Symbiosis and Genome Degeneration: Micro-niche Evolution

            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.

             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 HS.” This strain was isolated from a patient who had a hand wound following impalement with a tree branch. Phylogenetic analysis showed that the strain HS is a member of the Sodalis-allied clade of insect endosymbionts and that close relatives of strain HS gave rise to symbiotic association in a range of insect species. Using 165 rRNA genes, Clayton et al. (2012) showed that strain HS is closely related (by 98% sequence identity for synonymous sites) to the bacteria Solidas glossinidius and Sitophilus oryzae primary endosymbiont (SOPE) that are endosymbionts of grain weevils. The genome size (5.16 Mb) of HS was only slightly greater than those of S. glossinidius and SOPE (see Table 1). This result suggests that the latter two species have become endosymbionts only recently and HS is a free-living bacterium. (The symbiont bacterium (Buchnera aphidicola) of aphids has only 20% of the genome of the ancestral free bacteria.)

Table 1. General features of the strain HS, SOPE, and S. glossinidius genome sequences

            Clayton et al. (2012) and Oakeson et al. (2014) sequenced the genomes of HS and SOPE and compared the genomic sequences with the sequence of S. glossinidius, 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.

Figure 1. Alignments of three regions of the S. glossinidius, strain HS, and SOPE chromosomes. Alignments of three regions of the S. glossinidius, strain HS, and SOPE chromosomes, corresponding to SG0948–SG0977 (A), ps_SGL0466–SG0918 (B) and ps_SGL0318–ps_SGL0330 (C) in the most recent S. glossinidius 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 HS genes have intact reading frames, the status of their orthologs in S. glossinidius and SOPE 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 SOPE.

            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.

             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.

             Note also that because many mutations are not harmful under the symbiotic condition, even DNA repair genes such as recA and recF may be lost (Shigenobu et al. 2000; Itoh et al. 2002). In fact, the loss of recA has been confirmed even in the symbiont bacteria S. glossinidius and SOPE (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.

             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 Astyanax mexicanus 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 A. mexicanus 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.

             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.

References

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