The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.

Friday, December 20, 2013

Selective Advantage of New Mutations May Depend on Mutations in Other Sites

Contributed by: Zhenguo Zhang

 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 (1). An interesting case of epistatic interaction was recently observed in the hemoglobin of the deer mouse, Peromyscus maniculatus (2).

Figure 1. 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 in red.
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 et al. 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 (23 = 8) combinations of allelic group variants (Fig. 2), and tested the oxygen affinity of the recombinant proteins in vitro with or without allosteric effectors (Cl- and DPG).
Figure 2. The 8 genotypes of the recombinant deer mouse hemoglobin. (From Natarajan et al., Science, 2013). Each line denotes the amino acids of one recombinant hemoglobin at the polymorphic sites with the amino acids from the highland population in blue and those from the lowland population in red.
            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- 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 P50 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 ΔlogP50) 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 (2). This implies that the epistatic interactions of these mutations may be mediated by coordinated changes of protein topology.

   Table 1(From Natarajan et al., Science, 2013. P50 represents the oxygen pressure when 50% of the hemes of hemoglobins are saturated with oxygen. The genotype of each recombinant hemoglobin is denoted by three letters, for example, LH-L representing the L allele for α-globin exon 2, H allele for α-globin exon 3, and L allele for β-globin. H and L denote the alleles present in the highland and lowland populations, respectively)
            This study (2) demonstrates that the effect of a mutation on the oxygen affinity depends on the genetic background. Since epistasis is prevalent in the genome (3), 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 (4, 5). Genetic drift and environmental changes also may have played important roles.


Abstract of the original paper

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-O2 affinity depending on the allelic state of other sites. Structural analysis revealed that epistasis for Hb-O2 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.

1.         Lehner B: Molecular mechanisms of epistasis within and between genes. Trends Genet 2011, 27(8):323-331.
2.         Natarajan C, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF: Epistasis among adaptive mutations in deer mouse hemoglobin. Science 2013, 340(6138):1324-1327.
3.         Nei M, Ebooks Corporation: Mutation-driven evolution. In., 1st edn. Oxford: Oxford University Press; 2013: 1 online resource.
4.         Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JA: Initial mutations direct alternative pathways of protein evolution. PLoS Genet 2011, 7(3):e1001321.
5.         Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL: Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A 2009, 106(29):12025-12030.