Review Article | Published:

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

Nature Reviews Genetics volume 14, pages 559571 (2013) | Download Citation

Abstract

The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality — the purviews of evolutionary biology and biochemistry, respectively — are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do.

Key points

  • Evolutionary biochemistry aims to dissect the evolutionary processes and physical mechanisms by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution.

  • The historical separation between biochemists and evolutionary biologists is breaking down, allowing for powerful investigations of protein evolution at the interface of the two disciplines.

  • Among the key techniques for studying the biochemical mechanisms of protein evolution are ancestral protein reconstruction, directed laboratory evolution and high-throughput evolutionary analysis of protein sequence space.

  • Evolutionary analysis illuminates core questions in biochemistry because it can efficiently reveal the sequence determinants of differences in function, structure and other physical properties among proteins. It also provides the ultimate explanation for why any protein has the properties it has today.

  • Biochemical approaches illuminate core questions in molecular evolution because they can reveal the mechanisms by which historical mutations led to the emergence of new phenotypes, they can characterize the topology of the genotype–function space on which evolution occurred, and they can illuminate how the physical properties of biological molecules shaped the evolutionary processes.

  • Work in evolutionary biochemistry explains the interplay of contingency and determinism in molecular evolution as the result of the specific functional constraints and genetic interactions that are produced by the physical architecture of each protein.

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References

  1. 1.

    Molecular Basis of Evolution (John Wiley & Sons, 1959). This is a prescient early attempt by a Nobel-prize-winning biochemist to consider how chemistry might shape protein evolution.

  2. 2.

    Biochemical Evolution (Academic Press, 1949).

  3. 3.

    & Molecules as documents of evolutionary history. J. Theor. Biol. 8, 357–366 (1965).

  4. 4.

    & in Evolving Genes and Proteins (Bryson, 1965). Two chemists defend the potential contributions of biochemistry to evolutionary knowledge at a 1964 conference that brought molecular biologists and classical evolutionary biologists together.

  5. 5.

    & Chemical paleogenetics: molecular 'restoration studies' of extinct forms of life. Acta Chem. Scand. 17, S9–S16 (1963).

  6. 6.

    Gene evolution and the haemoglobins. Nature 189, 704–708 (1961).

  7. 7.

    Phylogeny and ontogeny at the molecular level. Evol. Biochem. 3, 12–51 (1963).

  8. 8.

    Paradox and persuasion: negotiating the place of molecular evolution within evolutionary biology. J. Hist. Biol. 31, 85–111 (1998).

  9. 9.

    Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959–1965. J. Hist. Biol. 31, 155–178 (1998).

  10. 10.

    'Molecules and monkeys': George Gaylord Simpson and the challenge of molecular evolution. Hist. Philos. Life Sci. 24, 441–465 (2002).

  11. 11.

    The status of the study of organisms. Am. Scientist 50, 36–45 (1962).

  12. 12.

    Organisms and molecules in evolution. Science 146, 1535–1538 (1964).

  13. 13.

    Biology, molecular and organismic. Am. Zool. 4, 443–452 (1964).

  14. 14.

    Homology: a personal view on some of the problems. Trends Genet. 16, 227–231 (2000).

  15. 15.

    & The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205, 581–598 (1979).

  16. 16.

    , & The tree-thinking challenge. Science 310, 979–980 (2005).

  17. 17.

    Allozymes in evolutionary genetics: self-imposed burden or extraordinary tool? Genetics 136, 11–16 (1994).

  18. 18.

    & Mechanistic approaches to the study of evolution: the functional synthesis. Nature Rev. Genet. 8, 675–688 (2007).

  19. 19.

    Bringing molecules back into molecular evolution. PLoS Comput. Biol. 8, e1002572 (2012).

  20. 20.

    & Is the evolution of insulin Darwinian or due to selectively neutral mutation? Nature 257, 197–203 (1975).

  21. 21.

