tomcod+Fig.+1.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><span style="font-family: "Times New Roman","serif"; font-size: 10pt; line-height: 200%;">Figure 1. Atlantic tomcod from the Hudson River<o:p></o:p></span><span style="font-size: small;">
</span></td></tr>
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<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">Over a million pounds of PCBs was
dumped by General Electric into the Hudson River between 1947 and 1976 before
the dumping was banned <a href="#r1">(1)</a>. Since PCBs are long lasting chemicals due to their sedimentation
in the soil and resistance to degradation, their influence in the Hudson River
was significant, and is still significant today <a href="#r2">(2)</a>. They cause serious health
issues in animals exposed to them such as cancer through their stimulation of
the aryl hydrocarbon receptor (AHR), which is an important transcription factor
<a href="#r2">(2)</a>. Two genes encode for the AHR (AHR1 and AHR2) <a href="#r1">(1)</a>. Although AHR1 and AHR2
are both expressed in fish, AHR2 is the more active protein <a href="#r1">(1)</a>. <o:p></o:p></span></div>
<span style="font-family: "Times New Roman","serif";"><o:p></o:p></span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJz5DE2HT5u3vum9lH0LX4jci0o7ccULGD0p10IUnde0Cd1n8UP2Rafu0UQNoFr21j2lTVezSaq5u1EiRtRa8hP9SkHjoZOoRn-m1sIss7k0RUCVIrQVEEsh9Xz34b6dz8k6pyAkCBRdg/s1600/Tomcod+Fig.+2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="343" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJz5DE2HT5u3vum9lH0LX4jci0o7ccULGD0p10IUnde0Cd1n8UP2Rafu0UQNoFr21j2lTVezSaq5u1EiRtRa8hP9SkHjoZOoRn-m1sIss7k0RUCVIrQVEEsh9Xz34b6dz8k6pyAkCBRdg/s400/Tomcod+Fig.+2.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div align="left">
<span style="font-family: "Times New Roman","serif"; font-size: 10pt;">Figure 2.<span style="mso-spacerun: yes;"> </span>Frequencies of AHR2-1 and AHR2-2 alleles in tomcod populations in and near the Hudson River. n indicates the number of specimens analyzed in a given location. From Wirgin et al. <a href="#r1">(1)</a>.<o:p></o:p></span></div>
</td></tr>
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<span style="font-family: "Times New Roman","serif";"><o:p> </o:p></span><br />
<br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style=" font-size: 12pt; font-family: "Times New Roman","serif";">Wirgin et al <a href="#r1">(1)</a> studied the
Atlantic tomcod population of the Hudson River and nearby estuaries and found
that there are two alleles, AHR2-1 and AHR2-2, at the AHR2 locus. These two
variants are distinguished by a mutation that evokes a functional difference.
The major difference between the two alleles is that the AHR2-1 exhibits a six
base pair deletion causing it to be two amino acids (Phe-Leu) shorter <a href="#r1">(1)</a>. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style=" font-size: 12pt; font-family: "Times New Roman","serif";">Fish expressing the AHR2-1
protein have a significantly lower affinity for toxins, preventing them from
turning on genes that should not be activated <a href="#r1">(1)</a>. Water contamination by PCBs
created a strong selection force in favor of the AHR2-1 allele, as it creates a
PCB resistant phenotype that enables the fish to survive and reproduce in a
toxic environment <a href="#r3">(3)</a>. The frequency of the AHR2-1 allele in the Hudson River
population is extremely high (99%), with the non-mutated allele (AHR2-2) only
observed in heterozygotes <a href="#r1">(1)</a>. The allele frequencies of AHR2-1 were also
examined in other Atlantic tomcod populations from 7 Atlantic Coast estuaries.
As shown in Figure 2, the allele frequency of AHR2-1 is significantly lower in
populations located more distantly from Hudson River. Specifically, the AHR2-1
allele is even absent in the four populations in distant locations.<span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">The different distributions of </span><span style="font-family: "Times New Roman","serif"; line-height: 200%; mso-bidi-font-size: 10.0pt;">AHR2-1
and AHR2-2 alleles suggest that the wild type allele AHR2-2 is dominant in
populations in non-PCBs polluted areas. The frequency of the PCB-resistant
allele </span><span style="font-family: "Times New Roman","serif";">AHR2-1 has apparently
increased rapidly </span><span style="font-family: "Times New Roman","serif"; line-height: 200%; mso-bidi-font-size: 10.0pt;">from a very low level to 99%</span><span style="font-family: "Times New Roman","serif";"> in ~ 60 years in the Hudson
River. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">In addition, the low frequency of
AHR2-1 in other fish populations suggests that the Atlantic tomcod population
of the Hudson River is relatively isolated, unlike the English peppered moth.
Thus the increase in frequency of the AHR2-1 allele was not hindered by factors
such as migration. The case of the Atlantic tomcod is noteworthy because for
the first time the selection coefficient can be estimated if the initial
frequency can be obtained in some way. Studies that aim to calculate the
selection coefficient in favor of the AHR2-1 allele in the Atlantic tomcod
population of the Hudson River are highly encouraged.<o:p></o:p></span></div>
<br />
<div id = "r1" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";"><o:p> </o:p></span></div>
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><strong>References</strong></span><br />
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="mso-spacerun: yes;"> </span></span><br />
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="mso-spacerun: yes;"><div class="MsoNormalCxSpFirst" style="line-height: 200%; margin: 0in 0in 10pt 0.5in; mso-add-space: auto; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;">1. <span style="mso-spacerun: yes;"> </span>Wirgin,
I., N.K. Roy, M. Loftus, R.C. Chambers, D.G. Franks, M.E. Hahn. 2011. <a href="http://www.sciencemag.org/content/331/6022/1322.full.pdf" target="_blank">Mechanistic Basis of Resistance to PCBs in Atlantic Tomcod from the Hudson River.</a> <i style="mso-bidi-font-style: normal;">Science </i>331: 1322-1324</span></div>
<div id = "r2" class="font-size: 12pt; MsoNormalCxSpMiddle" style="line-height: 200%; margin: 0in 0in 10pt 0.5in; mso-add-space: auto; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;">2. <span style="font-size: 12pt; mso-spacerun: yes;"> </span>“Toxic
River means rapid evolution for one fish species.” 2011.<i style="mso-bidi-font-style: normal;"> Understanding Evolution</i>. Web.<span style="mso-spacerun: yes;">
</span><</span><a href="http://evolution.berkeley.edu/evolibrary/news/110301_pcbresistantcod"><span style="font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="color: blue;">http://evolution.berkeley.edu/evolibrary/news/110301_pcbresistantcod</span></span></a><span style="font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;">>. </span></div>
<div id = "r3" class="font-size: 12pt; MsoNormalCxSpMiddle" style="line-height: 200%; margin: 0in 0in 10pt 0.5in; mso-add-space: auto; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif"; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;">3.<span style="font-size: 12pt; mso-spacerun: yes;"> </span>Roy,
N.K., S.C. Courtenay, R.C. Chambers, I.I. Wirgin. 2006. <a href="http://www.ncbi.nlm.nih.gov/pubmed/16519320?dopt=Abstract" target="_blank">Characterization of the aryl hydrocarbon receptor repressor and a comparison of its expression in Atlantic tomcod from resistant and sensitive populations. </a><i style="mso-bidi-font-style: normal;">Environmental Toxicology and Chemistry</i> 25: 560-571.<o:p></o:p></span></div>
</span><br /></span><br />Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-2402881259896185612013-02-27T12:12:00.000-05:002013-02-27T13:33:50.846-05:00ENCODE - All about "Functions"<b><span style="font-family: Times, Times New Roman, serif; font-size: 12pt">Contributed by: <a href="mailto:jianzhi@umich.edu" target="_blank">Jianzhi Zhang</a></span></b><br />
<div>
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><br /></span></div>
<div>
<div class="MsoNormal" style="line-height: 32px; text-indent: 0.5in;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">In 2012, the 288-million-dollar ENCyclopedia Of DNA Elements (ENCODE) project concluded in its 442-author <i>Nature</i> article that 80% of the human genome are functional. The completion of this massive study was regarded by both <i>Nature</i> and <i>Science</i> as one of the most important scientific accomplishments of the year. But are these 442 scientists correct?</span></div>
<div class="MsoNormal" style="line-height: 32px; text-indent: 0.5in;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">Dan Graur and five colleagues have now analyzed the ENCODE paper. Their conclusion is shocking, to say the least. They found that the ENCODE conclusion was erroneous and was reached mainly “<i>(1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect</i>”. The number and seriousness of the errors and inconsistencies they identified from the ENCODE paper are horrifying. One cannot help but wonder where the reviewers of the ENCODE project/paper were and what the 288 million dollars would accomplish if used to fund 200 NIH R01 grants. </span></div>
<div class="MsoNormal" style="line-height: 32px; text-indent: 0.5in;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">I recommend Graur et al.’s paper to all biologists, evolutionary or not, because it deals with some of the most fundamental concepts in biology with unusual clarity and wit. It also prompts one to ponder on the pros and cons of big science vs. small science. Last but not least, if you are intelligent, you will enjoy reading this 43-page PDF.<o:p></o:p></span></div>
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<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><br /></span></div>
<div class="MsoNormal" style="line-height: 32px;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt"><b>References</b> </span></div>
<div class="MsoNormal" style="line-height: 32px; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">The ENCODE Project Consortium. 2012. <a href="http://www.nature.com/nature/journal/v489/n7414/pdf/nature11247.pdf">An integrated encyclopedia of DNA elements in the human genome.</a> <i>Nature</i> 489: 57-74.<span style="text-indent: -0.5in;"> </span></span></div>
<div class="MsoNormal" style="line-height: 32px; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-family: Times, Times New Roman, serif; font-size: 12pt">Graur, D., Zheng, Y., Price, N., Azevedo, R. B. R., Zufall1 R. A., and Elhaik E. 2013. <a href="http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.full.pdf">On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE.</a> <i>Genome Biol. Evol.</i>, published February 20, 2013, doi:10.1093/gbe/evt028</span></div>
</div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com1tag:blogger.com,1999:blog-3378199995075509398.post-33887721807340702002012-12-12T13:01:00.000-05:002013-03-04T16:35:29.375-05:00Ortholog Conjecture Debated<!--[if gte mso 9]><xml>
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<span style="font-family: Times,"Times New Roman",serif;"><span style="color: black;">Most molecular biologists would agree that a gene tends to
be more similar to its orthologs than paralogs in terms of function.<span style="mso-spacerun: yes;"> </span>This fundamental tenet, recently termed the ortholog
conjecture, is a cornerstone of phylogenomics and is used by both computational
and experimental biologists in predicting, interpreting, and understanding gene
functions. <span style="mso-spacerun: yes;"> </span>But, is this conjecture wishful
thinking or empirically founded?</span></span></div>
<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGM3nD6nunh_f1qf770XjCK_tv17-NIoiytlvMa7XDYk0vBKo2O-fVJ_LKb6-Qqk32mWIkUJpKmt1CO-VlY7_fwZkFfz8PGWXAF8rq3ZCc5IGsr6Wl8ql5GN2XwY1G-IEXoz_HmhvnRlY/s1600/zhang+j+fig+1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGM3nD6nunh_f1qf770XjCK_tv17-NIoiytlvMa7XDYk0vBKo2O-fVJ_LKb6-Qqk32mWIkUJpKmt1CO-VlY7_fwZkFfz8PGWXAF8rq3ZCc5IGsr6Wl8ql5GN2XwY1G-IEXoz_HmhvnRlY/s1600/zhang+j+fig+1.jpg" /></a></td></tr>
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<span style="font-family: Times,"Times New Roman",serif;"><span style="font-size: 10pt;">Orthologous
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<span style="font-family: Times,"Times New Roman",serif;"><span style="font-size: 10pt;"> genes are generated by gene
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<span style="font-family: Times,"Times New Roman",serif;"><span style="font-size: 10pt;">Orthologs:
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<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;"><span style="color: black;">In a pioneering study, Nehrt et al. <a href="#q3">(3)</a> attempted to test
the ortholog conjecture using Gene Ontology (GO) annotations that were based on
experimental data.<span style="mso-spacerun: yes;"> </span>Contrary to
everyone’s expectation, they found that the functional similarity between
orthologs is lower than that between paralogs, when the level of sequence
divergence is controlled.<span style="mso-spacerun: yes;"> </span>Based on this
and other findings, the authors proposed th</span>at protein function evolution
is primarily determined by “the cellular context in which proteins act”. <span style="mso-spacerun: yes;"> </span>This would explain why within-species paralogs,
which are always in the same organism, were found functionally more similar than
orthologs, which by definition reside in different organisms.</span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">Nehrt et al.’s <a href="#q3">(3)</a>
finding stirred considerable controversies in cyberspace when published in the
summer of 2011, evidenced by numerous discussions in various blogs.<span style="mso-spacerun: yes;"> </span>The last 10 months have seen three papers
that challenged Nehrt et al.’s conclusion from different angles, although the
three papers do not completely agree with one another either.<span style="mso-spacerun: yes;"> </span></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">First, Thomas and
colleagues, representing the group that annotated GO, claimed that GO
annotation differences between homologous genes “do not reflect differences in
biological function, but rather complementarity in experimental approaches” <a href="#q4">(4)</a>.<span style="mso-spacerun: yes;"> </span>That is, gene function data are so sparse at
the present that GO annotations reflect ascertainment biases in experiments rather
than true functional differences.<span style="mso-spacerun: yes;"> </span></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">Second, Altenhoff
et al. <a href="#q1">(1)</a> identified a number of biases in GO.<span style="mso-spacerun: yes;">
</span>After correcting these biases, they found weak but significant evidence
for the ortholog conjecture.</span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">Most recently, Chen
and Zhang <a href="#q2">(2)</a> reanalyzed GO annotations and confirmed some of the biases
identified by Altenhoff and colleagues.<span style="mso-spacerun: yes;">
</span>Most disturbingly, however, was the finding of many errors in GO
annotation.<span style="mso-spacerun: yes;"> </span>Even in so-called
experiment-based annotations, across-species functional inferences were
frequently made.<span style="mso-spacerun: yes;"> </span>For example, an
experiment was conducted on a monkey gene, but the function was annotated in GO
for its human ortholog, based ironically on the ortholog conjecture.<span style="mso-spacerun: yes;"> </span></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">In one part of
their study, Chen and Zhang <a href="#q2">(2)</a> focused on pairs of orthologs or paralogs that have
identical protein sequences and were studied in the same papers.<span style="mso-spacerun: yes;"> </span>Surprisingly, while all nine such paralogous
pairs have 100% GO-based functional similarity, only nine of 31 such orthologous
pairs have 100% functional similarity.<span style="mso-spacerun: yes;">
</span>More extremely, eight of the 31 orthologous pairs show 0% functional
similarity, yet none of the papers that studied them explicitly mentioned their
functional dissimilarity.<span style="mso-spacerun: yes;"> </span>Apparently,
they reflect ascertainment biases rather than true functional differences.<span style="mso-spacerun: yes;"> </span>The authors also noted an upward trend in the
functional similarity of orthologs, relative to that of paralogs, when analyzing
the time series data of GO in the last five years.<span style="mso-spacerun: yes;"> </span></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;">These and other findings
led Chen and Zhang <a href="#q2">(2)</a> to conclude that the current GO is unsuitable for
testing the ortholog conjecture.<span style="mso-spacerun: yes;"> </span>They
thus turned to RNA-Seq gene expression data, which would be relative immune to
ascertainment bias and annotation error.<span style="mso-spacerun: yes;">
</span>They reported that orthologs are more similar to each other than to paralogs
in gene expression.<span style="mso-spacerun: yes;"> </span>But, regarding gene
function, the jury is still out. <span style="mso-spacerun: yes;"> </span>The
sheer difficulty of proving or rejecting the ortholog conjecture, one of the
most wildly assumed principles of molecular evolution, was completely unexpected,
and it still amazes me to this day. <span style="mso-spacerun: yes;"> </span></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="line-height: 200%;">
<br /></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-family: Times,"Times New Roman",serif;"><b style="font-size: 12pt; mso-bidi-font-weight: normal;"><span style="line-height: 200%; mso-bidi-font-size: 10.0pt;">References</span></b></span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" id="q1" style="font-size: 12pt; line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span style="font-family: Times,"Times New Roman",serif;">1.
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C (2012) <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002514" target="_blank">Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs</a>. PLoS Comput Biol 8(5): e1002514. </span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" id="q2" style="font-size: 12pt; line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span style="font-family: Times,"Times New Roman",serif;">2.
Chen X, Zhang J (2012) <a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002784" target="_blank">The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data</a>. PLoS Comput Biol 8(11):
e1002784. </span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" id="q3" style="font-size: 12pt; line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span style="font-family: Times,"Times New Roman",serif;">3.
Nehrt NL, Clark WT, Radivojac P, Hahn MW (2011) <a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002073" target="_blank">Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. </a>PLoS Comput Biol 7(6):
e1002073. </span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<div class="MsoNormal" id="q4" style="font-size: 12pt; line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span style="font-family: Times,"Times New Roman",serif;">4.
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA, et al. (2012) <a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002386" target="_blank">On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. </a>PLoS Comput Biol 8(2): e1002386. </span></div>
<span style="font-family: Times,"Times New Roman",serif;">
</span><br />
<br />Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-82217781378282307582012-12-04T16:48:00.001-05:002012-12-04T16:49:50.529-05:00Speciation Driven by Divergence in Heterochromatic Repeats <!--[if gte mso 9]><xml>
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<span style="font-family: Times,"Times New Roman",serif;"><b style="mso-bidi-font-weight: normal;"><span style="font-size: 12pt; line-height: 115%;">Contributed
by: <a href="mailto:zlin@rice.edu" target="_blank">Zhenguo Lin</a></span></b></span><br />
<br />
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: Times,"Times New Roman",serif;"><b style="mso-bidi-font-weight: normal;"><span style="font-size: 12pt; line-height: 115%;"> </span></b></span><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Darwin
used the title "On the origin of species" for his most famous book
published in 1859. In this book he explained how a single species changes over
time, but did not provide a proper explanation about how a species split into
two or more different species. The problem of speciation has now become an
important subject in evolutionary biology. From Hugo de Vries, Theodosius
Dobzhansky, and Ernst Mayr to contemporary workers such as Jerry Coyne and
Allen Orr, this problem has been studied extensively. </span></div>
<br />
<div class="MsoNormal" style="line-height: 200%; text-indent: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">In
this case it seems to be crucial to study speciation at the molecular level. In
their recent review article, Nei and Nozawa <a href="#p1">(1)</a> emphasized the importance of
mutations in speciation by presenting many cases of molecular studies. <span style="mso-spacerun: yes;"> </span>One of the mechanisms they considered is hybrid
incapacity associated with heterochromatin. Specifically, they stated that hybrid
sterility or inviability may occur by changes in repeat DNA elements in
heterochromatin regions of the genome. Two representative examples were presented
in the review article. (1) The different numbers of 359 bp repeats (zygote
hybrid rescue locus, <i style="mso-bidi-font-style: normal;">Zhr</i>) caused
hybrid inviability between <i style="mso-bidi-font-style: normal;">Drosophila
melanogaster</i> males and <i style="mso-bidi-font-style: normal;">D. simulans</i>
females.<span style="mso-spacerun: yes;"> </span>(2) The localization of Odysseus
homeobox (OdsH) protein to heterochromatic Y chromosome causes hybrid male
sterility between <i style="mso-bidi-font-style: normal;">D. mauritiana</i>
females and <i style="mso-bidi-font-style: normal;">D. simulans </i>males.<span style="mso-spacerun: yes;"> </span>Recently conducting a comparative study of the
genomic sequences from two closely related flycatcher bird species, Ellegren et
al. <a href="#p2">(2)</a> suggested that the divergence of complex genomic repeat structures
(centromere and telomeres) may have generated the two species.</span></div>
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<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgz12CUYX8f3mY2RdZDjdCPUpQpbQXZCPkSfqTxuMZk-qmB7-TkhQM0tL61PB0RfHjDCxnawPWu29hXyeH7zDltW-nSYvduw-0qT7hhqcx62j_7et3TH8MSIJ7xUcz0PP-24zy5gwVMn-w/s1600/zlin+fig1a+12412.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="137" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgz12CUYX8f3mY2RdZDjdCPUpQpbQXZCPkSfqTxuMZk-qmB7-TkhQM0tL61PB0RfHjDCxnawPWu29hXyeH7zDltW-nSYvduw-0qT7hhqcx62j_7et3TH8MSIJ7xUcz0PP-24zy5gwVMn-w/s400/zlin+fig1a+12412.jpg" width="400" /></a></td></tr>
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<span style="font-size: small;"><b><span style="font-family: "Times New Roman","serif"; line-height: 100%;">Figure
1 a</span></b><span style="font-family: "Times New Roman","serif"; line-height: 100%;">,
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<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;"> The
collared flycatcher <i style="mso-bidi-font-style: normal;">Ficedula albicollis</i>
and the pied flycatcher <i style="mso-bidi-font-style: normal;">Ficedula
hypoleuca</i> diverged less than 2 million years ago.<span style="mso-spacerun: yes;"> </span>They look very similar except for the
presence of white collar in the former species (Figure 1). The authors from
Uppsala University in Sweden have sequenced the ~1.1Gb genomic regions for 10
unrelated males in each species. By comparing these genomic regions, the author
identified 50 "divergence islands", which show significantly high
levels of sequence divergence between the two species. The length of an
"island" ranges from 100 kb to 3 Mb, with a mean of 625kb. Interestingly,
these “islands” are over-represented in the telomere or centromere regions,
which are rich in repeat structures (Figure 2). <span style="mso-spacerun: yes;"> </span>After detailed analyses of various
evolutionary patterns of these "divergence islands" , such as<span style="mso-spacerun: yes;"> </span>local mutation rates,<span style="mso-spacerun: yes;"> </span>levels of nucleotide diversity,<span style="mso-spacerun: yes;"> </span>allele-frequency spectra,<span style="mso-spacerun: yes;"> </span>levels of linkage disequilibrium and shared
polymorphisms,<span style="mso-spacerun: yes;"> </span>the authors confirmed
that these islands have experienced parallel selection in each species.
Although no direct evidence was provided to support how these "divergence
islands" contributed to the speciation, the authors believed that these
observations "raise the possibility that centromeres or other
heterochromatic repeats themselves are the driver of speciation" <a href="#p2">(2)</a>. </span></div>
<br />
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgviwyPhKEZ0HpuTBaTvTgGC1Xn-52hE-OolLTfeUv28z6nomAlijy9OLGAhj6ocIp5fVz_2cVK8WvwT1Kex5kQnVYchRYasaBIr0sONwRQfPXP8_2cpBkaEOSMfjCBvrXptRFShZDloig/s1600/zlin+fig1+12412.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="186" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgviwyPhKEZ0HpuTBaTvTgGC1Xn-52hE-OolLTfeUv28z6nomAlijy9OLGAhj6ocIp5fVz_2cVK8WvwT1Kex5kQnVYchRYasaBIr0sONwRQfPXP8_2cpBkaEOSMfjCBvrXptRFShZDloig/s400/zlin+fig1+12412.jpg" width="400" /></a></td></tr>
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<span style="font-size: small;"><b><span style="font-family: "Times New Roman","serif"; line-height: 100%;">Figure
2.</span></b><span style="font-family: "Times New Roman","serif"; line-height: 100%;">
Distribution of divergence measured as the density of fixed differences per bp
for 200-kb windows across the genome. Chromosomes are listed in numerical order
and are separated by gaps. Red horizontal bars show the approximate location of
centromeres in homologous chromosomes of zebra finch. Open read symbols are
used to indicate that avian microchromosomes are generally acro- or
telocentric. Both ends of these chromosomes are labeled as the orientation is
not known. For chromosomes 4, 6 and 8, there is a lack of an <i>in situ</i> mapped marker 5′ of the
centromere in zebra finch. (from Ellegren et al. <a href="#p2">(2)</a>).</span></span></div>
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(2012), '<a href="http://www.nature.com/nature/journal/v491/n7426/pdf/nature11584.pdf" target="_blank">The genomic landscape of species divergence in <i>Ficedula</i> flycatchers</a>', <i>Nature</i>.
doi:10.1038/nature11584</span></div>
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Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-44058939685934989422012-10-31T13:28:00.000-04:002012-10-31T13:45:19.281-04:00Evolution of Obligate Specialist Species: How Changes to a Single Gene Restricted Drosophila pachea to a Single Species of Cactus <div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt;">
<b>Contributed by: <a href="mailto:sws4@psu.edu" target="_blank">Steve </a><a href="http://www.blogger.com/blogger.g?blogID=3378199995075509398" target="_blank">Schaeffer</a></b><br />
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<![endif]--><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;"> The hormone ecdysone regulates many
developmental processes during metamorphosis in insects.<span style="mso-spacerun: yes;"> </span>In most Drosophila species, cholesterol is
the initial substrate for the pathway that synthesizes ecdysone.<span style="mso-spacerun: yes;"> </span>A recent study by Lang <i style="mso-bidi-font-style: normal;">et al</i>. (2012) provides evidence that amino acid substitutions in
the <i style="mso-bidi-font-style: normal;">neverland</i> gene are responsible
for an adaptive host shift of a Drosophila species. The enzyme produced by the <i style="mso-bidi-font-style: normal;">neverland</i> gene converts cholesterol to
7-dehydrocholesterol in the initial step in the ecdysone pathway.<span style="mso-spacerun: yes;"> </span><i style="mso-bidi-font-style: normal;">Drosophila
pachea</i> lives exclusively on senita cactus (<i style="mso-bidi-font-style: normal;">Lophocereus schottii</i>).<span style="mso-spacerun: yes;"> </span>The
senita cactus lacks appreciable levels of cholesterol, but does have other
sterols such as lathosterol that could be used to make ecdysone.<span style="mso-spacerun: yes;"> </span>The <i style="mso-bidi-font-style: normal;">neverland</i>
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amino acid changes in residues that are strongly conserved among Drosophila
species. Lang <i style="mso-bidi-font-style: normal;">et al</i>. (2012) used transgenic
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<i style="mso-bidi-font-style: normal;">neverland</i> knockdown mutants to test
the activity of the <i style="mso-bidi-font-style: normal;">D. pachea neverland</i>
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convert both cholesterol and lathosterol into 7-dehydrocholesterol while only
lathosterol is used by the extant <i style="mso-bidi-font-style: normal;">D.
pachea</i> enzyme to make 7-dehydrocholesterol. <span style="mso-spacerun: yes;"> </span>A population genetics analysis shows that
nucleotide diversity in the neverland gene region is consistent with a recent
selective sweep.<span style="mso-spacerun: yes;"> </span>This study is a nice
example of an integrative study that used molecular and population genetic
analysis to show how changes to a single enzyme can result in a species being
an obligate specialist.<span style="mso-spacerun: yes;"> </span>In this case, <i style="mso-bidi-font-style: normal;">D. pachea</i> became an obligate specialist
on senita cactus.<span style="mso-spacerun: yes;"> </span>This change may have
allowed <i style="mso-bidi-font-style: normal;">D. pachea</i> to have fewer
competitors on its new host.<span style="mso-spacerun: yes;"> </span>While this
change may currently be advantageous, if availability of the host is reduced, <i style="mso-bidi-font-style: normal;">D. pachea</i> could be an evolutionary
deadend.</span><br />
<br />
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<b>Abstract</b> <br />
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<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Most living
species exploit a limited range of resources. However, little is known about
how tight associations build up during evolution between such specialist
species and the hosts they use. We examined the dependence of <i style="mso-bidi-font-style: normal;">Drosophila pachea</i> on its single host,
the senita cactus. Several amino acid changes in the Neverland oxygenase
rendered <i style="mso-bidi-font-style: normal;">D. pachea </i>unable to
transform cholesterol into 7-dehydrocholesterol (the first reaction in the
steroid hormone biosynthetic pathway in insects) and thus made <i style="mso-bidi-font-style: normal;">D. pachea</i> dependent on the uncommon
sterols of its host plant. The <i style="mso-bidi-font-style: normal;">neverland</i>
mutations increase survival on the cactus</span><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%; mso-fareast-font-family: AdvTTdeec4450+20;">’</span><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">s unusual sterols and are in a genomic
region that faced recent positive selection. This study illustrates how
relatively few genetic changes in a single gene may restrict the ecological
niche of a species.</span></div>
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Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-71304774690438705712012-10-26T16:26:00.000-04:002012-10-31T13:39:18.171-04:00Changes of the XY and ZW Chromosomal Systems in a Frog Species<!--[if gte mso 9]><xml>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> It
is well known that the sex in mammals is determined by the X and Y chromosomes,
the XY being male and the XX being female, whereas the sex in birds is determined
by the Z and W chromosomes (ZZ males and ZW females). These XY and ZW systems
have a history of about 200 million years. Therefore, the sex determination
system seems to be quite stable once it is established <a href="#o1">(1)</a>.</span></span></div>
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<span style="font-size: small; line-height: 100%;"><span style="font-family: Times,"Times New Roman",serif;"><b>Fig.
1. </b>Four geographic
forms of <i>Rana rugosa</i>, differing in
the morphology of sex-determining chromosome 7. Three of these, indicated by
the dotted areas, have an XX/XY sex-determining system. The fourth form,
indicated by the black area, is characterized by a ZZ/ZW system. Three kinds of
sex chromosome 7 can be distinguished morphologically in these four geographic
forms. The Z, Y, and Hiroshima-type chromosomes are subtelocentric, the W and X
chromosomes are metacentric, and the Isehara-type chromosome is more
subtelocentric. S = subtelocentric; mS = more subtelocentric; M = metacentric.</span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> In
amphibians, however, this is not the case, and the same taxonomic family may
include species with both the XY and ZW systems <a href="#o2">(2)</a>. In an extreme case the
same species contains both the XY and ZW systems as polymorphism. This
situation is observed in the Japanese frog <i>Rana
rugosa</i>. This species inhabits almost the entire territory of Japan, but
depending on the geographical area the chromosomal system is either the XY or
the ZW (see Fig. 1). The ZW system is heterogametic, and therefore the male and
female can be distinguished by the chromosomal morphology. However, the XY
system is either heterogametic (Hamakita areas) or homogametic (Hiroshima and Isehara
areas) depending on the geographical area <a href="#o3">(3)</a>. Further studies have shown that
the gene sequence arrangements of the X and Y chromosomes from Hiroshima and
Isehara are different from each other (Fig. 1). How did these chromosomal
systems evolve? Solution of this question may allow us to understand the
general scheme of evolution of sex determination.</span></span></div>
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<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><b>Fig.
2. </b>A phylogenetic
tree of the ADP/ATP translocase gene from the six kinds of sex-determining
chromosome 7. The three kinds of chromosome 7 are shown on the right: S =
subtelocentric; mS = more subtelocentric; M = metacentric.</span></span></div>
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<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> Miura
et al. <a href="#o3">(3)</a> studied the evolutionary history of these sex chromosomes by using
the sex-linked gene, <i>AP/ATP translocase </i>gene,
on the sex chromosome (chromosome 7). The phylogenetic tree constructed from
this gene is presented in Fig. 2. On the basis of this phylogenetic tree, they
proposed the evolutionary scenario presented in Fig. 3. This scenario suggests
that the “subtelocentric chromosomes” in the Hiroshima area first generated the
“more subtelocentric chromosomes” similar to the chromosomes from the Isehara
area. The parental “subtelocentric chromosomes” are then hybridized with the “more
subtelocentric chromosomes” to produce the “metacentric chromosomes.” Finally,
these “metacentric chromosomes” and the Hiroshima “subtelocentric chromosomes”
generated the XY and the ZW chromosomal systems. These evolutionary changes are
believed to have occurred relatively recently.</span></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVbr5OjbLAvqezu4ceAnquYLtdFfu93lN31O3FbfhglhNzkmCEuWwwFfT4V-ehwvne39IbYwtmEhuZffyE0twGfcz_q7qdox1oXJssp9dxnCGoHHdnMo_ax8VDPZui07y78sackde_wI4/s1600/Nei+Frog+Fig.+3+10.25.12.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVbr5OjbLAvqezu4ceAnquYLtdFfu93lN31O3FbfhglhNzkmCEuWwwFfT4V-ehwvne39IbYwtmEhuZffyE0twGfcz_q7qdox1oXJssp9dxnCGoHHdnMo_ax8VDPZui07y78sackde_wI4/s400/Nei+Frog+Fig.+3+10.25.12.jpg" width="320" /></a></td></tr>
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<span style="font-size: small;"><span style="font-family: Times,"Times New Roman",serif;"><b>Fig.
3. </b>A phylogenetic
pathway of the sex-determining chromosome 7 inferred from the ADP/ATP
translocase gene tree. The subtelocentric chromosome is shown by a white area,
the more subtelocentric by shaded area, and the metacentric by black area.</span></span></div>
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<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> However,
there are several problems in this scenario. The first and most important one,
which the authors also recognized, is the nature and the location of
sex-determining genes on the sex chromosomes. The sex is determined not by
chromosomes but by genes, and therefore it is essential to identify the genes
that trigger the formation of testis or ovary. Chromosomal morphology can
change relatively easily by inversion and translocation, but the
sex-determining genes are generally more conserved, and therefore they are
likely to give a more accurate pattern of evolution of sex determination.
Furthermore, the morphological study of chromosomes does not give information
on small gene deletions, insertions, or pseudonization. It is therefore
difficult to reconstruct the evolutionary history of sex determination in the
present case.</span></span></div>
<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> For
the above reason, the authors have not clearly distinguished between the X and
Y chromosomes in the Hiroshima and Isehara areas (Fig. 1 and 3). Fig. 2,
however, indicates that the X and W chromosomes and the Y and Z chromosomes are
evolutionarily related, respectively. Although the phylogenetic tree was
constructed by using a sex-linked gene rather than the sex determining gene,
the results presented are interesting if we consider the mammalian sex determining
gene, <i>SRY</i>, that initiates the pathway
of testis formation. In this case the individual without the <i>SRY</i> gene becomes female as a default
option. In birds, which have the ZW system, the male (ZZ) is believed to form
testis because of the presence of two copies of the sex determining gene, <i>Dmrt1</i>, and the ZW female produces ovary
as a default option (<a href="#o2">2</a>, <a href="#o4">4</a>). </span></span></div>
<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> At
the present time we know nothing about the molecular basis of sex determination
in frogs. However, if we use the sex determination in mammals and birds as
guidance, the evolutionary changes of the XY and ZW systems may be studied at
the molecular level.</span></span></div>
<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> In
this connection, Miura et al. <a href="#o5">(5)</a> presented an interesting observation with
respect to the accumulation of lethal mutations in the Y and W chromosomes. In
frogs it is possible to generate the WW homozygotes by producing the ZW males with
a hormone treatment and by crossing the ZW males with the normal ZW females <a href="#o5">(5)</a>.
This WW homozygote did not survive well in the tadpole stage, and most of the
individuals died sooner or later. When the WW homozygotes were produced from
various geographical locations, it was clear that the W chromosome carries a
lethal mutation but the lethal mutation varies from location to location. In
other words, the W chromosome evolved independently in different locations. Therefore,
when the WW was produced by using the W chromosome from different locations,
the WW homozygotes could survive up to adulthood.</span></span></div>
<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> The
same type of experiment was done with the Y chromosome. In this case the YY
individual could not survive even if the two different Y’s were derived from
different locations. This suggests that the XY system evolved earlier than the
ZW system.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> It
has been argued that once a set of linked genes related to sex determination
evolve in a chromosome the recombination value of the linked gene region tends
to be reduced by modifier genes <a href="#o6">(6)</a> or chromosomal inversions <a href="#o7">(7)</a> and the
recessive lethal mutations gradually accumulate in the region (<a href="#o8">8</a>, <a href="#o9">9</a>). The rate
of accumulation of lethal mutations depends on the mutation rate, population
size, and evolutionary time. </span></span></div>
<div 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"> The
evolutionary change between the XY and ZW systems also occurs more frequently
in small populations than in large populations. Because the <i>R. rugosa</i> frogs generally inhabit the mountainous
areas, the effective population size must be very small. Probably for these
reasons, <i>R. rugosa</i> have undergone
rather rapid changes of the sex chromosome (chromosome 7) and the genes
controlling sex determination. However, the evolutionary changes of sex
determining genes are poorly understood at present. It is hoped that a more
detailed molecular study will be conducted for understanding the evolutionary mechanism
of sex determination in the future.</span></span></div>
<div class="MsoNormal" style="line-height: 200%;">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;"><b>References</b></span></span></div>
<div id = "o1" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">1. Graves JAM. 2008. <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091714" target="_blank">Weird animal genomes and the evolution of vertebrate sex and sex chromosomes.</a> Ann Rev Genet 42:565-586.</span></span></div>
<div id = "o2" 12pt="12pt" class="MsoNormal" font-size:="font-size:" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">2. Sarre SD, Ezaz T, and Georges A.
2011. <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev-genom-082410-101518" target="_blank">Transitions between sex-determining systems in reptiles and amphibians.</a>
Annu Rev Genomics Hum Genet 12:391-406.</span></span></div>
<div id = "o3" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">3.
Miura I, Ohtani H, Nakamura M, Ichikawa Y, and Saitoh K. 1998. <a href="http://mbe.oxfordjournals.org/content/15/12/1612.full.pdf" target="_blank">The origin and differentiation of the heteromorphic sex chromosomes Z, W, X, and Y in the frog <i>Rana rugosa</i>, Inferred from the sequences of a sex-linked gene, ADP/ATP translocase. </a>Mol Biol Evol
15(12):1612-1619.</span></span></div>
<div id = "o4" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">4.
Smith<sup> </sup>CA, Roeszler<sup> </sup>KN, Ohnesorg<sup> </sup>T, Cummins<sup> </sup>DM,
Farlie<sup> </sup>PG, Doran<sup> </sup>TJ, and & Sinclair AH. 2009. <a href="http://www.nature.com/nature/journal/v461/n7261/pdf/nature08298.pdf" target="_blank">The avian Z-linked gene <i>DMRT1</i> is required for male sex determination in the chicken. </a>Nature 461:267-271.</span></span></div>
<div id = "o5" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">5.
Miura I, Ohtani H, and Ogata M. 2012. <a href="http://www.springerlink.com/content/765wq104rrx80642/fulltext.pdf" target="_blank">Independent degeneration of W and Y sex chromosomes in frog <i>Rana rugosa</i>.</a>Chromosome Res 20:47-55.</span></span></div>
<div id = "o6" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">6.
Nei, M. 1969. <a href="http://www.personal.psu.edu/nxm2/1969%20Publications/1969-nei.pdf" target="_blank">Linkage modification and sex difference in recombination.</a> Genetics 63:681-699.</span></span></div>
<div id = "o7" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">7.
Ohno S. 1967. Sex chromosomes and sex-linked genes. Springer-Verlag, New York.</span></span></div>
<div id = "o8" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">8. Muller HJ. 1914. <a href="http://onlinelibrary.wiley.com/doi/10.1002/jez.1400170303/pdf" target="_blank">A gene for the fourth chromosome of <i>Drosophila</i>.</a> J Exp Zool 17:325-336.</span></span></div>
<div id = "o9" class="MsoNormal" style="line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="font-family: Times,"Times New Roman",serif;">9. Nei, M. 1970. <a href="http://www.personal.psu.edu/nxm2/1970%20Publications/1970-nei.pdf" target="_blank">Accumulation of nonfunctional genes on sheltered chromosomes. </a>Am. Nat. 104:311-322.</span></span></div>
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Masatoshi Neihttp://www.blogger.com/profile/15706545477678186676noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-68158198915690280432012-07-19T15:43:00.000-04:002012-07-19T15:43:19.042-04:00Ohno’s Hypothesis of X Chromosome Dosage Compensation Refuted<!--[if gte mso 9]><xml>
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<span style="font-size: 12pt;"><b><span style="color: black;">Contributed by: <a href="mailto:jianzhi@umich.edu" target="_blank">Jianzhi Zhang</a></span></b></span></div>
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<span style="font-size: 12pt;"><b style="font-family: Times,"Times New Roman",serif;"><span style="color: black;"></span></b><span style="color: black; font-family: Times,"Times New Roman",serif;"> </span></span>
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<span style="font-size: 12pt;"><span style="color: black;">The X and Y chromosomes of humans originated from a pair of
autosomes in the common ancestor of placental and marsupial mammals.<span> </span>In his classic book entitled </span><span>“<i>Sex Chromosomes and Sex-Linked Genes</i>”, Susumu
Ohno (1967) </span><span><a href="#n1">(1)</a></span><span> </span><span>wrote, </span><span>“During the course of evolution, an ancestor to placental mammals must
have escaped a peril resulting from the hemizygous existence of all the
X-linked genes in the male by doubling the rate of product output of each
X-linked gene,” (p. 99). </span><span><span> </span>This presumed
doubling of expression on X would cause X tetraploidy in females, which is
believed to be the driving force behind the evolution of the random
inactivation of one X chromosome in females.<span>
</span>As a result, the expressions of X-linked genes become equalized between
males and females.<span> </span></span></span></div>
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<span style="font-size: small;"><b><span>The prevailing
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<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; text-indent: 0.5in;">
<span style="font-size: 12pt;"><span>So, are
expressions of X-linked genes doubled to compensate the loss of their Y
homologs, as Ohno hypothesized 45 years ago?<span>
</span>In the last few years, a number of groups tested Ohno’s hypothesis
indirectly by comparing the expressions of X-linked and autosomal genes in
humans or mice </span><span><a href="#n2">(2-11)</a></span><span>.<span> </span>These authors reached different conclusions
either supporting or refuting Ohno’s hypothesis, depending on the transcriptome
data used and the genes compared.<span> </span>This
controversy is now resolved by a direct comparison of the expression levels of
human X-linked genes with those of their one-to-one orthologs in chicken.<span> </span></span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; text-indent: 0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">Julien et al. <span><a href="#n12">(12)</a></span> and
Lin et al. <span><a href="#n13">(13)</a></span> analyzed the same RNA-Seq
data published </span>last year.<span> </span>They
found that the expression ratio between a human X-linked gene and its
one-to-one ortholog in the “proto-X” chromosome in chicken has a median of
~0.5.<span> </span>That is, the per-allele expression
level of X-linked genes is on average unchanged!<span> </span>This finding conclusively refutes Ohno’s
hypothesis. </span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; text-indent: 0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">Does this finding imply that a two-fold change in gene
expression has such a small fitness effect that dosage compensation is hardly
needed?<span> </span>The answer appears different for
different genes.<span> </span>First, following a
recent analysis <span><a href="#n14">(14)</a></span>, Lin et al. found
that proto-X genes that encode members of large protein complexes did
experience an on average two-fold up-regulation during sex chromosome
evolution, likely because of the high dose sensitivity of large protein complex
members.<span> </span>But these genes constitute only
~5% of all X-linked genes and therefore do not show up in the chromosome-wide
analysis.<span> </span>Second, there are X-linked
genes that have now migrated to autosomes, which may have been a strategy to
avoid a dose change. <span> </span>Third, a
genome-wide study showed that haploinsufficiency is rare in yeast.<span> </span>It is possible that the same is true in
mammals.<span> </span>Fourth, even for one-to-one
orthologous genes in autosomes, a two-fold expression difference between human
and chicken is not uncommon, suggesting that perhaps expression levels need not
be so finely regulated and conserved.<span>
</span>Together, the analyses suggest that, for most genes on the proto-X, a
50% expression reduction is quite tolerable and need not be compensated. </span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; text-indent: 0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">Because Ohno’s hypothesis is the basis of the current model
of male:female X chromosome dosage compensation, its invalidation opens the
research for a new evolutionary explanation of X inactivation in female
mammals.<span> </span></span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%;">
<br /></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%;">
<span style="font-size: 12pt;"><b><span style="color: black;">References</span></b></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%;">
<br /></div>
<div id = "n1" class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">1. Ohno S (1967) Sex Chromosomes and
Sex-Linked Genes. New York: Springer-Verlag.</span></span></div>
<div id = "n2" class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">2. Gupta V, Parisi M, Sturgill D, Nuttall
R, Doctolero M, et al. (2006) <a href="http://jbiol.com/content/pdf/jbiol30.pdf" target="_blank">Global analysis of X-chromosome dosage compensation.</a> J Biol 5: 3.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">3. Nguyen DK, Disteche CM (2006) <a href="http://www.nature.com/ng/journal/v38/n1/pdf/ng1705.pdf" target="_blank">Dosage compensation of the active X chromosome in mammals. </a>Nat Genet 38: 47-53.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">4. Lin H, Gupta V, Vermilyea MD, Falciani
F, Lee JT, O'Neill LP, and Turner, BM (2007) <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050326" target="_blank">Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes.</a> PLoS Biol 5: e326.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">5. Xiong Y, Chen X, Chen Z, Wang X, Shi S, Wang X, Zhang J, and He X (2010) <a href="http://www.nature.com/ng/journal/v42/n12/pdf/ng.711.pdf" target="_blank">RNA sequencing shows no dosage compensation of the active X-chromosome.</a> Nat Genet 42: 1043-1047.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">6. Deng X, Hiatt JB, Nguyen DK, Ercan S,
Sturgill D, Hillier L, Schlesinger F, Davis C, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, and Disteche CM (2011) <a href="http://www.nature.com/ng/journal/v43/n12/pdf/ng.948.pdf" target="_blank">Evidence for compensatory upregulation of expressed X-linked genes in mammals, <i>Caenorhabditis elegans</i> and <i>Drosophila melanogaster</i>.</a>
Nat Genet 43: 1179-1185.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">7. Kharchenko PV, Xi R, Park PJ (2011)
<a href="http://www.nature.com/ng/journal/v43/n12/pdf/ng.991.pdf" target="_blank">Evidence for dosage compensation between the X chromosome and autosomes in mammals.</a> Nat Genet 43: 1167-1169.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">8. Lin H, Halsall JA, Antczak P, O'Neill
LP, Falciani F, and Turner BM (2011) <a href="http://www.nature.com/ng/journal/v43/n12/pdf/ng.992.pdf" target="_blank">Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis.</a> Nat Genet 43:
1169-1170.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">9. Yildirim E, Sadreyev RI, Pinter SF, Lee
JT (2012) <a href="http://www.nature.com/nsmb/journal/v19/n1/pdf/nsmb.2195.pdf" target="_blank">X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription.</a> Nat Struct Mol Biol 19: 56-61.</span></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt;"><span style="color: black;">10. He X, Chen X, Xiong Y, Chen Z, Wang X, Shi S, Wang X, and Zhang J (2011) <a href="http://www.nature.com/ng/journal/v43/n12/pdf/ng.1010.pdf" target="_blank">He et al. reply.</a> Nat Genet 43: 1171-1172.</span></span></div>
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<span style="font-size: 12pt;"><span style="color: black;">11. Castagne R, Rotival M, Zeller T, Wild
PS, Truong V, Tregouet DA, Munzel T, Ziegler A, Cambien F, Blankenberg S, and Tiret L (2011) <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023956" target="_blank">The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome.</a>
PLoS One 6: e23956.</span></span></div>
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<span style="font-size: 12pt;"><span style="color: black;">12. Julien P, Brawand D, Soumillon M,
Necsulea A, Liechti A, Schutz F, Daish T, Grutzner F, and Kaessmann H (2012) <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001328" target="_blank">Mechanisms and evolutionary patterns of mammalian and avian dosage compensation</a>. PLoS Biol 10: e1001328.</span></span></div>
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<span style="font-size: 12pt;"><span style="color: black;">13. Lin F, Xing K, Zhang J, He X (2012)
<a href="http://www.pnas.org/content/109/29/11752.full.pdf" target="_blank">Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation. </a>Proc Natl Acad Sci U S A 109: 11752-11757.</span></span></div>
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<span style="font-size: 12pt;"><span style="color: black;">14. Pessia E, Makino T, Bailly-Bechet M,
McLysaght A, Marais GA (2012) <a href="http://www.pnas.org/content/109/14/5346.full.pdf" target="_blank">Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome.</a>
Proc Natl Acad Sci U S A 109: 5346-5351.</span></span></div>
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<br /></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-19416970524419344332012-07-16T17:11:00.000-04:002012-12-06T17:04:47.169-05:00Dawn of Molecular Biology of Infrared Vision<div style="font-family: Times,"Times New Roman",serif;">
<span style="font-size: 12pt;"><b>Contributed by: <a href="mailto:syokoya@emory.edu" target="_blank">Shozo Yokoyama</a></b></span></div>
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<span style="font-size: 12pt;">Humans visualize a
narrow range, 400-700 nanometer (nm), of electromagnetic radiation (light),
which is reflected from the surfaces of various objects in nature. In addition to the photochemical detection of
light, certain animals and insects have acquired infrared (IR) vision during
evolution. IR is electromagnetic
radiation with longer wavelength (750 nm - 1 mm) than those of the visible
light. Much of the energy we receive
from the sun is IR radiation, but the IR radiation also includes the thermal radiation emitted by animals. Organisms with IR vision detect the thermal
radiation (750-1,200 nm) for hunting and thermoregulation. </span></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2Tly86-2BFle9LvuOLwZglW6oVsDu5oEiJ4mOffLMw1yTPzWB0xrulHGdnpwa3SaAIRCdcUkUNYrgPEkuzGlFMSjZU7usJIZsgVt8eP5TObdR7LDSGFkGZYAYD7uIL17udlsWM8nhz_o/s1600/Fig.+1+pit+viper.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="310" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2Tly86-2BFle9LvuOLwZglW6oVsDu5oEiJ4mOffLMw1yTPzWB0xrulHGdnpwa3SaAIRCdcUkUNYrgPEkuzGlFMSjZU7usJIZsgVt8eP5TObdR7LDSGFkGZYAYD7uIL17udlsWM8nhz_o/s320/Fig.+1+pit+viper.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div align="center" class="MsoNormal" style="text-align: center;">
<b style="mso-bidi-font-weight: normal;">Fig. 1</b>. Pit viper pit organ.</div>
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<span style="font-size: 12pt;">Only four
vertebrates (pit vipers, boas, pythons, and vampire bats) are known to detect
and localize sources of infrared (IR) radiation. Their infrared “eyes” can be one pair (pit vipers
and vampire bats) or as many as 13 pairs (boas and pythons) of deep cavities
located beneath their eyes, called pit organs <a href="#mfig1">(Fig. 1)</a>. In the rattlesnake, the pit organs contain an
inner chamber that is separated by a thin (15 mm), concave IR-sensitive
membrane <a href="#mfig2">(Fig. 2)</a> <a href="#m1">(<i>1</i>)</a>. The IR and
visible-light information are integrated in the brain to yield a unique
wide-spectrum picture of the world <a href="#m2">(<i>2</i>)</a>. Since the postulation that such pit organs
can be capable of detecting subtle environmental stimuli <a href="#m3">(<i>3</i>)</a>, the
anatomy of the pit organs and the behavioural consequences of IR vision have
been extensively studied. Having no IR
receptors in hand, however, little is known about the molecular basis of IR
vision. Thanks to the discovery of the
IR receptors by David Julius and his colleagues at UCSF (<a href="#m4"><i>4</a>, <a href="#m5">5</i></a>), this 80-year
stalemate is going to be overcome.
Before these papers were published, it had been suspected that IR
receptors operate on a thermal principle rather than photochemical principle
(e.g. <a href="#m6">(<i>6</i>)</a>),
suggesting that the transient receptor potential (TRP) ion channels may be
involved.</span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUz7zeuy-wso_XzJ5agWlKCJJrLUqKvfY5EQrZBdD8WO4CtFf8iO79JIMDJ1WCF4YNQ1XJdTStPl_RgvfEuhF-K3d1XgCDTXxbtJE6obc1gIBUXVz4yQfWd2CnsGxIFi_CfNe_phcOWVI/s1600/Fig.+2+Rattlesnake+pit+organ.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="340" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUz7zeuy-wso_XzJ5agWlKCJJrLUqKvfY5EQrZBdD8WO4CtFf8iO79JIMDJ1WCF4YNQ1XJdTStPl_RgvfEuhF-K3d1XgCDTXxbtJE6obc1gIBUXVz4yQfWd2CnsGxIFi_CfNe_phcOWVI/s400/Fig.+2+Rattlesnake+pit+organ.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "Times New Roman","serif"; font-size: 11pt;"> </span><span style="font-family: "Times New Roman","serif"; font-size: 11pt;">Fig. 2. Rattlesnake pit organ, (<i style="mso-bidi-font-style: normal;">1</i>). </span><span style="font-family: "Times New Roman","serif"; font-size: 11pt;"> </span></td></tr>
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<span style="font-size: 12pt;">The TRP ion channels are involved in a diverse range of biological
processes, including calcium and magnesium homeostasis, neuronal growth,
temperature sensation, and pain sensation (<a href="#m7"><i>7</a>, <a href="#m8">8</i></a>). Based on sequence similarity, the TRP
superfamily can be divided into seven subfamilies: TRPC (canonical), TRPV
(vanilloid), TRPM (melastatin), TRPA (ankyrin), TRPN (NOMPC), TRPP
(polycystin), and TRPML (mucolipin) (Fig. 3).
The total numbers of TRP channels in worm (<i>C. elegans</i>), fruit fly (<i>D.
melanogaster</i>), mouse (<i>M. musculus</i>),
and human vary between 13 and 28 <a href="#m8">(<i>8</i>)</a>. So, which TRP receptor is involved in the IR
vision? </span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjs8Ib-ZYE0eNovPkS2TbPtICBkcK-qPqKZI97MeFAfp7iKvRhq9TWA1_L_YbJjQLiQcdFuFlGgkhx-z45Po3zs-uUyh_32qrYE7tGqiu3HPg7Sho0K8rGZsOgMDVJPI5QhM92w0AyYOxk/s1600/Fig.+3+TRP+Channels.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="171" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjs8Ib-ZYE0eNovPkS2TbPtICBkcK-qPqKZI97MeFAfp7iKvRhq9TWA1_L_YbJjQLiQcdFuFlGgkhx-z45Po3zs-uUyh_32qrYE7tGqiu3HPg7Sho0K8rGZsOgMDVJPI5QhM92w0AyYOxk/s400/Fig.+3+TRP+Channels.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "Times New Roman","serif"; font-size: 11pt;">Fig. 3. Some examples of TRP receptors, (<i style="mso-bidi-font-style: normal;">8</i>).</span></td></tr>
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<span style="font-size: 12pt;">The best candidates for the IR receptors are TRPVs because of their
sensitivities to body-heat and external temperatures. For example, TRPV1, 2, 3, and 4 are activated
at 43, 52, 39, and 27-34 <sup>o</sup>C, respectively. However, in the first paper <a href="#m4">(<i>4</i>)</a>,
Gracheva et al. have shown that the IR receptors isolated from the western
diamondback rattlesnake (<i>Crotalus atrox</i>), ball python (<i>Python regius</i>),
and garden tree boa<i> </i>(<i><span style="color: #292526;">Corallus hortulanus</span></i><span style="color: #292526;">)
are </span>TRPA1s. Many people
may have personally experienced the fiery sensation caused by wasabi when
eating sushi. This sensation is
initiated by our TRPA1 receptors. The
paper contains an enormous amount of data on the molecular cloning and
expression of TRPA1s, omics, and some molecular evolution not only of the three
evolutionarily distantly related rattlesnake, python, and boa but also of the
Texas rat snake (<i><span style="color: #292526;">Pantherophis obsoletus
lindheimeri</span></i><span style="color: #292526;">) without IR vision. Interestingly, the rattlesnake is evolutionarily
more closely related to the rat snake than to the python or the boa, suggesting
the independent origin of IR vision among the snakes.</span></span></div>
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<span style="font-size: 12pt;">Knowing that the snakes use TRPA1 for their IR vision, we might now think
that vampire bats<span style="color: #292526;"> (<i>Desmodus rotundus</i>) also modified TRPA1 to detect IR. We are wrong again! The second and equally wonderful paper <a href="#m5">(<i>5</i>)</a></span>
reveals that the vampire bat after all uses one of the TRPVs, TRPV1, for its IR
vision. One fascinating feature is that
the bat IR-detection has been achieved through alternative splicing of the
TRPV1 transcript that produces a truncated receptor, which is caused by a newly
acquired extra exon of 29 nucleotides. </span></div>
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<span style="font-size: 12pt;">The discoveries of the IR receptors in the snakes and vampire bat will
open an exciting new chapter in the molecular analyses of signal transduction
underlying IR detection. Molecular
evolutionary studies of the two sets of IR-sensitive and other TRP receptors
will be helpful not only in understanding the mechanisms of IR vision but also
in elucidating the mechanisms of phenotypic differentiation of diverse TRP
superfamily members.<b> </b></span></div>
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<span style="font-size: 12pt;"><b>References</b></span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m1" style="font-size: 12pt;">1. E. A. Newman, P. H. Hartline, The infrared
'vision' of snakes. <i>Sci. Amer.</i> <b>20</b>, 116 (1982).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m2" style="font-size: 12pt;">2. E. A. Newman, P. H. Hartline, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4eFBMV3JZbHFRM0U" target="_blank">Integration of visual and infrared information in bimodal neurons in the rattlesnake optic tectum.</a> <i>Science</i> <b>213</b>, 789 (Aug 14, 1981).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m3" style="font-size: 12pt;">3. W. G. Lynn, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4VmR6eldxSGNHM1k" target="_blank">The structure and function of the facial pit of the pit vipers.</a> <i>American Journal
of Anatomy</i> <b>49</b>, 97 (1931).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m4" style="font-size: 12pt;">4. E. O. Gracheva<i> et al.</i>, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4YTExT25BX3pRTkE" target="_blank">Molecular basis of infrared detection by snakes. </a><i>Nature</i> <b>464</b>, 1006 (Apr 15, 2010).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m5" style="font-size: 12pt;">5. E. O. Gracheva<i> et al.</i>, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4VDdHT2p5V1J6bUU" target="_blank">Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats.</a> <i>Nature</i> <b>476</b>, 88 (Aug 4, 2011).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m6" style="font-size: 12pt;">6. J. F. Harris, R. I. Gamow, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4WU04UFhCQklBZnM" target="_blank">Snake infrared receptors: thermal or photochemical mechanism?</a> <i>Science</i> <b>172</b>, 1252 (Jun
18, 1971).</span></div>
<div class="aug" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "m7" style="font-size: 12pt;">7. R. Gaudet, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4RWE4VWRycUJTWnM" target="_blank">A primer on ankyrin repeat function in TRP channels and beyond.</a> <i>Mol
Biosyst</i> <b>4</b>, 372 (May, 2008).</span></div>
<div class="aug" style="line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span id = "m8" style="font-family: Times,"Times New Roman",serif; font-size: 12pt;">8. K. Venkatachalam, C. Montell, <a href="https://docs.google.com/open?id=0BylAIZ8juWh4b192eW1UVVY1b2M" target="_blank">TRP channels.</a> <i>Annu Rev Biochem</i> <b>76</b>, 387 (2007).</span></div>
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</div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-80419914320986620842012-07-10T17:02:00.000-04:002012-07-10T17:03:53.304-04:00Mystery of Pod Corn (Tunicate maize) Solved<div style="font-family: Times,"Times New Roman",serif;">
<span style="font-size: 12pt;"><b>Contributed by: <a href="mailto:jnam@caltech.edu" target="_blank">Jongmin Nam</a></b></span></div>
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<span style="font-size: 12pt;"> Pod corn (<i>Zea mays </i>var.<i> tunicata</i>) is a variety of maize that has kernels enclosed in elongated
glumes (Figure 1), which is caused by a dominant gain-of-function mutation at
the <i>Tunicate</i> (<i>Tu</i>) locus. The <i>Tu</i> also has
a gene dosage effect, as there are several partial phenotypic revertants.
Because the <i>Tunicate</i> phenotype is a
universal characteristic of wild grasses and is different from naked
kernels in maize varieties common today, pod corn is thought to be a progenitor
of maize by some researchers. Despite long-standing interest in the evolution of this phenotype,
molecular identity of the locus has remained unclear.</span></div>
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<span style="font-size: small;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXeHW6BQj1eUvRV6u9-8qJ3TX8fZhqRAK6Nrn73eKDWwnNBjyNO4as10X-lLO_79wUa3Pi0qrwCdHl5gedT4iiU9qu8giMCjPoYWc2HX7La4g0hMLyvlglHbijRir0xIU7O69SB77Bf0E/s1600/Nam+Pod+Corn+Fig.+1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="255" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXeHW6BQj1eUvRV6u9-8qJ3TX8fZhqRAK6Nrn73eKDWwnNBjyNO4as10X-lLO_79wUa3Pi0qrwCdHl5gedT4iiU9qu8giMCjPoYWc2HX7La4g0hMLyvlglHbijRir0xIU7O69SB77Bf0E/s400/Nam+Pod+Corn+Fig.+1.jpg" width="400" /></a></span></div>
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<span style="font-size: 12pt;"> In a recent
paper published in PNAS <a href="#k1">(1)</a>, Wingen et
al. tested the hypothesis that genomic changes in a maize MADS-box
transcription factor gene, ZMM19, are responsible for the <i>Tunicate</i> phenotype. They then obtained the following results that
support the hypothesis: 1) The genomic location of ZMM19 is very close to the <i>Tu</i> locus; 2) Ectopic expression of
ZMM19, a gene normally expressed only in vegetative tissues, in male and female
inflorescence is observed in all pod corn lines tested; 3) Constitutive
expression of ZMM19 in Arabidopsis resulted in enlarged sepals with unusual
vegetative characters, which is similar to the <i>Tunicate</i> phenotype; 4) Insertions of a transposable element-like
sequence in the 5' upstream region of the gene is observed, although the effect
of this insertion has not been shown yet; 5) Perhaps most interestingly, the tandem
duplication of ZMM19 specifically in pod corns and loss of one of the
duplicates in several partial phenotypic revertant lines explain the gene
dosage effect of the <i>Tu</i>. Moreover,
this study suggests that pod corn is not a progenitor of common maize
varieties, because the same insertion of transposable elements and gene
duplication in the ZMM19 locus were not observed in wild grasses.</span></div>
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<span style="font-size: 12pt;"> This study is
a neat example of how a detailed molecular genetic study can help solving
long-standing evolutionary questions, though in this case reciprocal
engineering experiment of the ZMM19 locus between pod corn and common maize
varieties is necessary to prove the authors' hypothesis.</span></div>
<div class="MsoNormalCxSpMiddle" style="font-family: Times,"Times New Roman",serif; line-height: 200%;">
<span style="font-size: 12pt;"> In
principle, any mutation has the potential to cause phenotypic evolution, and
this is not the first study suggesting that gene expression change and gene
copy number variation resulted in a phenotypic change. However, we still need
more case studies to draw general principles of phenotype-mutation
relationship, so I would never get tired of reading this type of paper.</span></div>
<div class="MsoNormalCxSpMiddle" style="font-family: Times,"Times New Roman",serif; line-height: 200%; text-indent: 0.5in;">
<span style="font-size: 12pt;">The abstract of their paper is as
follows.</span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; line-height: 200%;"></span><br />
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<tbody>
<tr>
<td bgcolor="#ffffcc"><div align="left">
<br />
<div 200%;?="" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0.5in 10pt;">
<b>Abstract</b> <br />
<div align="left" class="MsoNormal" style="font-size: 12pt;">
<br />
<div class="MsoNormalCxSpFirst" style="line-height: 200%; margin: 0in 0.3in 0.0001pt 0.3in;">
Pod corn is a classic
morphological mutant of maize in which the mature kernels of the cob are
covered by glumes, in contrast to generally grown maize varieties in which
kernels are naked. Pod corn, known since pre-Columbian times, is the result of
a dominant gain-of-function mutation at the <i>Tunicate</i>
(<i>Tu</i>) locus. Some classic articles of
20th century maize genetics reported that the mutant <i>Tu</i> locus is complex, but molecular details remained elusive. Here,
we show that pod corn is caused by a <i>cis</i>-regulatory
mutation and duplication of the ZMM19 MADS-box gene. Although the <i>WT</i> locus contains a single-copy gene
that is expressed in vegetative organs only, mutation and duplication of ZMM19
in <i>Tu</i> lead to ectopic expression of
the gene in the inflorescences, thus conferring vegetative traits to
reproductive organs.</div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin: 0in 0.3in 0.0001pt 0.3in;">
<b>PMID: 22517751</b></div>
</div>
<div style="line-height: 200%;">
<span style="color: black;">
<o:p></o:p>
</span></div>
</div>
</div>
</td>
</tr>
</tbody></table>
<span style="font-size: 12pt; line-height: 200%;">
</span></div>
<div style="font-family: Times,"Times New Roman",serif;">
<span style="font-size: 12pt;"><br /></span></div>
<div style="font-family: Times,"Times New Roman",serif;">
<span style="font-size: 12pt;"><br /></span></div>
<div style="font-family: Times,"Times New Roman",serif;">
</div>
<div class="MsoNormalCxSpFirst" style="font-family: Times,"Times New Roman",serif; line-height: 200%;">
<span style="font-size: 12pt;"><b>References</b></span></div>
<div class="MsoNormal" style="font-family: Times,"Times New Roman",serif; line-height: 200%; margin-left: 0.5in; text-indent: -0.5in;">
<span id = "k1" style="font-size: 12pt;">1. Wingen LU, Munster T, Faigl W, Deleu W, Sommer H, Saedler H, Theißen G. 2012. <a href="http://www.pnas.org/content/109/18/7115.full.pdf" target="_blank">Molecular genetic basis of pod corn (Tunicate maize). </a>Proceedings of the National Academy of Sciences of
the United States of America 109: 7115-7120.</span></div>
<br />
<br />
<br />
<br />Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-88409018904378392822012-07-06T16:52:00.000-04:002012-07-06T16:52:39.537-04:00Gene Transfer from Organelles to Nuclei Visualized<div style="font-family: Times,"Times New Roman",serif; font-size: 12pt;">
<b>Contributed by: <a href="mailto:zlin1@uchicago.edu" target="_blank">Zhenguo Lin</a></b></div>
<br />
<br />
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; text-indent: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">It has been generally accepted that mitochondria
and chloroplasts in eukaryotic cells originated from ancestral free-living
prokaryotes through endosymbiosis. Compared with their free-living sibling prokaryotes
(proteobacteria and cyanobacteria), which contain over 3,000 genes, the genome
sizes of mitochondria and chloroplasts are much smaller. The mitochondrial
genome encodes a few to about 70 proteins, whereas the chloroplast genome produces
20 to 200 proteins. Therefore, a major challenge of the endosymbiosis
hypothesis is to explain the difference in genome size between the organelles
and their free-living counterparts. </span></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; text-indent: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">It has been shown that many proteins
encoded by the nuclear genome are essential for the function of chloroplasts
and mitochondria, suggesting that genes have been relocated from the ancestral
organelle to the nucleus during evolution. The gene transfer from organelles to
nuclei has been supported by many bioinformatics and genomics studies. In one
of the well-known studies, Martin el al. showed that approximately 18% of the
nuclear genes in <i style="mso-bidi-font-style: normal;">Arabidopsis</i> come
from the ancestral chloroplast genome <a href="#j1">(1)</a>. In addition, several experimental
studies showed that the translocation of genes from organelles to nuclei indeed
occurs and that the translocation process is still ongoing. In fact, using the nucleus-specific
marker gene approach, Huang et al. <a href="#j2">(2)</a> showed that the marker gene was
integrated into a nuclear chromosome in 16 out of 250,000 tobacco seedlings,
which provided the first experimental measurement of the frequency of gene
transfer from chloroplasts to nuclei.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; text-indent: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Although the optimal growth temperature
for tobacco plants is around 25 °C, they regularly encounter much higher temperature
in nature and the temperature might exceed 40 °C in leaf due to radiant heating
effect. In a recent PNAS paper <a href="#j3">(3)</a>, Wang et al. reported that gene transfer from
organelles to nuclei can be increased up to 10-fold under mild heat
stress. In this study, the authors
placed a nucleus-specific reporter gene (<i style="mso-bidi-font-style: normal;">gus</i>)
into the tobacco chloroplast genome.
Because the expression of the reporter <i style="mso-bidi-font-style: normal;">gus</i> is driven by 35S promoter and terminator and the gene contain a nuclear
intron, the translation of <i style="mso-bidi-font-style: normal;">gus</i> in chloroplasts
cannot occur. The reporter <i style="mso-bidi-font-style: normal;">gus</i> gene
can be expressed only if the gene is transferred to nuclei, and the expression can
be visualized as blue sectors in cells by histochemical staining of the <i style="mso-bidi-font-style: normal;">gus</i> product. Using this technique, the
authors have examined the effects of various stress conditions on the organelle
to nucleus gene transfer: including the treatment with heat, salt, hydrogen peroxide
and paraquat. The authors found that mild heat stress (45 °C) has the strongest
effect on the gene transfer <a href="#jFig">(Figure 1)</a>. </span></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; text-indent: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Why does heat stress increase the gene transfer?
To answer this question, the authors treated a tobacco plant containing GFP (Green Florescence Protein) in its chloroplast
genome with heat stress. They found that the GFP florescence was widespread in
the cell after heat stress, while in the plant without heat treatment GFP florescence
colocalized in chloroplasts. The authors concluded that heat stress disrupts chloroplast
membranes and release DNA into the cytosol, which could facilitate the transfer
of organellar genes into nuclei. Considering that the translocation of
organellar genes to nuclei is remarkably high under ideal growth condition <a href="#j2">(2)</a> and
the growth condition in real world is much more variable, the influx of
organellar genes into nuclei could be much more frequent than generally recognized
and this process could be an important source of mutations for nuclear genomes.</span></div>
<div id = "jFig" class="MsoNormal" style="line-height: 200%; margin-bottom: 0.0001pt; text-indent: 0.5in;">
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbRaaygqy44WMccHDe3hm3lT42yKAvhrzlDiHNgolsnqNoB7-11WZFClAjD4Bb8nfCfVOgk7WFTPmcw-XlskIfEuDeSNIMxUDTq-0VdwN2zztYA9KeDiqptrgr_O1Z3dMXEmfLXxvHcVQ/s1600/Lin+Heat+Stress+Photo.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbRaaygqy44WMccHDe3hm3lT42yKAvhrzlDiHNgolsnqNoB7-11WZFClAjD4Bb8nfCfVOgk7WFTPmcw-XlskIfEuDeSNIMxUDTq-0VdwN2zztYA9KeDiqptrgr_O1Z3dMXEmfLXxvHcVQ/s1600/Lin+Heat+Stress+Photo.jpg" /></a></td></tr>
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<span style="font-size: small;"><b><span style="font-family: "Times New Roman","serif";">Figure. 1.</span></b><span style="font-family: "Times New Roman","serif";">
Plastid-to-nucleus gene transfer in heat-stressed tobacco seedlings: time
course of heat treatment. (A) Histochemical staining of whole seedlings. Seedlings
were grown for 2 weeks at 25 °C, treated at 45 °C for the indicated times, and
allowed to recover at 25 °C for 2 days before staining for <i>gus</i> expression. (B) RT-PCR of <i>gus</i>
mRNA with (+) and without (−) reverse transcriptase after heat stress (hr). The
positive control gs1.1 (20) is a plant line containing a nuclear copy of <i>gus</i>. rpl25 mRNA RT-PCR was used as a
technical and loading control. (C) Spliced <i>gus</i>
mRNA levels relative to rpl25 mRNA. <i>Gus</i>
mRNA was significantly increased in the 5 hour sample compared with the 0 hour control
(P < 0.05, two-sample Independent t test). (D) The memory of heat stress.
The 2-week-old plants with two leaves and two cotyledons were treated at 45 °C
for 0 or 5 hours and allowed to recover for 1 month before GUS staining. (Scale
bars: 3 mm.) (Scale bars: 3 mm.)</span></span></div>
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">References</span></b></div>
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<span id = "j1" style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">1.
Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T.,
Leister, D., Stoebe, B., Hasegawal, M., and Penny, D. 2002. <a href="http://www.pnas.org/content/99/19/12246.full.pdf" target="_blank">Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus.</a> Proc.
Natl Acad. Sci. USA 99, 12246–12251. </span></div>
<div class="MsoNormal" style="line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span id = "j2" style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">2.
Huang, CY., Ayliffe, MA., and Timmis, JN. 2003. <a href="http://www.nature.com/nature/journal/v422/n6927/pdf/nature01435.pdf" target="_blank">Direct measurement of the transfer rate of chloroplast DNA into the nucleus. </a>Nature 422, 72–76.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin-left: .5in; text-indent: -.5in;">
<span id = "j3" style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">3.
Wang, D., Lloyd, AH., and Timmis, JN . 2012. <a href="http://www.pnas.org/content/early/2012/01/27/1117890109.full.pdf" target="_blank">Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants.</a> Proc Natl Acad
Sci U S A. 109(7):2444-8.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin-bottom: 0.0001pt; text-indent: 0.5in;">
<br /></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-48616612319707668712012-06-06T15:17:00.000-04:002012-06-06T15:20:32.568-04:00Instant Insecticide Resistance by Symbiosis<!--[if gte mso 9]><xml>
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<b style="mso-bidi-font-weight: normal;"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 115%;">Contributed by: <a href="mailto:zlin1@uchicago.edu" target="_blank">Zhenguo Lin</a></span></b></div>
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<br /></div>
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<br /></div>
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<span style="background: none repeat scroll 0% 0% white; color: black; font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">In the first half of the 20<sup>th</sup> century,
chemical pesticides began to be widely used to control a variety of pest
species. In her 1962 groundbreaking book Silent Spring, Rachel Carson argued that
insects are building up resistance to pesticides. Sadly, as Carson foretold, cases
of resistance surfaced within two to 20 years after the introduction of every kind
of new insecticide.</span></div>
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<span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">It is generally believed that the development of
pesticide resistance is generated by changes of genetic information in the
pest's genomes and it takes many generations for the pesticide resistant genes to
spread in the population. However, some short cuts of acquiring pesticide resistance
actually exist. As discussed in my <a href="http://molecularevolutionforum.blogspot.com/2012/04/evolution-of-poison-resistance-gene.html">previous
blog</a>, it is found that European house mice stole a rodenticide resistant
gene through hybridization with Algerian mice <a href="#i1">(1)</a>. In a recent PNAS paper <a href="#i2">(2)</a> ,
Kikuchi et al. found an unexpected mechanism of rapid acquisition of insecticide
resistance from bacterial symbionts in bean bugs and stinky bugs, which are
major pests in agriculture. </span></div>
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<span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Fenitrothion
is an </span></span><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">organophosphate insecticide
that acts as an inhibitor of cholinesterase, so that the nerve function is
damaged in insects, humans, and many other animals. Fenitrothion has been
heavily used to kill a wide range of pests. <span class="apple-converted-space">However,
it has been found that repeated application of fenitrothion leads to rapid
increase of fenitrothion-degrading microbes, including some species in the bacterial
genus of <i style="mso-bidi-font-style: normal;">Burkholderia</i>. These bacteria
are able to breakdown feritrothion into products that can be used as their carbon
source. </span></span></div>
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<span class="apple-converted-space"><i style="mso-bidi-font-style: normal;"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Burkholderia</span></i></span><span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;"> are able
to inhabit prosperously in the midgut of the bean bugs as symbionts. The
infected bean bugs tend to grow bigger than uninfected bugs, showing mutual
benefits of symbiosis.<span style="mso-spacerun: yes;"> </span></span></span><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Kikuchi et al. <span class="apple-converted-space">infected
the bean bugs with six different <i style="mso-bidi-font-style: normal;">Burkholderia</i>
species (strains): three of them are fenitrothion-degrading and the others are non-degrading
<a href="#ifigure1">(Figure 1)</a> . They found that the bean bug infected with fenitrothion-degrading <i style="mso-bidi-font-style: normal;">Burkholderia</i> has much higher survival
rates than those bugs infected with non-degrading <i style="mso-bidi-font-style: normal;">Burkholderia</i>, because the degraded fenitrothion is almost non-toxic
to bugs. This study indicates that the insects can become resistant to
fenitrothion instantly after they swallow these fenitrothion-degrading bacteria.</span></span></div>
<div class="MsoNormal" style="line-height: 200%; text-indent: 0.5in;">
<span class="apple-converted-space"><span style="background: none repeat scroll 0% 0% white; color: black; font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Interestingly,
unlike many other insects, the offspring of bean bugs does not inherit <i style="mso-bidi-font-style: normal;">Burkholderia</i> from their mothers. The bean
bugs need to pick the <i style="mso-bidi-font-style: normal;">Burkholderia</i> symbionts
from surrounding soils each generation before reaching the adult stage. This
seems to be inefficient, but it reduces the possibility that the
fenitrothion-degrading bacteria become so dependent on their hosts that they lose
their chemical-detoxifying genes. In addition, the authors found that the
resistant <i style="mso-bidi-font-style: normal;">Burkholderia</i> species can
increase rapidly in soil after treated with fenitrothion even though these
bacteria are very rare in natural environments. The fenitrothion-degrading species
rapidly become the most dominant group (>80%) in the <i style="mso-bidi-font-style: normal;">Burkholderia</i> population after merely one month of fenitrothion
treatment. Therefore, bean bugs can easily acquire pesticide resistance because
the resistance may have already developed in the bacterial population even before
the arrival of insects. In addition, considering that the highly diversified
enzymatic functions of bacteria are able to detoxify many different pesticide, the
acquisition of instant pesticide resistances from these bacterial symbionts
will definitely bring new challenges for the efficiency of insecticides.</span></span></div>
<br />
<br />
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<span style="font-size: small;"><b><span style="color: black; font-family: "Times New Roman","serif";">Figure 1.</span></b></span><span style="font-family: "Times New Roman","serif"; font-size: 18.0pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";"></span></div>
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<span style="font-size: small;"><span style="color: black; font-family: "Times New Roman","serif";">Insecticide resistance
of</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>R. pedestris</i> </span><span style="color: black; font-family: "Times New Roman","serif";">infected with
fenitrothion-degrading</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i> </span><span style="color: black; font-family: "Times New Roman","serif";">strains. (</span><i><span style="color: black; font-family: "Times New Roman","serif";">A</span></i><span style="color: black; font-family: "Times New Roman","serif";"> </span><span style="color: black; font-family: "Times New Roman","serif";">and</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>B</i></span><span style="color: black; font-family: "Times New Roman","serif";">) Survival of third instar nymphs of</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>R.
pedestris</i> </span><span style="color: black; font-family: "Times New Roman","serif";">infected
with the fenitrothion-degrading and nondegrading</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i> </span><span style="color: black; font-family: "Times New Roman","serif";">strains when reared on
fenitrothion-coated soybean seeds. Results under the host genetic background
TKS-1 (</span><i><span style="color: black; font-family: "Times New Roman","serif";">A</span></i><span style="color: black; font-family: "Times New Roman","serif";">) and TKA-7 (</span><i><span style="color: black; font-family: "Times New Roman","serif";">B</span></i><span style="color: black; font-family: "Times New Roman","serif";">) are shown. Mean and SE
of 10 replicates are indicated at each data point. Each asterisk indicates that
survival rate of the insects infected with the fenitrothion-degrading</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i></span><span style="color: black; font-family: "Times New Roman","serif";">strain is significantly higher than survival rate of the insects
infected with the allied nondegrading strain (likelihood ratio test;</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>P</i> </span><span style="color: black; font-family: "Times New Roman","serif";">< 0.01). (</span><i><span style="color: black; font-family: "Times New Roman","serif";">C</span></i><span style="color: black; font-family: "Times New Roman","serif";">and</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>D</i></span><span style="color: black; font-family: "Times New Roman","serif";">) Resistance of</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i></span><span style="color: black; font-family: "Times New Roman","serif";">-infected</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>R. pedestris</i> </span><span style="color: black; font-family: "Times New Roman","serif";">to percutaneous application (</span><i><span style="color: black; font-family: "Times New Roman","serif";">C</span></i><span style="color: black; font-family: "Times New Roman","serif";">) and oral
administration (</span><i><span style="color: black; font-family: "Times New Roman","serif";">D</span></i><span style="color: black; font-family: "Times New Roman","serif";">) of fenitrothion. Third
instar nymphs, which were infected either with the fenitrothion-degrading</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i> </span><span style="color: black; font-family: "Times New Roman","serif";">strain (SFA1) or with the nondegrading</span><span style="color: black; font-family: "Times New Roman","serif";"> <i>Burkholderia</i> </span><span style="color: black; font-family: "Times New Roman","serif";">strain (RPE67), were administrated with 30 pmol of fenitrothion,
and their survival was inspected 24 h later. On each of the columns is shown
number of surviving insects/total number of treated insects. Statistically
significant differences in the survival rates are shown (Fisher’s exact
probability test). <a href="#i2">(2)</a></span></span></div>
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<span class="apple-converted-space"><b style="mso-bidi-font-weight: normal;"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">References</span></b></span></div>
<div id = "i1" class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: 0in; margin-top: 0in; text-indent: -.5in;">
<span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">1. Song,
Y.,<span style="mso-spacerun: yes;"> </span>Endepols, S.,<span style="mso-spacerun: yes;"> </span>Klemann, N., Richter, D.,<span style="mso-spacerun: yes;"> </span>Matuschka, F.R., Shih, C.H., Nachman, M.W.,
and Kohn, M.H. 2011. <a href="http://www.cell.com/current-biology/abstract/S0960-9822%2811%2900716-0" target="_blank">Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice.</a> Current Biology
21:1296-1301</span></span></div>
<div id = "i2" class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: 0in; margin-top: 0in; text-indent: -.5in;">
<span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">2. Kikuchi
Y, Hayatsu M, Hosokawa T, Nagayama A, Tago K, Fukatsu T. 2012.
<a href="http://www.pnas.org/content/109/22/8618.full.pdf" target="_blank">Symbiont-mediated insecticide resistance.</a> Proc Natl Acad Sci USA 109:8618–8622</span></span></div>
<div id = "i3" class="MsoNormal" style="line-height: 200%; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: 0in; margin-top: 0in; text-indent: -.5in;">
<span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">3.</span></span><span style="font-family: "Times New Roman","serif";"> </span><span class="apple-converted-space"><span style="background: white; color: black; font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 200%;">Kikuchi Y,
Hosokawa T, Fukatsu T. 2007. <a href="http://aem.asm.org/content/73/13/4308.full.pdf" target="_blank">Insect-microbe mutualism without vertical transmission: A stinkbug acquires a beneficial gut symbiont from the environment every generation.</a> Appl Environ Microbiol 73:4308–4316</span></span></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-59305634792385168292012-06-01T16:20:00.000-04:002012-06-05T15:06:41.032-04:00Rodents with No Y Chromosome and Decay of the Human Y<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>In
my previous commentary on the sex determination of <i style="mso-bidi-font-style: normal;">Tokudaia</i> spiny rats dated </span><a href="http://molecularevolutionforum.blogspot.com/2012/05/rodents-with-no-y-chromosome-and-no-sry.html" target="_blank"><span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">May 21, 2012</span></a><span style= "font-size: 12pt; font-family: Times, "Times New Roman", serif;">, I mentioned that Amami and
Tokunoshima spiny rats (<i style="mso-bidi-font-style: normal;">T. osimensis</i>
and <i style="mso-bidi-font-style: normal;">T. tokunoshimensis</i>) have no Y
chromosome and no <i style="mso-bidi-font-style: normal;">Sry</i> gene and their
sex chromosome type is XO in both males and females and that the gene contents
of the male X and the female X chromosomes must be different. However,
examining ten genes that are related to sex determination, Kuroiwa et al. <a href="#h1">(1)</a>
concluded that the two chromosomes contain the same set of genes. This suggests
that my statement was incorrect (A. Kuroiwa, personal communication). </span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>However,
this does not necessarily exclude the possibility that there may be some
sex-determining genes located on the X chromosomes. This possibility is
supported to some extent by the mechanism of formation of XO zygotes. Because
both males and females have the XO chromosome type, they should produce the
gametes with one X or no X chromosome in both sexes. Therefore, the offspring may
have genotypes XX, XO, and OO with the probabilities of ¼, ½, and ¼,
respectively. However, genotypes XX and OO are not observed, so that they must
be lethal. Why is the genotype XX lethal? If the male X (X<sup>m</sup>) and the
female X (X<sup>f</sup>) are identical and normal, the genotype X<sup>m</sup>X<sup>f</sup>
should be viable and be able to establish the XX genotype in the population. One
possible explanation for the absence of XX (or X<sup>m</sup>X<sup>f</sup>) and
the persistence of only XO could be that X<sup>m</sup> and X<sup>f</sup> carry
the male and the female-determining genes which are incompatible with each
other and therefore X<sup>m</sup>X<sup>f</sup> individuals will die. Of course,
this is an overstretched interpretation at present, and we need to study the
genes located on the male X and the female X chromosomes more extensively.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>Kuroiwa
et al. identified copies of <i style="mso-bidi-font-style: normal;">Cbx2</i>
genes on two autosomal chromosomes in each of the two <i style="mso-bidi-font-style: normal;">Tokudaia</i> species, and the number of copies was higher in males than
in females. One of the two chromosomes is linked to the <i style="mso-bidi-font-style: normal;">Sox9</i> gene, as in the case of other mammalian species, and therefore
the <i style="mso-bidi-font-style: normal;">Cbx2</i> gene located on this
chromosome appears to be the original one, and other <i style="mso-bidi-font-style: normal;">Cbx2</i> genes located on the other chromosome are considered to be the
genes transferred from the original chromosome and then duplicated. Kuroiwa et
al. speculated that these duplicate <i style="mso-bidi-font-style: normal;">Cbx2</i>
genes are responsible for testis formation because the <i style="mso-bidi-font-style: normal;">Cbx2</i> genes are known to suppress ovary development in humans and
mice. Kuroiwa (personal communication) then suggests that the new chromosome
carrying more <i style="mso-bidi-font-style: normal;">Cbx2</i> genes has become a
neo-Y chromosome and the homologous chromosome carrying a smaller number of <i style="mso-bidi-font-style: normal;">Cbx2</i> genes has become a neo-X
chromosome. <span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>This
is an interesting suggestion, but it is not without deficiencies. First, there
is no proof that a larger number of <i style="mso-bidi-font-style: normal;">Cbx2</i>
copies is really responsible for sex determination. Second, there must be a
recombination reduction in the duplicate gene region to keep the duplicate
genes together. Otherwise, the neo-Y chromosome cannot be isolated from the neo-X
chromosome <a href="#h2">(2)</a>. Once no recombination system evolves in this region, lethal
mutations are expected to accumulate particularly in small populations <a href="#h3">(3)</a>. At
the present time, no such evidence seems to exist. </span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>Of
course, identification of the sex determination gene in these species would be very
difficult because the population size of Amami and Tokunoshima spiny rats is
very small and protected by the Japanese government. Therefore, one cannot get even
small samples easily. Nevertheless, it would be important to clarify the
evolutionary mechanism of the XO/XO type, because this would give some insight
into the general pattern of Y chromosome evolution.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYbLyfgrvb0A4GgB0X4wal6XkKfG11MYf6Goozb2l1_IC4l5GFj__1J19nD_Z9FFct-_PXezgeQ2wXmntQs4nGa0BEcHlymaFtNo0U-q4OVr9YOl1XbFvEpH7OKfGiTgsx4J_LE7wE1GE/s1600/8+Degeneration+of+sex+specific+element.tif" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYbLyfgrvb0A4GgB0X4wal6XkKfG11MYf6Goozb2l1_IC4l5GFj__1J19nD_Z9FFct-_PXezgeQ2wXmntQs4nGa0BEcHlymaFtNo0U-q4OVr9YOl1XbFvEpH7OKfGiTgsx4J_LE7wE1GE/s400/8+Degeneration+of+sex+specific+element.tif" width="255" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><div align="left" class="MsoNormal" style="margin: 0in 0.5in 0pt;">
<span style="font-size: small;"><span style="font-family: Times, "Times New Roman", serif;"><b style="mso-bidi-font-weight: normal;">Fig.1.</b>
Degeneration of the sex-specific element (Y or W) from an original autosome <i style="mso-bidi-font-style: normal;">(purple)</i> to form more or less
differentiated XY <i style="mso-bidi-font-style: normal;">(blue) </i>or ZW <i style="mso-bidi-font-style: normal;">(pink)</i> sex chromosome pairs. Degraded Y
chromosomes harbor male-specific genes <i style="mso-bidi-font-style: normal;">(blue
lines)</i> and W harbor female-specific genes <i style="mso-bidi-font-style: normal;">(pink lines).</i> Examples of vertebrate species that exhibit this
level of differentiation of XY or ZW chromosomes are given on the left or
right, respectively. Dotted lines represent pairing and recombination.<span style="mso-tab-count: 1;"> </span>From Graves <a href="#h5">(5)</a>.</span></span></div>
<span style="font-size: small;">
</span></td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<br /></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
</div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; mso-tab-count: 1;"> <span style="font-family: Times, "Times New Roman", serif;"> </span></span><span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">Jennifer
Graves (<a href="#h4">4</a>; <a href="#h5">5</a>; <a href="#h6">6</a>) has repeatedly argued that the human Y chromosome is subject
to a high rate of deleterious mutation and appears to become extinct in about
ten million years. It is known that only 50 out of the 1,500 genes that existed
in the original Y chromosome are surviving currently in the human chromosome.
She states: “Accelerated degeneration of the Y chromosome is found in 5 – 15%
of severely infertile men whose infertility is caused by wholesale deletion of
parts of this chromosome.” She envisages that once the Y chromosome is lost, a
new set of sex chromosomes like those of <i style="mso-bidi-font-style: normal;">Tokudaia</i>
spiny rats must be generated.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>In
principle, I disagree with her, because strong purifying is operating for
keeping all Y chromosome genes required for male fertility and formation of
male phenotype. However, if contraception practice becomes more popular and
each married couple produces a smaller number of offspring, the purifying
selection will be weaker. It is then possible that infertile men increase and
the probability of decay of the Y chromosome genes may be enhanced. In this
case the formation of a new sex determination system similar to that of <i style="mso-bidi-font-style: normal;">Tokudaia</i> could be one solution. However,
because humans can control their evolution, it is unlikely for this event to
happen.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-family: Times, "Times New Roman", serif;">
</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<br /></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-family: Times, "Times New Roman", serif;">
</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<b style="font-size: 12pt; mso-bidi-font-weight: normal;"><span style="font-family: Times, "Times New Roman", serif;">References</span></b></div>
<div id = "h1" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">1.
Kuroiwa A, Handa S, Nishiyama C, Chiba E, Yamada F, Abe S, and Matsuda Y. 2011.
<a href="http://www.springerlink.com/content/y711266126v16074/fulltext.pdf" target="_blank">Additional copies of CBX2 in the genomes of males of mammals lacking SRY,the Amami spiny rat (<em>Tokudaia osimensis</em>) and the Tokunoshima spiny rat (<em>Tokudaia tokunoshimensis</em>). </a>Chromosome Res 19:635-644.</span></div>
<div id = "h2" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">2.
Nei, M. 1969. <a href="https://homes.bio.psu.edu/people/faculty/nei/Lab/1969-nei.pdf" target="_blank">Linkage modification and sex difference in recombination.</a> <i>Genetics</i>
63:681-699.</span></div>
<div id = "h3" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">3.
Nei, M. 1970. <a href="https://homes.bio.psu.edu/people/faculty/nei/Lab/1970-nei.pdf" target="_blank">Accumulation of nonfunctional genes on sheltered chromosomes.</a> <i>Am.
Nat. </i>104:311-322.</span></div>
<div id = "h4" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">4.
Aitken RJ, and Marshall Graves JA. 2002. <a href="http://www.nature.com/nature/journal/v415/n6875/pdf/415963a.pdf" target="_blank">The future of sex. </a>Nature 415:963.</span></div>
<div id = "h5" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">5.
Graves JAM. 2008. <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091714" target="_blank">Weird animal genomes and the evolution of vertebrate sex and sex chromosomes.</a> Ann Rev Genet 42:565-586.</span></div>
<div id = "h6" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-size: 12pt; font-family: Times, "Times New Roman", serif;">6.
<span style="mso-bidi-font-family: "Times New Roman";">Griffin DK. 2012. <a href="http://www.springerlink.com/content/u41822557416j633/fulltext.pdf" target="_blank">Is the Y chromosome disappearing?--both sides of the argument.</a> Chromosome Res 20:35-45.</span></span></div>Masatoshi Neihttp://www.blogger.com/profile/15706545477678186676noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-17273055382999291882012-05-29T16:55:00.001-04:002012-06-04T14:17:26.150-04:00How Can There Be Orphan Genes?<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Contributed by: <a href="mailto:kenweiss@psu.edu" target="_blank">Ken Weiss<o:p></o:p></a></span></b><br />
<div class="MsoNormal" font="" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Earlier discussions about genome
evolution in this and other blogs coincided with my being reminded of a <i style="mso-bidi-font-style: normal;">Trends in Genetics</i> paper in 2009 by Khalturin
et al. <a href="#g1">(1)</a> on the subject of ‘orphan’ genes, and there have been two recent
papers on this topic, Tautz et al. <a href="#g2">(2)</a> and Ranz & Parsch <a href="#g3">(3)</a> that seem
worthy of comment here. Orphan<i style="mso-bidi-font-style: normal;"> </i>genes
are individual genes or small gene families that are sequestered within
specific taxonomic groups, but have no known related genes outside the group.<span style="mso-spacerun: yes;"> </span>The term is of course a misnomer, and could
be highly misleading, because unless you’re a Creationist the DNA that’s a gene
today had to be in some genome somewhere ancestrally.<span style="mso-spacerun: yes;"> </span>But in what form and how did it arise?<span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" font="" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">An important generalization at
the core of modern molecular evolution is that evolution occurs by duplication
events. The idea is that genes have from early days been so structured that
they cannot arise just by random mutation of single nucleotides.<span style="mso-spacerun: yes;"> </span>But duplication is clearly only part of the
story: since every gene needs to be regulated, and regulatory elements are
shorter, more fluid in number and location than the genes they regulate, they
can arise more easily by mutation alone than whole genes can.<span style="mso-spacerun: yes;"> </span>Thus even in modern theory a combination of
duplication and ‘ordinary’ mutation is responsible for genome evolution.<span style="mso-spacerun: yes;"> </span>But if genes themselves (and/or their exons)
arise by duplication, that creates a family of related sequences.<span style="mso-spacerun: yes;"> </span>So how can there be orphan genes, without a
trace of relatives?</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">The above authors point out that in
every taxonomic group so far studied up to 20% or even more of its genes have
no recognizable homologues in other species.<span style="mso-spacerun: yes;">
</span>Or, more properly, they are ‘Taxonomically Restricted Genes’ (TRG’s)
with perhaps a small gene family that is, however, found only within a specific
taxonomic clade.<span style="mso-spacerun: yes;"> </span>Given the idea that
genomes evolve by duplication, the prevalence of orphans needs some
explanation, and these authors basically provide three.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">First, the authors argue that the
existing evidence suggests that the orphan genes fulfill some restricted
taxon-specific adaptive needs (e.g., specific functional cell-types in
cnidarians).<span style="mso-spacerun: yes;"> </span>If that is the case, the
relatives in collateral taxa must have lost their function, their trace erased
by mutation or deletion not opposed by selection.<span style="mso-spacerun: yes;"> </span>Khalturin et al. <a href="#g1">(1)</a> suggest that “once a
certain evolutionary time has elapsed” sequence similarity to the ancestral
gene will be erased.<span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Mutational erasure is clearly possible
over time.<span style="mso-spacerun: yes;"> </span>Marshall et al.<span style="mso-spacerun: yes;"> </span><a href="#g4">(4)</a> tried to quantify the idea in 1994,
concluding that after about 10 million years, genes mutated into pseudogenhood
could no longer be revived by mutation (but retain enough sequence to still be
recognized as pseudogenes). </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">For this to be the case, we have
to assume the ‘parental’ gene(s), that must have existed if genes at the time
of the taxonomic split had previously been important when the new species branched
off, but then were later removed by drift or selection from the descendants of
the parental clade, while serving some strong, or new adaptive function in the
new clade. Presumably the parental taxa didn’t include a large gene family
related to the orphan, because if they did a large gene family would have been
serving one—or many—important functions at the time and there would likely
still be at least some of them around today.<span style="mso-spacerun: yes;">
</span></span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">We know that gene families can
persist in widespread branches of life, without sequence easily recognized by BLAST
or other homology searches, based on work by Kazz Kawasaki <a href="#g5">(5)</a> in my group for
unusual kinds of proteins, such as the disordered proteins like those involved in
biomineralization, in which the protein 3D structure is not as important for
function as its ion-binding capacity.<span style="mso-spacerun: yes;"> </span>At
least one of the genes in the SCPP gene family (Amelogenin, responsible for
capturing Ca+ ions in forming dental enamel crystals) was considered an orphan
gene, until we identified its relatives <a href="#g6">(6)</a>.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Second, the orphan-paper authors
acknowledge that BLAST searching and our genome data bases are imperfect, so
that<span style="mso-spacerun: yes;"> </span>relatives of some of these orphans
may be eventually identified.<span style="mso-spacerun: yes;"> </span>However,
it seems unlikely that that will account for all of them, and there should be
some gene-age consequences both for the adaptive function (something new in the
clade, for example) and time for the ancestral genes to be erased.<span style="mso-spacerun: yes;"> </span>Some evidence cited by Tautz <a href="#g2">(2)</a> is ambiguous
in regard to the estimated age and functions of orphans, so the picture is not
wholly clear.<span style="mso-spacerun: yes;"> </span>Is it more plausible that in
so many cases the homologies just haven’t been recognized for some reason,
including incomplete genomic data currently available? </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Three, the explanation that is
most interesting is that orphan genes really are orphans in the sense of having
arisen <i style="mso-bidi-font-style: normal;">de novo</i>, without being copies
of functional genes.<span style="mso-spacerun: yes;"> </span>Tautz <a href="#g2">(2)</a> and Ranz <a href="#g3">(3)</a>
both suggest that regulatory sequences might arise near to DNA that has enough
of the structure of genes (start, stop, and splice sequences, proper coding
exons, polyA addition sites) to be transcribed as well as translated, and serve
some function that over-rode any possible toxicity a new protein might have in
the cell.<span style="mso-spacerun: yes;"> </span>Regulatory sequences usually
involve many different TF-binding elements, so may have been put in these
places by translocation events of such elements from other genes.<span style="mso-spacerun: yes;"> </span>Or in examples cited, the new gene may be in
an exon of an existing (and hence already regulated) gene.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Tautz <a href="#g2">(2)</a> provide a step-by-step
scenario for <i style="mso-bidi-font-style: normal;">de novo</i> gene
creation.<span style="mso-spacerun: yes;"> </span>These authors recognize the
stretched plausibility of such ideas, given the seemingly miniscule probability
that functional genes—with strongly advantageous effects—could arise this
way.<span style="mso-spacerun: yes;"> </span>This is certainly a challenge to
Ohno!</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">One possibility mentioned is that
the recent discovery that much or most of DNA, including non-coding DNA, is
transcribed into RNA.<span style="mso-spacerun: yes;"> </span>The cell obviously
tolerates this RNA litter, which could make it more likely that occasionally
such an RNA has translatable properties.<span style="mso-spacerun: yes;">
</span>Of course, one might suggest that any such RNA sequences are actually
the unrecognized fragmentary trash of long-dead genes.<span style="mso-spacerun: yes;"> </span>If <i style="mso-bidi-font-style: normal;">de
novo</i> creation were to happen often, most of the time selection would
perhaps remove it.<span style="mso-spacerun: yes;"> </span>But over millions of
years maybe it happens enough.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Could it be that the history of
discovery has misled us to become Ohno-ized?<span style="mso-spacerun: yes;">
</span>We discovered interrupted genes, which led to theories of gene origin by
exon duplication (and many genes have repeat exons with high
duplication/deletion properties).<span style="mso-spacerun: yes;"> </span>Then
we discovered gene families, and this led to the obvious conclusion that
duplication was ‘the’ mode of genome evolution.<span style="mso-spacerun: yes;">
</span>We excepted enhancer evolution which can easily come and go by normal
point mutation.<span style="mso-spacerun: yes;"> </span>But this led to the
discovery of the generality of gene families and focused attention on them, and
the networks in which they participate, and the related but diverging functions
they fill.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Could it be that instead, new
genes often really do arise by <i style="mso-bidi-font-style: normal;">de novo</i>
mechanisms, and disappear by deletion before they generate large gene
families?<span style="mso-spacerun: yes;"> </span>If they are old enough, they
and their paralogs would be less taxonomically restricted than if they are
recent.<span style="mso-spacerun: yes;"> </span>After all if you had a
phylogenetic dart board and randomly through darts, most would hit on some
branch, not at the very top: their descendants would be ‘taxonomically
restricted’.<span style="mso-spacerun: yes;"> </span>So it’s the lack of
collateral relatives rather than the taxonomic restriction that seems most
curious to me.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Other authors have suggested that
human orphan genes are often expressed in the brain, but that seems to me to be
yet another kind of forced human exceptionalism, because most genes old or new
are expressed in the brain.<span style="mso-spacerun: yes;"> </span>Likewise,
Khalturin <a href="#g1">(1)</a> propose that taxon-specific genes “drive morphological
specification,” as part of “rewiring” of the networks of regulatory genes.<span style="mso-spacerun: yes;"> </span>But isn’t this always the case?<span style="mso-spacerun: yes;"> </span>Except in some special circumstances, traits
are usually affected by many interacting genes.<span style="mso-spacerun: yes;">
</span>They seem to evolve by gradually diverging functions emerging from
selection acting (again gradually) on the diversity made possible by the
redundancy generated by gene duplication.<span style="mso-spacerun: yes;">
</span>It seems rather unlikely that a newcomer of basically random structure
could participate in such a network (or be properly expressed in a relevant
tissue context) to experience strong positive selection.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Orphan genes may be simply be
lucky genes in complex systems that happened to survive for us to observe them--different
contributing genes, for different reasons including drift, surviving in
different taxa.<span style="mso-spacerun: yes;"> </span>The 20% of such genes
that are orphans may just be the normal passengers on the train of duplication
and deletion.<span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">If <i style="mso-bidi-font-style: normal;">de novo</i> evolution is common, or more common than we thought
relative to gene duplication, we may have to revisit the strong evidence for
the evolution of gene evolution by exon duplication and the proliferation of
ancient gene families.<span style="mso-spacerun: yes;"> </span>Have we missed
something? </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">This could be a startling
realization.<span style="mso-spacerun: yes;"> </span>I’m sure many Mol. Evol. r<a href="http://www.blogger.com/" name="_GoBack"></a>eaders will know more about this than I do, and I’d like to
see what you think.<o:p></o:p></span></div>
<br />
<br />
<br />
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif";">References</span></b></div>
<div id = "g1" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span lang="EN" style="font-family: "Times New Roman","serif"; mso-ansi-language: EN;">1. <span style="mso-spacerun: yes;"> </span>Khalturin, K, Hemmrich, G, Fraune, S, Augustin,
R, and Bosch, TCG. </span><span style="font-family: "Times New Roman","serif";"><a href="http://www.sciencedirect.com/science/article/pii/S0168952509001450" target="_blank">More
than just orphans: are taxonomically-restricted genes important in
evolution?</a><span style="mso-spacerun: yes;"></span><i style="mso-bidi-font-style: normal;">Trends in Genetics</i> 25(9): 404-413, 2009.</span></div>
<div id = "g2" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; mso-no-proof: yes;">2. <span style="mso-spacerun: yes;"> </span>Tautz, D, and Domazet-Loso, T.<span style="mso-spacerun: yes;"> </span><a href="http://www.nature.com/nrg/journal/v12/n10/pdf/nrg3053.pdf" target="_blank">The evolutionary origin of orphan genes.</a> <i style="mso-bidi-font-style: normal;">Nature Reviews Genetics</i> 12(10):692-702,
2011.</span></div>
<div id = "g3" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif";">3. <span style="mso-spacerun: yes;"> </span>Ranz, J, and Parsch, J.<span style="mso-spacerun: yes;"> </span><a href="http://onlinelibrary.wiley.com/doi/10.1002/bies.201100177/pdf" target="_blank">Newly evolved genes: Moving from comparative genomics to functional studies in model systems.</a><span style="mso-spacerun: yes;"> </span>BioEssays 34: 477-83, 2012.</span></div>
<div id = "g4" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif";">4. <span style="mso-spacerun: yes;"> </span>Marshall, CR, Raff, EC, and Raff, RA.<span style="mso-spacerun: yes;"> </span><a href="http://www.pnas.org/content/91/25/12283.long" target="_blank">Dollo’s law and the death and resurrection of genes.</a><span style="mso-spacerun: yes;"> </span><i style="mso-bidi-font-style: normal;">PNAS</i> 91(25): 12283-7, 1994.</span></div>
<div id = "g5" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif";">5. <span style="mso-spacerun: yes;"> </span>Kawasaki, K, Buchanan, AV, and Weiss, KM.
<a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev-genet-102108-134242" target="_blank">Biomineralization in humans: making the hard choices in life.</a><span style="mso-spacerun: yes;"> </span>Ann. Rev Genet,43: 119-142, 2009.</span></div>
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<span style="font-family: "Times New Roman","serif";">6. <span style="mso-spacerun: yes;"> </span>Kawasaki, K, and Weiss, K.<span style="mso-spacerun: yes;"> </span><a href="http://www.pnas.org/content/100/7/4060.full.pdf+html" target="_blank">Mineralized tissue and vertebrate evolution: the secretory calcium-binding phosphoprotein gene cluster.</a><span style="mso-spacerun: yes;"> </span>PNAS 100:4060-65, 2003.<o:p></o:p></span></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-19116195914764343302012-05-21T14:10:00.000-04:002012-06-04T14:21:41.650-04:00Rodents with No Y Chromosome and No Sry Gene<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">In mammalian species
sex is determined by the X and Y chromosomes. Individuals with two X
chromosomes (XX) become female, and those with one X chromosome and one Y
chromosome (XY) will be male. This occurs because the Y chromosome carries an <i style="mso-bidi-font-style: normal;">Sry </i>gene, which is a transcription
factor and triggers the developmental pathway for testis formation. In the
absence of the <i style="mso-bidi-font-style: normal;">Sry</i> gene, the
developmental pathway for ovary formation is chosen as a default option.</span></div>
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; mso-bidi-font-size: 11.0pt;">Fig. 1.</span></b><span style="font-family: "Times New Roman","serif"; font-size: 12pt; mso-bidi-font-size: 11.0pt;"> Evolution of
sex chromosomes, <i style="mso-bidi-font-style: normal;">SRY</i>, and <i style="mso-bidi-font-style: normal;">CBX2</i> in the genus <i style="mso-bidi-font-style: normal;">Tokudaia</i>. <b style="mso-bidi-font-weight: normal;">a</b> Evolutionary
events inferred from the present study (<i style="mso-bidi-font-style: normal;">red</i>)
and previous studies (<i style="mso-bidi-font-style: normal;">black</i>) are
shown in the phylogeny, together with the geographical distribution of <i style="mso-bidi-font-style: normal;">Tokudaia</i> species. Ma: million years ago.
<b style="mso-bidi-font-weight: normal;">b</b> Adult female of Okinawa spiny rat.
<b style="mso-bidi-font-weight: normal;"><span style="mso-spacerun: yes;"> </span>c</b>
Sub-adult male <a href="#f2">(2)</a>. <o:p></o:p></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8WOuxRbGFrYZnN7wEFb2HaiIcPqNV9IveG0RkYu-sfLBHz-pWgfEIfYcJu6VXoD6HHhSffRTv_OCGoILuqeeK410DHYcdevph4czPnMYoPDsCuoiUfbI3UAPVN85JpqF9SZ3Lx6MAJI8/s1600/Fig.+2..png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8WOuxRbGFrYZnN7wEFb2HaiIcPqNV9IveG0RkYu-sfLBHz-pWgfEIfYcJu6VXoD6HHhSffRTv_OCGoILuqeeK410DHYcdevph4czPnMYoPDsCuoiUfbI3UAPVN85JpqF9SZ3Lx6MAJI8/s640/Fig.+2..png" width="294" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><strong>Fig. 2.</strong></span><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"> Karyotypes of Amami and Tokunoshima spiny rats <a href="#f3">(3)</a>.<o:p></o:p></span></td></tr>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">However, there are
exceptional species in rodents. Two species of the genus <i style="mso-bidi-font-style: normal;">Tokudaia </i>living in small islands called Amami Oshima (<i style="mso-bidi-font-style: normal;">T. osimensis</i>) and Tokunoshima (<i style="mso-bidi-font-style: normal;">T. tokunoshimensis</i>) near Okinawa, Japan,
have neither the Y chromosome nor the <i style="mso-bidi-font-style: normal;">Sry
</i>gene (<b style="mso-bidi-font-weight: normal;">Fig. 1</b>). Furthermore, both
males and females of these species have only one X chromosome, so that their
sex chromosome type is XO in both sexes. In addition, the number of autosomal
chromosomes is different between the two species. <i style="mso-bidi-font-style: normal;">T. osimensis</i> (Amami spiny rat) has 24 autosomal chromosomes,
whereas <i style="mso-bidi-font-style: normal;">T. tokunoshimensis</i>
(Tokunoshima spiny rat) has 44 autosomal chromosomes (<b style="mso-bidi-font-weight: normal;">Fig. 2</b>). The genus <i style="mso-bidi-font-style: normal;">Tokudaia</i>
have three species, and the remaining one (<i style="mso-bidi-font-style: normal;">T.
muenninki</i>) lives in Okinawa Island. This Okinawa spiny rat has the normal
sex chromosome type XX/XY, and the number of autosomal chromosomes is 42.</span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">Molecular phylogenetic
analysis has suggested that Okinawa spiny rats diverged from the other two <i style="mso-bidi-font-style: normal;">Tokudaia </i>species about 2.5 million years
ago and Amami and Tokunoshima spiny rats diverged about one million years ago.
Therefore, the chromosome number has changed rapidly in these species by means
of fusion, fission, inversion, deletion, translocation, etc. In fact, there is
evidence that the chromosomes of Okinawa spiny rat have also experienced
structural changes frequently. However, these chromosomal changes are not
surprising because chromosomes can change quite often in small populations.</span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">The surprising finding here
is that the<i style="mso-bidi-font-style: normal;"> Sry</i> gene has been lost
and the male and the female are determined by the male and the female X
chromosomes, respectively. Therefore, the gene contents of the male and the
female X chromosomes must be different. In a recent paper Kuroiwa et al. <a href="#f1">(1)</a>
studied this problem by examining the copy number and chromosomal location of
10 genes (<i style="mso-bidi-font-style: normal;">Artx, Cbx2, Dmrt1, Fgf9, NroB1,
Nr5A1, Rspo1, Sox9, Wnt4, Wnt1</i>) that are concerned with the differentiation
of gonads into testis or ovary. The reason why they studied these genes is that
duplicates of these genes are often used as signal proteins for sex
determination in other organisms such as birds, frogs, and medaka fish. They
then found that there are multiple copies of <i style="mso-bidi-font-style: normal;">Cbx2</i> genes in the <i style="mso-bidi-font-style: normal;">Tokudaia</i>
species and that there are two or more copies of <i style="mso-bidi-font-style: normal;">Cbx2 </i>genes in males than in females in both Amami and Tokunoshima
spiny rats. Because the <i style="mso-bidi-font-style: normal;">Cbx2 </i>gene is
known to repress ovarian development in mice and humans, they concluded that a
larger number of <i style="mso-bidi-font-style: normal;">Cbx2</i> genes in males
is probably responsible for testis development. However, this hypothesis has
not been confirmed by isolating and characterizing the <i style="mso-bidi-font-style: normal;">Cbx2</i> genes.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">There are two more rodent
species which have the XO/XO sex chromosome type in both males and females. They
are mole voles <a href="#f4">(4)</a>, and their effective population size again appears to be small.
At present, the evolutionary change of the sex determination system in mammals is
believed to be rare, but this may not be the case if we examine the sex chromosomes
in species of small population size.</span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">In reptiles, amphibians,
and fish the sex determination system is known to change rapidly in the evolutionary
process. Particularly in reptiles, there are the genetic sex determination
(GSD) including both the XY and ZW systems and the temperature dependent sex
determination (TSD), and these systems are interchangeable in the evolutionary
process <a href="#f5">(5)</a>. It is also known that one species of frog, <i style="mso-bidi-font-style: normal;">Rana rugosa</i>, contains geographical races with the XY and ZW
systems, and the XY ↔ ZW change appears to have occurred recently by an
inversion event in the sex chromosomes <a href="#f6">(6)</a>.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">In vertebrates <i style="mso-bidi-font-style: normal;">Dmrt</i> genes are believed to be
responsible for imitating the developmental pathway for the formation of male
and female phenotypes, but various signal proteins that trigger the function of
<i style="mso-bidi-font-style: normal;">Dmrt</i> genes are used in different
species <a href="#f7">(7)</a>.<i style="mso-bidi-font-style: normal;"> Dmrt</i>-triggering genes
are apparently subject to a rapid evolutionary change. How this evolutionary
change occurs is not well understood.</span><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><o:p> </o:p></span></div>
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">References</span></b></div>
<div id = "f1" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">1. Kuroiwa A, Handa S,
Nishiyama C, Chiba E, Yamada F, Abe S, and Matsuda Y. 2011. <a href="http://www.springerlink.com/content/y711266126v16074/fulltext.pdf" target="_blank">Additional copies of CBX2 in the genomes of males of mammals lacking <em>SRY</em>, the Amami spiny rat (<em>Tokudaia osimensis</em>) and the Tokunoshima spiny rat (<em>Tokudaia tokunoshimensis</em>).</a>Chromosome Res 19:635-644.</span></div>
<div id = "f2" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">2. Murata C, Yamada F,
Kawauchi N, Matsuda Y, and Kuroiwa A. 2012. <a href="http://www.springerlink.com/content/72125n5114w85171/fulltext.pdf" target="_blank">The Y chromosome of the Okinawa spiny rat, <em>Tokudaia muenninki</em>, was rescued through fusion with an autosome.</a> Chromosome Res 20:111-125.</span></div>
<div id = "f3" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">3. Sutou S, Mitsui Y,
and Tsuchiya K. 2001. <a href="http://www.springerlink.com/content/tb0gyegkx22tdyjc/fulltext.pdf" target="_blank">Sex determination without the Y chromosome in two Japanese rodents <em>Tokudaia osimensis osimensis</em> and <em>Tokudaia osimensis spp</em>.</a> Mamm
Genome 12:17-21.</span></div>
<div id = "f4" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">4. Bagheri-Fam S,
Sreenivasan R, Bernard P, Knower KC, Sekido R et al. 2012. <a href="http://www.springerlink.com/content/h88v02t26t252824/fulltext.pdf" target="_blank"><em>Sox9</em> gene regulation and the loss of the XY/XX sex-determining mechanism in the mole vole <em>Ellobius lutescens.</em></a> Chromosome Res 20:191-199.</span></div>
<div id = "f5" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">5. Sarre SD, Ezaz T,
and Georges A. 2011. <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev-genom-082410-101518" target="_blank">Transitions between sex-determining systems in reptiles and amphibians.</a> Annu Rev Genomics Hum Genet 12:391-406.</span></div>
<div id = "f6" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">6. Miura I, Ohtani H,
and Ogata M. 2012. <a href="http://www.springerlink.com/content/765wq104rrx80642/fulltext.pdf" target="_blank">Independent degeneration of W and Y sex chromosomes in frog <i style="mso-bidi-font-style: normal;">Rana rugosa</i>. </a>Chromosome Res 20:47-55.</span></div>
<div id = "f7" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">7.</span><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="font-family: Calibri;"> </span></span><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">Kopp A. 2012. <a href="http://www.sciencedirect.com/science/article/pii/S0168952512000170" target="_blank"><em>Dmrt</em> genes in the development and evolution of sexual dimorphism.</a> Trends Genet 28:175-184.</span></div>Masatoshi Neihttp://www.blogger.com/profile/15706545477678186676noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-66056160291335266832012-05-14T16:10:00.000-04:002012-06-04T14:24:24.928-04:00Loss of Sweet Taste Genes in Carnivores<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Contributed by:
<a href="mailto:takezaki@med.kagawa-u.ac.jp" target="_blank">Naoko Takezaki</a> <o:p></o:p></span></b><br />
<br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="color: black; font-family: "Times New Roman","serif";">It is generally
believed that most mammals perceive five basic taste qualities: sweet, umami
(tasty), bitter, salty, and sour. The receptors for sweet, umami and bitter
tastes are G protein-coupled receptors (GPCRs). Sweet taste is mediated largely
by a heteromer of two closely related Tas1r (type 1 taste receptor) family
GPCRs: Tas1r2 and Tas1r3. Tas1r1, another member of the Tas1r family, in
combination with Tas1r3, forms an umami taste receptor. Tas1r receptors are
class C GPCRs. Unlike sweet and umami tastes, bitter taste is mediated by Tas2r
family GPCRs, which belong to class A GPCRs and are structurally unrelated to
Tas1r family receptors. The genes encoding Tas2r receptors, the <em>Tas2r</em>
genes, differ substantially in gene number and primary sequences among species,
most likely reflecting the likelihood that these genes are required for
detecting toxic or harmful substances in a species’ ecological niche.</span></div>
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<span style="font-family: "Times New Roman","serif";">Sweet taste <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes are pseudogenized in domestic cats which show indifference
to sweet taste. Similarly, in other members (e.g., tiger and cheetah) of the
cat family <i style="mso-bidi-font-style: normal;">Tas1r2 </i>genes are
pseudogenized. In a recent study Jiang et al. <a href="#e1">(1)</a> sequenced all exons of <i style="mso-bidi-font-style: normal;">Tas1r2 </i>genes from several carnivore species
including obligate carnivores (e.g., domestic and wild cats), relatively
omnivorous species (e.g., bears), and strict herbivores (e.g., giant panda). They
found that loss-of-function mutations occurred in different positions of exons
of <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes of obligate
carnivores (Fig. 1), which are scattered on the phylogenetic tree (Fig. 2).
This result indicates that pseudogenization of <i style="mso-bidi-font-style: normal;">Tas1r2 </i>genes resulting in loss of sweet taste occurred
independently in several carnivore lineages in relatively short periods of
time. <o:p></o:p></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwhgEw5-INn88GHdd7T_5fvJqMJS4x5cYetO_f_K-33BAZOQKVPQldXnM8GhaaOc-UAE9HusoZ7aeblAnSfBbEDGQ_CkwRv3OWdxQUB1b2SIMkIbCTPXDmEAJDF4giY8o8acd4K9os5a0/s1600/F1_largeR.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="102" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwhgEw5-INn88GHdd7T_5fvJqMJS4x5cYetO_f_K-33BAZOQKVPQldXnM8GhaaOc-UAE9HusoZ7aeblAnSfBbEDGQ_CkwRv3OWdxQUB1b2SIMkIbCTPXDmEAJDF4giY8o8acd4K9os5a0/s400/F1_largeR.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><br />
<div align="left" class="MsoNormal" style="margin: 0in 0in 0pt 0.25in; text-align: left;">
<span style="font-size: small;"><b><span style="font-family: "Times New Roman","serif";">Fig. 1. </span></b><span style="font-family: "Times New Roman","serif";">Widespread pseudogenization of
the sweet-taste receptor gene <i>Tas1r2</i>. The above diagram shows the
positions of ORF-disrupting mutations in <i>Tas1r2</i> from selected species of
carnivores. The functional dog <i>Tas1r2</i> gene structure is shown as a
reference. The positions where ORF-disrupting mutations occurred are marked
with a red asterisk (*).<o:p></o:p></span></span></div>
<span style="font-size: small;">
</span></td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCG1aursYL-tvSJfNIU9pCsk6Enzi3H0offmNHt4_2ihbQ2fraKnGh3LSVyKi-gCQpADacvxwSNXtueT0W7CYw2hx5jnYmZQzJGGqflPkV_CkmnkBESA1FMfi_pfKGnZzdwLoPTuatL_U/s1600/F2_large.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCG1aursYL-tvSJfNIU9pCsk6Enzi3H0offmNHt4_2ihbQ2fraKnGh3LSVyKi-gCQpADacvxwSNXtueT0W7CYw2hx5jnYmZQzJGGqflPkV_CkmnkBESA1FMfi_pfKGnZzdwLoPTuatL_U/s400/F2_large.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><br />
<div align="left" class="MsoNormal" style="line-height: 150%; margin: 0in 0in 0pt 0.25in; text-align: left;">
<span style="font-size: small;"><b><span style="font-family: "Times New Roman","serif";">Fig.
2. </span></b><span style="font-family: "Times New Roman","serif"; mso-bidi-font-weight: bold;">E</span><span style="font-family: "Times New Roman","serif";">volutionary
tree of <i>Tas1r2</i> genes from 18 species of carnivores. Species with a
pseudogenized <i>Tas1r2</i> are marked with a diamond (red and gray depict
species characterized in this study and the previous study, respectively).<o:p></o:p></span></span></div>
<span style="font-size: small;">
</span></td></tr>
</tbody></table>
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<br />
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Furthermore, Jiang et al. showed
that in sea lion (Carnivora) and dolphin (Cetacea) which swallow whole food and
have a reduced number of taste buds on tongue <i style="mso-bidi-font-style: normal;">Tas1r1</i> and <i style="mso-bidi-font-style: normal;">Tas1r3</i> genes
are pseudogenized. They also failed to find intact <i style="mso-bidi-font-style: normal;">Tas2r</i> genes that encode bitter taste receptors in the dolphin
genome. This result indicates the loss of umami taste as well as the loss of
sweet taste in sea lion and dolphin and suggests the loss of bitter taste in
the latter. </span><span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Jiang
et al. present the view that the loss of taste receptor genes is a consequence
of dietary specialization in mammals <a href="#e1">(1)</a>.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt;"><span style="mso-tab-count: 1;"> </span>However, Zhao and Zhang <a href="#e2">(2)</a> pointed
out that (i) although <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes
are pseudogenized only in obligate carnivores in Jiang et al. <a href="#e1">(1)</a>, ferret and
Canadian otter, which are also obligate carnivores, still possess intact <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes and (ii) although three
pinnipeds share the common ancestry of obligate meat-eating, none of the null
mutations in <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes are shared by
these species. Moreover, a previous study of Zhao and Zhang’s group <a href="#e3">(3)</a> showed
that (iii) <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes are
pseudogenized in vampire bats which feed solely on blood containing
carbohydrate and (iv) <i style="mso-bidi-font-style: normal;">Tas1r2</i> genes
are missing in herbivorous horse and omnivorous pig as well as in all available
birds’ genome sequences irrespective of their diet. <i style="mso-bidi-font-style: normal;">Tas1r1</i> genes that encode umami taste receptors are pseudogenized in
all bats regardless of their diet (fruit, insect, blood) <a href="#e4">(4)</a>. In Zhao and
Zhang’s view the relationship between the diet of species and the loss of
function of taste receptor genes is quite complex and sometimes inconsistent.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Jiang et al. <a href="#e5">(5)</a> responded to
Zhao and Zhang <a href="#e2">(2)</a> stating that (i) prefect correspondence between the exclusive
meat-eating diet and the loss of taste receptor genes should not be expected
because the loss of sweet taste receptor genes occurs stochastically and
therefore is a time-dependent and ongoing process after diet switch, (ii) whether
the common ancestor depended solely on meat-eating diet is not known, (iii) vampire
bats unlikely require sweet taste because of the very small amount of carbohydrate
in blood, and (iv) some studies showed the presence of <i style="mso-bidi-font-style: normal;">Tas1r2 </i>genes in horse and pig and these species show preference of
sweet taste.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Although Jiang et al. <a href="#e5">(5)</a>
responded to Zhao and Zhang’s <a href="#e2">(2)</a> questions, some questions remain unanswered.
For example, why are no sweet taste receptor genes found in birds regardless of
their diets?</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Although the two groups of authors
have different opinions on the relationship of the diet and loss of taste
receptor genes, both of them recognize a need for better understanding of
physiological mechanisms of taste and taste receptors to understand the
relationship between diet and gene loss (<a href="#e1">1</a>, <a href="#e2">2</a>). <o:p></o:p></span></div>
<br />
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 0pt; text-indent: 48pt;">
<span style="font-family: "Times New Roman","serif";">The abstract of Jiang et al.’s
paper <a href="#e1">(1)</a> is as follows.<o:p></o:p></span></div>
<br />
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"></span><br />
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<tbody>
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<td bgcolor="#ffffcc"><div align="left">
<br />
<div 200%;?="" class="MsoNormal" style="line-height: 200%; margin: 0in 0.5in 10pt;">
<strong>Abstract</strong> <br />
<div style="line-height: 200%;">
</div>
<div align="left" class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; mso-layout-grid-align: none; mso-pagination: widow-orphan; text-align: left;">
<span style="font-family: "Times New Roman","serif"; mso-font-kerning: 0pt;">Mammalian
sweet taste is primarily mediated by the type 1 taste receptor Tas1r2/Tas1r3,
whereas Tas1r1/Tas1r3 act as the principal umami taste receptor. Bitter taste
is mediated by a different group of G protein-coupled receptors, the Tas2rs,
numbering 3 to <b>~ </b>66, depending on the species. We showed previously that
the behavioral indifference of cats toward sweet-tasting compounds can be
explained by the pseudogenization of the <i style="mso-bidi-font-style: normal;">Tas1r2</i>
gene, which encodes the Tas1r2 receptor. To examine the generality of this
finding, we sequenced the entire coding region of <i style="mso-bidi-font-style: normal;">Tas1r2</i> from 12 species in the order Carnivora. Seven of these
nonfeline species, all of which are exclusive meat eaters, also have
independently pseudogenized <i style="mso-bidi-font-style: normal;">Tas1r2</i>
caused by ORF-disrupting mutations. Fittingly, the purifying selection pressure
is markedly relaxed in these species with a pseudogenized <i style="mso-bidi-font-style: normal;">Tas1r2</i>. In behavioral tests, the Asian otter (defective <i style="mso-bidi-font-style: normal;">Tas1r2</i>) showed no preference for sweet
compounds, but the spectacled bear (intact Tas1r2) did. In addition to the
inactivation of <i style="mso-bidi-font-style: normal;">Tas1r2</i>, we found that
sea lion <i style="mso-bidi-font-style: normal;">Tas1r1</i> and <i style="mso-bidi-font-style: normal;">Tas1r3</i> are also pseudogenized,
consistent with their unique feeding behavior, which entails swallowing food
whole without chewing. The extensive loss of Tas1r receptor function is not restricted
to the sea lion: the bottlenose dolphin, which evolved independently from the
sea lion but displays similar feeding behavior, also has all three <i style="mso-bidi-font-style: normal;">Tas1r</i>s inactivated, and may also lack
functional bitter receptors. These data provide strong support for the view
that loss of taste receptor function in mammals is widespread and directly
related to feeding specializations.<o:p></o:p></span></div>
<div style="line-height: 200%;">
<span style="color: black;">
<o:p></o:p>
</span></div>
</div>
</div>
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</span></div>
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<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; text-indent: -0.5in;">
<b style="mso-bidi-font-weight: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">References<o:p></o:p></span></b></div>
<br />
<div id = "e1" align="left" class="ColorfulList-Accent11" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-align: left; text-indent: -0.5in;">
<span style="font-size: 12pt;font-family: "Times New Roman","serif";">1. Jiang P, Josue J, Li X, Galser D, Li W, Brand JG,
Margolskee RF, Reed DR, Beauchamp GK. 2012. <a href="http://www.pnas.org/content/109/13/4956.full.pdf+html" target="_blank">Major taste loss in carnivorous mammals.</a> Proc. Natl. Acad. Sci. USA. 109:4956-4961.</span></div>
<div id = "e2" align="left" class="ColorfulList-Accent11" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-align: left; text-indent: -0.5in;">
<span style="font-size: 12pt;font-family: "Times New Roman","serif";">2. Zhao H, Zhang J. 2012. </span><span style="font-size: 12pt;color: #0e0e0e; font-family: "Times New Roman","serif"; mso-bidi-font-weight: bold; mso-font-kerning: 0pt;"> <a href = "http://www.pnas.org/content/early/2012/05/03/1205205109.full.pdf+html" target="_blank"> Mismatches between feeding ecology and taste
receptor evolution: An inconvenient truth.</a></span><span style="font-size: 12pt;font-family: "Times New Roman","serif";"> Proc. Natl. Acad. Sci.</span><span style="font-size: 12pt;color: #1a1a1a; font-family: "Times New Roman","serif"; mso-font-kerning: 0pt;">USA, doi: 10.1073/pnas.1205205109.</span></div>
<div id = "e3" align="left" class="ColorfulList-Accent11" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-align: left; text-indent: -0.5in;">
<span style="font-size: 12pt;font-family: "Times New Roman","serif";">3. Zhao H, Zhou Y, Pinto CM, Charles-Dominique P,
Galindo-Gonzalez J, Zhang S, Zhang J. 2010. <a href="http://mbe.oxfordjournals.org/content/27/11/2642.full.pdf+html" target="_blank">Evolution of the sweet taste receptor gene <em>Tas1r2</em> in bats.</a> Mol. Biol. Evol. 27; 2642-2650.</span></div>
<div id = "e4" align="left" class="ColorfulList-Accent11" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-align: left; text-indent: -0.5in;">
<span style="font-size: 12pt;font-family: "Times New Roman","serif";">4. Zhao H, Xu D, Zhang S, Zhang J. 2012. <a href="http://gbe.oxfordjournals.org/content/early/2011/11/24/gbe.evr126.full.pdf+html" target="_blank">Genomic and genetic evidence for the loss of umami taste in bats.</a> Genome Biol. Evol. 4:73-79.</span></div>
<div id = "e5" align="left" class="ColorfulList-Accent11" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-align: left; text-indent: -0.5in;">
<span style="font-size: 12pt;font-family: "Times New Roman","serif";">5. Jiang P, Josue J, Li X, Galser D, Li W, Brand JG,
Margolskee RF, Reed DR, Beauchamp GK. 2012. <a href = "http://www.pnas.org/content/early/2012/05/03/1205581109.full.pdf+html" target="_blank"> Reply to Zhao and Zhnag: Loss of
taste receptor function in mammals is directly related to feeding
specializations.</a> Proc. Natl. Acad. Sci. USA, doi: </span><span style="font-size: 12pt;color: #1a1a1a; font-family: "Times New Roman","serif"; mso-font-kerning: 0pt;">10.1073</span><span lang="EN" style="font-size: 12pt;color: #1a1a1a; font-family: "Times New Roman","serif"; mso-ansi-language: EN; mso-bidi-font-style: italic; mso-font-kerning: 0pt;">/pnas.1205581109.</span><span style="font-family: "Times New Roman","serif";"><o:p></o:p></span></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-62136931951342321992012-05-09T15:11:00.000-04:002012-06-04T14:25:17.138-04:00Endosymbiosis and Photosynthetic Animals<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif";"><span style="font-family: Times, "Times New Roman", serif; font-size: 12pt;">Contributed by:
<a href="mailto:hxm16@psu.edu" target="_blank">Hong Ma<o:p></o:p></a></span></span></b><br />
<span style="font-family: Times, "Times New Roman", serif;">
</span><br />
<div <span="" class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: Times, "Times New Roman", serif;"><span style="mso-tab-count: 1;"> </span>Endosymbiosis is thought to be
crucial for the early evolution of eukaryotic cells, including the origins of
the mitochondrion and the chloroplast, which is essential for photosynthesis.
Photosynthesis is generally associated with plants, algae, and bacteria such as
cyanobacteria, making these organisms the major primary producers. It is widely
accepted that photosynthesis originated in bacteria and that chloroplasts in
eukaryotic photosynthetic organisms were derived via ancient endosymbiosis
after the capture of a cyanobacterium by an early eukaryote (Fig.1).<span style="mso-spacerun: yes;"> </span>This primary endosymbiosis resulted in the
ancestor of red algae and green algae. One branch of green algae then evolved
into the green plants on land, such as mosses, ferns, and seed plants. The
cyanobacterium taken in by the eukaryotic host cell evolved into the organelle
chloroplast, which has a greatly reduced genome, whereas most of the original
cyanobacterial genes were either lost or transferred into the host nuclear
genome. For example, many of the proteins for photosynthesis are now encoded by
nuclear genes. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
<span style="font-family: Times, "Times New Roman", serif;">After the origins of red and
green algae, secondary symbiotic events (Fig.1) following the capture of one of
the red or green algae by other eukaryotes generated a number of highly
divergent algae, such as brown algae; however, the origins and histories of
many of these algae and other organisms are still uncertain. In these algae,
chloroplasts have one or two additional membranes compared with those in red or
green algae (and the land plant descendents of green algae), with partial or
complete loss of the nuclear genome of the captured red/green algal cells.
Because both primary and secondary endosymbioses were both very ancient events,
and there are few, if any, intermediate cases, the origin and history of these
processes are not well understood.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh41vm-4RbdTd_PwphVVijlwzjJw3iiK6C_MS3CjVZYwRDQZzaTfg457WcbQ8tgbapeng8URL7kqXkxXsoB7Dec9U3tN56ptjETHRvoMFHVUb6p-55rzZcs69HVb2S9GzzlB_nsFWC4y2g/s1600/Ma+Fig+1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="365" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh41vm-4RbdTd_PwphVVijlwzjJw3iiK6C_MS3CjVZYwRDQZzaTfg457WcbQ8tgbapeng8URL7kqXkxXsoB7Dec9U3tN56ptjETHRvoMFHVUb6p-55rzZcs69HVb2S9GzzlB_nsFWC4y2g/s400/Ma+Fig+1.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><br />
<div align="left" class="MsoNormal" style="font-size: 12pt; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="font-size: small;"><b style="mso-bidi-font-weight: normal;">Fig.1.</b>
Diagrams illustrating primary and secondary endosymbiosis. Top: a eukaryotic
cell (brown with flagella) takes up a cyanobacterium (blue) and then evolved
into red and green algae, as well as glaucophytes (golden algae). Bottom, red
algae and green algae are again taken up in secondary endosymbiotic events, one
of which gave rise to <i style="mso-bidi-font-style: normal;">Vaucheria</i>. </span></span></div>
<span style="font-size: small;">
</span></td></tr>
</tbody></table>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
</div>
<span style="font-family: Times, "Times New Roman", serif;"></span><br />
<span style="font-family: Times, "Times New Roman", serif;"></span><br />
<span style="font-family: Times, "Times New Roman", serif;"></span><br />
<span style="font-family: Times, "Times New Roman", serif;"><div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Animals derive nutrients from
foods that are ultimately produced by photosynthetic organisms. Lesser known
are the amazing symbiotic relationships between members of diverse groups of
invertebrates and single-cell photosynthetic algae or bacteria. Such symbiosis
is found in sponges, corals, and some giant clams, and provides fixed carbon to
the animals, whereas the photosynthetic algae or cyanobacteria also benefit
from this relationship in the form of protection and nutrients from the animal
partners, such as nitrogen and other minerals. In these mutually beneficial
relationships, as much as 90% of the energy needed by the animals can be from
the photosynthetic symbionts. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>In the primary and secondary
endosynbiotic relationships for plants, algae and other organisms, the
ancestral free-living photosynthetic cells had evolved into an organelle, the
chloroplast, that depends on the host nuclear genes for biogenesis and
function. In addition, chloroplast (or plastid) is maintained throughout the
life cycle of plants or algae. In contrast, the relationships between the
animal hosts and their photosynthetic symbionts are less intimate, with the
symbionts still retaining their cellular structure and complete genomes.
Furthermore, the symbiotic relationship is established de novo during animal
development. Therefore, the relationships between animals and their symbionts
are fundamentally different from those in the primary and secondary
endosymbiotic relationships between the plant and algal hosts and their
chloroplasts. It is thus difficult to draw inference from the animal – algal
symbiotic relationships regarding the evolutionary history of the primary and
secondary endosymbioses of the chloroplast.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>Recently, Rumpho et al. (1) described
an unusual relationship between a sea slug (<i style="mso-bidi-font-style: normal;">Elysia
chlorotica</i>) and an alga (<i style="mso-bidi-font-style: normal;">Vaucheria
litorea</i>). <i style="mso-bidi-font-style: normal;">Elysia chlorotica</i> is a
green marine animal commonly known as eastern emerald elysia and is found in
Eastern US coastal marshes.<span style="mso-spacerun: yes;"> </span>It is
usually 20-30 mm long, but can grow to as long as 60 mm (Fig. 2). Its food at
the juvenile stage is the intertidal <i style="mso-bidi-font-style: normal;">Vaucheria
litorea,</i> a yellow-green alga and member of the Heterokonts, a diverse group
that also includes brown algae. Before feeding on <i style="mso-bidi-font-style: normal;">V. litorea</i>, the sea slug has a brown color with red spots and
feeding on <i style="mso-bidi-font-style: normal;">V. litorea </i>is necessary
for the green color. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifptrWQH9GNWXv_demiTb91007W3WFmiqmt3ECRpBOPxMJI7TF-_0xOCtg2xVQMnu-y-eN1G4_9ZtnRqAcw5aH0pjbjywOze_AlLycAoApw3KfYrnsvT9xmrHwmCSUcZBEJZqH04cYhSc/s1600/Ma+Fig+2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="393" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifptrWQH9GNWXv_demiTb91007W3WFmiqmt3ECRpBOPxMJI7TF-_0xOCtg2xVQMnu-y-eN1G4_9ZtnRqAcw5aH0pjbjywOze_AlLycAoApw3KfYrnsvT9xmrHwmCSUcZBEJZqH04cYhSc/s400/Ma+Fig+2.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;"><span style="font-family: "Times New Roman","serif"; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: Cambria; mso-fareast-language: EN-US;"><strong>Fig. 2.</strong></span><span style="font-family: "Times New Roman","serif"; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: Cambria; mso-fareast-language: EN-US;"> <i style="mso-bidi-font-style: small;">Elysia
chlorotica</i>, showing highly branched digestive system and green color</span>.</span> </td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 10pt;">
<br /></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif";">Using an artificial sea-water
culture system, Rumpho and coworkers observed that metamorphosis of <i style="mso-bidi-font-style: normal;">E. chlorotica</i> from larva to juvenile
depends on the presence of <i style="mso-bidi-font-style: normal;">V. litorea, </i>and<i style="mso-bidi-font-style: normal;"> </i>newly formed juvenile starts to feed on
the algae immediately. As the sea slug feeds on <i style="mso-bidi-font-style: normal;">V. litorea</i>, it breaks the unicellular filamentous alga, and sucks
the contents, accumulating chloroplasts in its highly branched digestive system
distributed throughout its body. The chloroplasts are taken up by and stored
within the cells of the digestive system of the animal in a precess called
“kleptoplasty” (Fig. 3), making the body green. The feeding continues until the
number of chloroplasts accumulates to a sufficient level, then the sea slug can
live as a photosynthetic organism without eating for several months. This
ability to use photosynthesis as the sole energy source has endowed the name
“solar-powered” sea slug. If, however, the sea slug is removed from the algae
within a few days of the start of feeding, then there are insufficient
chloroplasts and development arrests.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt; text-indent: 0.5in;">
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix0bmKVXRwyf_hBsQifg-si8GLuTGiCxHwA1dvMweQTsIaZATN46sMZHePYPH6Lvn3y-dpc158RR-CQFPR-lHUuUULmEKszw0kX9uSEsMVq5UvJn8rMAD3jVyfGn9YMxvz_Yp1s_AZyGQ/s1600/Ma+Fig+3.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="215" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEix0bmKVXRwyf_hBsQifg-si8GLuTGiCxHwA1dvMweQTsIaZATN46sMZHePYPH6Lvn3y-dpc158RR-CQFPR-lHUuUULmEKszw0kX9uSEsMVq5UvJn8rMAD3jVyfGn9YMxvz_Yp1s_AZyGQ/s400/Ma+Fig+3.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div align="left">
<span style="font-family: Times New Roman; font-size: small;">
</span><span style="font-size: small;"><b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif";">Fig.3.</span></b><span style="font-family: "Times New Roman","serif";"> Kleptoplasty, by which cells of
the digestive systems of the sea slug take up chloroplasts from <i style="mso-bidi-font-style: normal;">V. litorea</i>, and maintain the function of
the chloroplasts. </span></span></div>
</td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 10pt;">
<br /></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>Although the <i style="mso-bidi-font-style: normal;">V. litorea</i> chloroplasts have four outer membranes, characteristic
of such secondary endosymbiotic chloroplasts of heterokonts, the chloroplasts
retained in the sea slug seem to lack the two outer membranes. In addition, the
<i style="mso-bidi-font-style: normal;">V. litorea</i> nuclei or mitochondria
were not detected in the sea slug cells, suggesting that only the chloroplasts
(without their outer two membranes) are taken up by the cells of the host
digestive tract. In other words, the algal nuclei that normally contain the
needed gene functions to maintain chloroplast functions appear to be absent in
the sea slug cells. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>Therefore, this sea slug –alga
relationship is similar to other animal-algal symbiotic relationships in having
to establish it de dovo during development, and unlike the endosymbiotic
relationship between plants/algae and chloroplasts. However, the <i style="mso-bidi-font-style: normal;">E. chlorotica</i> - <i style="mso-bidi-font-style: normal;">V. litorea</i> symbiosis is distinct from other animal-algae
relationship because the <i style="mso-bidi-font-style: normal;">V. litorea</i>
chloroplasts are taken up by the <i style="mso-bidi-font-style: normal;">E.
chlorotica</i> digestive cells, and <i style="mso-bidi-font-style: normal;">V.
litorea cells </i>are not maintained in the animal<i style="mso-bidi-font-style: normal;">. </i>It is striking that during the time when the sea slug is not
feeding, even for months, chloroplasts in its digestive cells are functional.
One of consequences of the photosynthesis is damage to chloroplast proteins;
thus new protein synthesis is needed for the maintenance of chloroplast
function. Therefore, the sea slug should be able to provide needed protein
activities to repair photo-oxidative damage to chloroplast proteins. </span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>An attractive hypothesis that
explains the ability of <i style="mso-bidi-font-style: normal;">E. chlorotica</i>
to maintain chloroplast function is that, through repeated uptake of <i style="mso-bidi-font-style: normal;">V. litoria</i> cellular content, crucial
genes for chloroplast functions have been transferred to the <i style="mso-bidi-font-style: normal;">E. chlorotica</i> nuclear genome. Indeed,
several lines of evidence support gene transfer from <i style="mso-bidi-font-style: normal;">V. litoria</i> to <i style="mso-bidi-font-style: normal;">E. chlorotica</i>:
de novo protein synthesis of a nuclear-encoded light-harvesting protein,
synthesis of the nuclear-encoded PRK protein and light-induced expression of
the <i style="mso-bidi-font-style: normal;">prk</i> gene in algal-starved sea
slugs, and detection of sequences highly similar to <i style="mso-bidi-font-style: normal;">V. litoria</i> nuclear genes encoding chloroplast proteins. However,
recently a partial transcriptome analysis has failed to identify cDNA sequences
that are similar to algal nuclear genes. Nevertheless, the absence of
supporting evidence for gene transfer is not evidence for the absence of gene
transfer. It is possible that such transferred genes are not expressed highly
enough to be detected in the partial transcriptome analysis. Alternatively, the
chloroplast functions might be supported via novel mechanisms. Therefore, more
extensive and definitive evidence for gene transfer is needed to support the
above hypothesis.</span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
<span style="font-family: "Times New Roman","serif";"><span style="mso-tab-count: 1;"> </span>Regardless of the exact mechanisms, <i style="mso-bidi-font-style: normal;">E. chlorotica</i> clearly can take up
functional chloroplasts intracellularly and maintain their functions for
extended periods of several months. These features make this relationship more
advanced than other animal-algal symbiotic relationships with intact cellular
symbionts and closer to endosymbiotic relationships present in algae. It will
be instructive to understand the mechanistic interaction between <i style="mso-bidi-font-style: normal;">E. chlorotica</i> and <i style="mso-bidi-font-style: normal;">V. litoria</i> and more will be uncovered as much more extensive
sequencing efforts are underway. It is possible that in the future, when the
soma-germline barrier can be broken for the chloroplast, and when the symbiont
chloroplasts can replicate in the sea slug, the relationship will then have
evolved into true endosymbiosis.<span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt;">
</div>
<div class="MsoNormal" style="font-size: 12pt; margin: 0in 0in 10pt;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif";">References</span></b></div>
<div class="MsoNormal" style="font-size: 12pt; line-height: 200%; margin: 0in 0in 10pt 0.5in; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif";">1. Rumpho ME, Pelletreau KN,
Moustafa A, Bhattacharya D. 2011. <a href="http://jeb.biologists.org/content/214/2/303.full.pdf+html" target="_blank">The making of a photosynthetic animal.</a> J.
Exp. Biol. 214, 303-311.</span></div>
</span><br />
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</div>
Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-12017572188890081162012-05-02T13:54:00.000-04:002012-06-04T14:26:57.844-04:00Epigenetics and Speciation<div class="MsoNormal" style="margin: 0in 0in 0pt;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt;">Contributed by:
<a href="mailto:mnozawa@nig.ac.jp" target="_blank">Masafumi Nozawa<o:p></o:p></a></span></b></div>
<br />
<br />
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 42pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Epigenetic
variation has recently been recognized as an additional layer of genetic
changes. After the discovery of epigenetic variation, many researchers have studied
its importance in adaptation and evolution. However, the role of epigenetic
variation in speciation remains largely unexplored.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 42pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Durand
et al. (1) recently showed that natural epigenetic variation in <i style="mso-bidi-font-style: normal;">Arabidopsis thaliana</i> contributes to the
cause of genetic incompatibility responsible for post-zygotic reproductive isolation.
When they crossed the Columbia-0 (col) strain with the Shahdara (sha) strain,
some F2 hybrids showed reduced seed production by 80-90%. Linkage
disequilibrium analysis identified two genomic regions, K4 and K5, that are responsible
for the incompatibility. Further fine mapping revealed that K5 contains gene <i style="mso-bidi-font-style: normal;">AtFOLT1</i>, which encodes a folate
transporter, and K4 contains a duplicate locus, <i style="mso-bidi-font-style: normal;">AtFOLT2</i>, only in sha. <i style="mso-bidi-font-style: normal;">AtFOLT1</i>
is expressed in col but not in sha, whereas <i style="mso-bidi-font-style: normal;">AtFOLT2</i>
exists only in sha. Interestingly, F2 hybrids become incompatible only when
there is no <i style="mso-bidi-font-style: normal;">AtFOLT</i> transcript. Therefore,
the lack of <i style="mso-bidi-font-style: normal;">AtFOLT</i> transcripts is
responsible for the incompatibility (Fig. 1).<o:p></o:p></span></div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6hiGP1W6M-nnU3SJw7eyOgMSm7xuLPGZooBNnLkfbLoymlq5IOnNGjF9w99FEOybCrJ3MMamGeXbE1EuYMBDHPV_ELcB0VQCPc_z6NQCjD4cA_tcEuB9MYOrO2LAzohF28wO6CUXV-qE/s1600/Fig1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6hiGP1W6M-nnU3SJw7eyOgMSm7xuLPGZooBNnLkfbLoymlq5IOnNGjF9w99FEOybCrJ3MMamGeXbE1EuYMBDHPV_ELcB0VQCPc_z6NQCjD4cA_tcEuB9MYOrO2LAzohF28wO6CUXV-qE/s400/Fig1.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><br />
<div align="left" class="MsoNormal" style="margin: 0in 29.2pt 0pt 0.5in; mso-layout-grid-align: none;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt;">Fig.
1.</span></b><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt;"> Mechanism of the allelic
incompatibility. </span><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPSMT; mso-font-kerning: 0pt;">In col, the promoter and the first part of the gene </span><i><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPS-ItalicMT; mso-font-kerning: 0pt;">AtFOLT1 </span></i><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPSMT; mso-font-kerning: 0pt;">are totally
unmethylated but they are in sha. The homologous region of </span><i><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPS-ItalicMT; mso-font-kerning: 0pt;">AtFOLT2 </span></i><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPSMT; mso-font-kerning: 0pt;">is also
methylated in sha, the gene being transcribed (black arrow) from the
unmethylated upstream promoter (green box). Modified from Durand et al. (1).<o:p></o:p></span></div>
<span style="font-size: small;">
</span></td></tr>
</tbody></table>
<br />
<br />
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Therefore,
they examined SNPs that might be responsible for the suppression of <i style="mso-bidi-font-style: normal;">AtFOLT1</i> in sha and identified 29 such SNPs
between sha and col. However, another strain named Ishikawa was shown to express
<i style="mso-bidi-font-style: normal;">AtFOLT1</i> even if the nucleotide
sequence of <i style="mso-bidi-font-style: normal;">AtFOLT1</i> is exactly the
same as that of sha. This indicates that epigenetic changes cause the silencing
of <i style="mso-bidi-font-style: normal;">AtFOLT1</i>. Indeed, <i style="mso-bidi-font-style: normal;">AtFOLT1</i> in sha was highly methylated.</span></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">They
further investigated how the methylation is induced and found that <i style="mso-bidi-font-style: normal;">AtFOLT2</i> in sha generates small RNAs
which directly induce DNA methylation on promoter regions of <i style="mso-bidi-font-style: normal;">AtFOLT1</i> and <i style="mso-bidi-font-style: normal;">AtFOLT2</i>. Yet, because <i style="mso-bidi-font-style: normal;">AtFOLT2</i>
in sha has an irregular promoter region which is not methylated, sha can express
<i style="mso-bidi-font-style: normal;">AtFOLT2</i> and therefore be fertile
(Fig. 1). Interestingly, this small RNA is sufficient to induce <i style="mso-bidi-font-style: normal;">de novo </i>DNA methylation in the <i style="mso-bidi-font-style: normal;">AtFOLT</i> region, because after several
generations the unmethylated <i style="mso-bidi-font-style: normal;">AtFOLT1</i>
region was methylated (Fig. 2).</span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNY00CAG8qpIXeCc_e4A_mAhJOGy47iRgcp8pBwgsFgs6mMZrT9kM7TRI7pMpJImtRyG7AqE3BVV9ta2O_3aXYLEP8PlHoIj21Aogmpdzp1r__XGRPHsPytgi4sOl3tMy5BehfwVj8yYM/s1600/Fig2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNY00CAG8qpIXeCc_e4A_mAhJOGy47iRgcp8pBwgsFgs6mMZrT9kM7TRI7pMpJImtRyG7AqE3BVV9ta2O_3aXYLEP8PlHoIj21Aogmpdzp1r__XGRPHsPytgi4sOl3tMy5BehfwVj8yYM/s400/Fig2.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">
</span><br />
<div align="left" class="MsoNormal" style="margin: 0in 29.2pt 0pt 0.5in; mso-layout-grid-align: none;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPSMT; mso-font-kerning: 0pt;">Fig. 2.</span></b><span style="font-family: "Times New Roman","serif"; font-size: 11pt; mso-bidi-font-size: 12.0pt; mso-fareast-font-family: TimesNewRomanPSMT; mso-font-kerning: 0pt;"> <i style="mso-bidi-font-style: normal;">De novo</i> DNA methylation of <i style="mso-bidi-font-style: normal;">AtFOLT1</i> by small RNAs in the <i style="mso-bidi-font-style: normal;">AtFOLT2</i> region. In F1, <i style="mso-bidi-font-style: normal;">AtFOLT1</i> from col is expressed because
the region is not methylated. However, small RNAs at the <i style="mso-bidi-font-style: normal;">AtFOLT2</i> region derived from sha stochastically and progressively
induce DNA methylation on the <i style="mso-bidi-font-style: normal;">AtFOLT1</i>
region. Consequently, <i style="mso-bidi-font-style: normal;">AtFOLT1</i> is not
expressed after seven generations.<o:p></o:p></span></div>
<span style="font-size: small;">
</span></td></tr>
</tbody></table>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-align: left; text-indent: 0.5in;">
<br /></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt; text-indent: 0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">In
summary, this study represents the first case of a natural epiallele that has
strong deleterious phenotypic consequences steadily maintained in the progenies
of crosses between strains, which play roles in establishing reproductive
isolation. I think this type of processes might be much more frequent than
currently appreciated.</span></div>
<br />
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">References</span></b><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-fareast-font-family: "Times New Roman";"><span style="mso-list: Ignore;"></span></span></div>
<div class="MsoListParagraph" style="line-height: 200%; margin: 0in 0in 0pt 0.5in; mso-para-margin-left: 0gd; text-indent: -0.5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">1. Durand S, Bouche N, Strand EP,
Loudet O, and Camilleri C. (2012) <a href="http://ac.els-cdn.com/S0960982211014679/1-s2.0-S0960982211014679-main.pdf?_tid=6c59b739349d1a6f002bbe457844f1b9&acdnat=1338834576_6a72368b95f3cccf318ab72157efd719" target="_blank">Rapid establishment of genetic incompatibility through natural epigenetic variation</a>. <i style="mso-bidi-font-style: normal;">Curr Bio</i> 22: 326-31.</span></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-1875946849260724862012-04-19T15:02:00.000-04:002012-06-04T14:27:41.830-04:00Evolution of Milk Casein Genes from Tooth Genes<div class="MsoNormal" style="margin: 0in 0in 10pt;">
<strong>Contributed by: <a href="mailto:kuk2@psu.edu" target="_blank">Kazuhiko Kawasaki</a></strong><br />
<br /></div>
<div class="MsoNormal" style="line-height: 200%; margin: 0in 0in 0pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><span style="mso-tab-count: 1;"> </span>
In most mammals, caseins are the
most abundant proteins in milk. Caseins associate with calcium and stabilize it
at a high concentration, which helps infants to develop bone and teeth. Despite
the critical role of caseins in mammalian evolution, their origin has been
unknown or highly speculative. Association of caseins with calcium is mediated
by negatively charged amino acids, and no rigid 3-dimensional structure is
required for this function. Mainly for this reason, caseins evolve rapidly, and
hence the amino acid or nucleotide sequence similarity is not very useful for exploring their evolution. For this reason, we studied similarities in the
exon-intron structure of the genes, which is more conserved during evolution (1).
The results suggest that two of the three casein genes have evolved by
duplication of the <i style="mso-bidi-font-style: normal;">SCPPPQ1</i> gene,
whereas the third casein gene originated from the <i style="mso-bidi-font-style: normal;">FDCSP</i> gene. In addition, the <i style="mso-bidi-font-style: normal;">SCPPPQ1</i>
and <i style="mso-bidi-font-style: normal;">FDCSP</i> genes share a common
ancestral gene called <i style="mso-bidi-font-style: normal;">ODAM</i>.
Interestingly, all these three precursor genes are expressed in dental tissues
and probably encode calcium-binding proteins. We therefore argue that all
casein genes arose from tooth genes and that the calcium-binding ability of
caseins was inherited from their ancestor.<o:p></o:p></span>
<br />
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<v:shapetype coordsize="21600,21600" filled="f" o:preferrelative="t" o:spt="75" path="m@4@5l@4@11@9@11@9@5xe" stroked="f"><span style="font-family: Times; font-size: small;"><v:stroke joinstyle="miter"><v:path gradientshapeok="t" o:connecttype="rect" o:extrusionok="f"><o:lock aspectratio="t" v:ext="edit"><strong>Figure:</strong> A likely scenario of the evolution of case in genes</o:lock></v:path></v:stroke></span></v:shapetype><br />
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<v:shapetype coordsize="21600,21600" filled="f" o:preferrelative="t" o:spt="75" path="m@4@5l@4@11@9@11@9@5xe" stroked="f"><span style="font-family: Times; font-size: small;"><v:stroke joinstyle="miter"><v:path gradientshapeok="t" o:connecttype="rect" o:extrusionok="f"><o:lock aspectratio="t" v:ext="edit"></o:lock></v:path></v:stroke></span></v:shapetype><v:shapetype coordsize="21600,21600" filled="f" o:preferrelative="t" o:spt="75" path="m@4@5l@4@11@9@11@9@5xe" stroked="f"><span style="font-family: Times; font-size: small;"><v:stroke joinstyle="miter"><v:path gradientshapeok="t" o:connecttype="rect" o:extrusionok="f"><o:lock aspectratio="t" v:ext="edit">[Gene symbols]</o:lock></v:path></v:stroke></span></v:shapetype></div>
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<v:shapetype coordsize="21600,21600" filled="f" o:preferrelative="t" o:spt="75" path="m@4@5l@4@11@9@11@9@5xe" stroked="f"><span style="font-size: small;"><v:stroke joinstyle="miter"><v:path gradientshapeok="t" o:connecttype="rect" o:extrusionok="f"><o:lock aspectratio="t" v:ext="edit"><span style="font-family: Times, "Times New Roman", serif;">ODAM: odontogenic ameloblast-associated</span></o:lock></v:path></v:stroke></span></v:shapetype></div>
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<span style="font-family: Times, "Times New Roman", serif;">SCPPPQ1: secretory calcium-binding phosphoprotein proline and glutamine rich 1</span></div>
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<span style="font-family: Times, "Times New Roman", serif;">FDCSP: follicular dendritic cell secreted peptide</span></div>
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Caseins are among cardinal proteins that evolved in the lineage leading
to mammals.<span style="mso-spacerun: yes;"> </span>In milk, caseins and calcium
phosphate (CaP) form a huge complex, called casein micelle.<span style="mso-spacerun: yes;"> </span>By forming the micelle, milk maintains high
CaP concentrations, which help altricial mammalian neonates to grow bone and
teeth.<span style="mso-spacerun: yes;"> </span>Two types of caseins are
known.<span style="mso-spacerun: yes;"> </span>Ca-sensitive caseins<span style="font-family: Symbol;"> (a</span><sub>s</sub>- and <span style="font-family: Symbol;">b</span>-caseins) bind Ca but precipitate at high Ca concentrations,
whereas Ca-insensitive casein (<span style="font-family: Symbol;">k</span>-casein)
does not usually interact with Ca but instead stabilizes the micelle.<span style="mso-spacerun: yes;"> </span>Thus, it is thought that these two types of
caseins are both necessary for stable micelle formation.<span style="mso-spacerun: yes;"> </span>Both types of caseins show high substitution
rates, which make it difficult to elucidate the evolution of caseins.<span style="mso-spacerun: yes;"> </span>Yet, recent studies have revealed that all
casein genes belong to the secretory calcium-binding phosphoprotein (SCPP) gene
family that arose by gene duplication.<span style="mso-spacerun: yes;">
</span>In the present study, we investigated exon-intron structures and
phylogenetic distributions of casein and other SCPP genes, particularly the
odontogenic ameloblast associated (<i style="mso-bidi-font-style: normal;">ODAM</i>)
gene, the SCPP-Pro-Gln-rich 1 (<i style="mso-bidi-font-style: normal;">SCPPPQ1</i>)
gene, and the follicular dendritic cell secreted peptide (<i style="mso-bidi-font-style: normal;">FDCSP</i>) gene.<span style="mso-spacerun: yes;"> </span>The results suggest
that contemporary Ca-sensitive casein genes arose from a putative common
ancestor, which we refer to as <i style="mso-bidi-font-style: normal;">CSN1/2</i>.<span style="mso-spacerun: yes;"> </span>The six putative exons comprising <i style="mso-bidi-font-style: normal;">CSN1/2</i> are all found in <i style="mso-bidi-font-style: normal;">SCPPPQ1</i>, although <i style="mso-bidi-font-style: normal;">ODAM</i> also shares four of these exons.<span style="mso-spacerun: yes;"> </span>By contrast, the five exons of the
Ca-insensitive casein gene are all reminiscent of <i style="mso-bidi-font-style: normal;">FDCSP</i>.<span style="mso-spacerun: yes;"> </span>The phylogenetic
distribution of these genes suggests that both <i style="mso-bidi-font-style: normal;">SCPPPQ1</i> and <i style="mso-bidi-font-style: normal;">FDCSP</i> arose
from <i style="mso-bidi-font-style: normal;">ODAM</i>.<span style="mso-spacerun: yes;"> </span>We thus argue that all casein genes evolved
from <i style="mso-bidi-font-style: normal;">ODAM</i> via two different pathways;
Ca-sensitive casein genes likely originated directly from <i style="mso-bidi-font-style: normal;">SCPPPQ1</i>, whereas the Ca-insensitive casein genes directly
differentiated from <i style="mso-bidi-font-style: normal;">FDCSP</i>.<span style="mso-spacerun: yes;"> </span>Further, expression of <i style="mso-bidi-font-style: normal;">ODAM</i>, <i style="mso-bidi-font-style: normal;">SCPPPQ1</i>, and <i style="mso-bidi-font-style: normal;">FDCSP</i> was detected in dental tissues,
supporting the idea that both types of caseins evolved as Ca-binding
proteins.<span style="mso-spacerun: yes;"> </span>Based on these findings, we
propose two alternative hypotheses for micelle formation in primitive milk.<span style="mso-spacerun: yes;"> </span>The conserved biochemical characteristics in
caseins and their immediate ancestors also suggest that many slight genetic
modifications have created modern caseins, proteins vital to the sustained
success of mammals.<span style="mso-spacerun: yes;"> </span></div>
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<b style="mso-bidi-font-weight: normal;">References<o:p></o:p></b></span></div>
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1.
Kawasaki, K., Lafont, A.G., and Sire, J.Y. 2011. <a href="http://mbe.oxfordjournals.org/content/28/7/2053.full.pdf" target="_blank">The evolution of milk casein genes from tooth genes before the origin of mammals</a>. Mol. Biol. Evol.
28(7):2053-2061.</span></div>
</div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-68374741969918998212012-04-16T16:13:00.000-04:002012-04-16T16:13:35.395-04:00Parallel Adaptive Evolution and Genomic Changes in Stickleback Fish
<strong>Contributed by: </strong><a href="mailto:jnam@caltech.edu" target="_blank"><strong>Jongmin Nam</strong></a><br />
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><span style="mso-tab-count: 1;"> </span>The
molecular basis of phenotypic evolution is largely unknown, and identification
of exact DNA changes underlying a specific morphological, physiological, or
behavioral evolution is very hard, though it is a fascinating subject. Despite
these difficulties, stickleback fish have been a great model system for
studying the molecular basis of adaptive evolution, because they have
experienced rapid parallel adaptation from salt to freshwater life in multiple
geographical locations. They are therefore good organisms for studying
recurrent adaptive evolution.<o:p></o:p></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><o:p> </o:p></span><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><span style="mso-tab-count: 1;"> </span>In
a recent Nature paper, Jones et al. (1) sequenced the genomes of multiple,
independently evolved marine-freshwater pairs of sticklebacks (see Figure 1).
They then examined sequence changes that are shared by most freshwater fishes
but are different from typical sequences shared by most saltwater fishes. Not
only did they detect what was already known, but they also detected about 60
strong candidate genomic regions for recurrent adaptive evolution. About 40% -
80% of them had either changes in noncoding regions or synonymous substitutions
in protein coding regions, and only about 17% contained changes causing amino
acid substitutions. Genes within or near these protein-coding regions varied
widely from differentiation genes to regulatory genes. It would be of great
interest to study molecular function of these regions in relation to the
changes of specific phenotypic characters.<o:p></o:p></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZiKSytbMCQDqEPybN39aXpYGQHVdWp-Ak6CGpntAkrnTRfxIKp2h5HZP8G2GKKWBCyhkTM9s8-yz7boG_FBYq0b303p97uYKfVkx8CDe-4r5tEpJta35BTM-QT8dMGQKiHrF_2X1fVDY/s1600/Nam+Parallel+Adaptive+Evolution+Picture.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZiKSytbMCQDqEPybN39aXpYGQHVdWp-Ak6CGpntAkrnTRfxIKp2h5HZP8G2GKKWBCyhkTM9s8-yz7boG_FBYq0b303p97uYKfVkx8CDe-4r5tEpJta35BTM-QT8dMGQKiHrF_2X1fVDY/s1600/Nam+Parallel+Adaptive+Evolution+Picture.jpg" /></a></td></tr>
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<span style="font-family: "Times New Roman","serif"; mso-bidi-font-size: 11.0pt;"><span style="font-size: small;"><strong>Figure 1.</strong> Genome scans for parallel marine–freshwater divergence.<span style="mso-spacerun: yes;"> </span>Marine (red) and freshwater (blue) stickleback populations were surveyed from diverse locations.</span></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><span style="mso-tab-count: 1;"> </span><o:p></o:p></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;"><span style="mso-tab-count: 1;"> </span>Conducting
killer experiments to show causality of these regulatory changes to specific
phenotype evolution is still challenging, partly because we do not know how
these functional elements work in complex regulatory networks and partly
because experimental tools for re-engineering functional elements in the genome
are not yet available in most species. Nevertheless, there are at least a good
number of candidate regions for studying adaptive evolution to begin with, and
this is a big step forward.</span></div>
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<p style="line-height: 200%;"><strong>Abstract</strong> </p>
<p style="line-height: 200%;">Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature. <span style="color: black;">
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">References</span></b></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%; mso-bidi-font-size: 11.0pt;">1. Jones, F. C.,
Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford,
R., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J.,
Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R.,
Knecht, A. K., Brady, S. D., Zhang, H., Pollen, A. A., Howes, T., Amemiya, C.,
Baldwin, J., Bloom, T., Jaffe, D. B., Nicol, R., Wilkinson, J., Lander, E. S.,
Di Palma, F., Lindblad-Toh, K., Kingsley, D. M. 2012. <a href="http://www.nature.com/nature/journal/v484/n7392/pdf/nature10944.pdf" target="_blank">The genomic basis of adaptive evolution in threespine sticklebacks.</a> Nature 484: 55-61.<o:p></o:p></span></div>
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Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0tag:blogger.com,1999:blog-3378199995075509398.post-79984456479974162222012-04-13T15:09:00.000-04:002012-04-13T15:13:05.258-04:00Evolution of a Poison-Resistance Gene through Introgression<strong>Contributed by: </strong><a href="mailto:zlin1@uchicago.edu" target="_blank"><strong>Zhenguo Lin</strong></a><br />
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Warfarin is an anticoagulant that inhibits
the synthesis of clotting factors. Because it causes internal bleeding in rats
and mice, warfarin has been widely used a rodenticide since 1948. Warfarin decreases
blood coagulation by inhibiting the vitamin K epoxide reductase (VKOR), an
enzyme involved in the carboxylation of several blood coagulation proteins.<o:p></o:p></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;"> After
merely 10 years of introduction of warfarin as a rodenticide, warfarin resistant
mouse or rats have been found. The resistance to warfarin of house mice (<i style="mso-bidi-font-style: normal;">Mus musculus domesticus</i>) was found to be
due to some nonsynonymous single-nucleotide polymorphisms (SNPs) in the vitamin
K epoxide reductase subcomponent 1 (vkorc1) that encodes the warfarin-sensitive
component of VKOR.<o:p></o:p></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">Song et al. (2011) recently found that
the polymorphisms of vkorc1 in resistant house mice were acquired from the
Algerian mouse (<i style="mso-bidi-font-style: normal;">Mus spretus</i>), a
species known to be naturally resistant to warfarin, through introgressive
hybridization (1).<o:p></o:p></span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">The Algerian mouse and house mouse
diverged 1.5–3 million years ago and the distributions of the two species has
some overlaps in Spain and northern Africa. The hybridization between the two
species is not common and only some female offspring are fertile. However, it
is surprising that the piece of DNA that contain warfarin resistant gene can spread
quickly in the house mouse populations in a few decades. For example, the vkorc1
gene in 27 of 29 house mice examined in Spain was entirely or partly originated
from Algerian mice. Similar cases were also observed in 16 of 50 house mice in
Germany, where Algerian mice do not exist (1). Although it is believed that interspecific
hybrids have severe disadvantages, this study suggests that hybridization can be
an important way for the evolution of a specific character.<o:p></o:p></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDxb2ZT4Yo8yl72J7AhSETBhVJHfFBtyrND4U44eh5B8FxJslwqoBMJ_xMM4r7xIl2OEwiSEQ7lmVbM4EeMukCzfbj4xlmS_HCFRC_6I_dPMK4i0EHSDHJcRPP8upL7raAfIZPGHlC7zA/s1600/Algerian+mice+photo.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDxb2ZT4Yo8yl72J7AhSETBhVJHfFBtyrND4U44eh5B8FxJslwqoBMJ_xMM4r7xIl2OEwiSEQ7lmVbM4EeMukCzfbj4xlmS_HCFRC_6I_dPMK4i0EHSDHJcRPP8upL7raAfIZPGHlC7zA/s400/Algerian+mice+photo.jpg" width="341" /></a></td></tr>
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<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Times New Roman","serif";"><span style="font-size: small;">Distribution of vkorc1 genotypes
in Western European <i style="mso-bidi-font-style: normal;">M. m. domesticus</i>.</span></span></b><span style="font-family: "Times New Roman","serif";"><span style="font-size: small;"> The hatched area depicts the
native range of <i style="mso-bidi-font-style: normal;">M. spretus</i>. The house
mouse (<i style="mso-bidi-font-style: normal;">Mus musculus spp</i>.) has become
a cosmopolitan species and now is occurring across the entire area depicted and
beyond. Pie charts show the frequencies of pure vkorc1 of <i style="mso-bidi-font-style: normal;">M. m. domesticus</i> origin (vkorc1</span><sup><span style="font-size: x-small;">dom</span></sup><span style="font-size: small;">) (pink, genotypes 1–6
in A), genotypes that correspond to the complete <i style="mso-bidi-font-style: normal;">M. spretus</i> vkorc1 allele or share parts of it in the form of
heterozygosity and/or intragenic recombination (all vkorc1</span><sup><span style="font-size: x-small;">spr</span></sup><span style="font-size: small;">,
yellow, genotypes 8–20 in A), and ambiguous genotypes (genotype 7, green).
Countries sampled in this study are shaded in gray. Sampling locations (some
overlapping as a result of proximity) are shown as triangles (pink, vkorc1</span><sup><span style="font-size: x-small;">spr</span></sup><span style="font-size: small;">
absent; yellow, vkorc1</span><sup><span style="font-size: x-small;">spr</span></sup><span style="font-size: small;"> present). <b style="mso-bidi-font-weight: normal;">From Song et al. (2011).<o:p></o:p></b></span></span></div>
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<strong>References</strong><br />
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<span style="font-family: "Times New Roman","serif"; font-size: 12pt; line-height: 200%;">1.
Song, Y., <span style="mso-spacerun: yes;"> </span>Endepols, S.,<span style="mso-spacerun: yes;"> </span>Klemann, N., Richter, D., <span style="mso-spacerun: yes;"> </span>Matuschka, F.R., Shih, C.H., Nachman, M.W., and
Kohn, M.H. 2011. <a href="http://www.sciencedirect.com/science/article/pii/S0960982211007160" target="_blank">Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice.</a> Current Biology
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<br /></div>Tina Kushnerhttp://www.blogger.com/profile/08101451188926956175noreply@blogger.com0