    Species adaptation in a protein molecule. Mol. Biol. Evol. 1, 1–28 (1983). This is the first article in the inaugural issue of Molecular Biology and Evolution. It lays out an agenda for experimental studies of protein evolution, using biochemical and structural studies of haemoglobin in a phylogenetic context as a template.

  22. 22.

    , , , & Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345, 86–89 (1990).

  23. 23.

    , & Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J. Mol. Biol. 233, 305–312 (1993).

  24. 24.

    & The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355–369 (1998).

  25. 25.

    & Exploring protein fitness landscapes by directed evolution. Nature Rev. Mol. Cell Biol. 10, 866–876 (2009).

  26. 26.

    & Protein engineers turned evolutionists. Nature Meth 4, 991–994 (2007).

  27. 27.

    , & Experimental illumination of a fitness landscape. Proc. Natl Acad. Sci. USA 108, 7896–7901 (2011). A high-throughput experimental evolution study is presented that directly characterizes the distribution of fitness effects of a very large number of possible mutations in heat shock protein 90 (HSP90).

  28. 28.

    , & Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179, 2037–2043 (2008).

  29. 29.

    & Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360–366 (2010).

  30. 30.

    & Optimizing non-natural protein function with directed evolution. Curr. Opin. Chem. Biol. 15, 201–210 (2011).

  31. 31.

    et al. Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proc. Natl Acad. Sci. USA 106, 14450–14455 (2009). This multifaceted study links ecological context and population-level variation in haemoglobin allele frequencies to the experimentally measured oxygen affinity of those alleles.

  32. 32.

    , , & Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl Acad. Sci. USA 105, 13480–13485 (2008).

  33. 33.

    , , , & Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185, 293–303 (2010).

  34. 34.

    , & Pervasive cryptic epistasis in molecular evolution. PLoS Genet. 6, e1001162 (2010). This elegant experiment demonstrates that functionally equivalent, orthologous proteins can have different tolerances for identical mutations.

  35. 35.

    , & Direct demonstration of an adaptive constraint. Science 314, 458–461 (2006).

  36. 36.

    , , & Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317, 1544–1548 (2007).

  37. 37.

    , & An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461, 515–519 (2009). References 36 and 37 describe the first experimental identification of permissive and restrictive mutations, which open and close evolutionary trajectories despite being functionally neutral themselves; this paper also reports the first X-ray crystallographic structures of reconstructed ancestral proteins.

  38. 38.

    , & Forced evolution of a regulatory RNA helix in the HIV-1 genome. Nucl. Acids Res. 25, 940–947 (1997).

  39. 39.

    & Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406, 625–628 (2000).

  40. 40.

    , & Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature 474, 92–95 (2011).

  41. 41.

    , , & Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA. PLoS ONE 7, e44376 (2012).

  42. 42.

    The structure of protein evolution and the evolution of protein structure. Curr. Opin. Struct. Biol. 18, 170–177 (2008).

  43. 43.

    & Understanding protein evolution: from protein physics to Darwinian selection. Annu. Rev. Phys. Chem. 59, 105–127 (2008).

  44. 44.

    in Proceedings of the Sixth International Congress of Genetics 356–366 (1932).

  45. 45.

    Genetics and the Origin of Species (Columbia Univ. Press, 1937).

  46. 46.

    Natural selection and the concept of a protein space. Nature 225, 563–564 (1970).

  47. 47.

    Evolution and speciation on holey adaptive landscapes. Trends Ecol. Evol. 12, 307–312 (1997).

  48. 48.

    The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces (Cambridge Univ. Press, 2006).

  49. 49.

    & Colloquium paper: adaptive landscapes and protein evolution. Proc. Natl Acad. Sci. USA 107, 1747–1751 (2009).

  50. 50.

    et al. High-resolution mapping of protein sequence-function relationships. Nature Meth 7, 741–746 (2010).

  51. 51.

    et al. Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proc. Natl Acad. Sci. USA (2013). This paper presents an evolutionary biochemical study that uses ancestral reconstruction to identify two historical substitutions that cause a massive historical shift in binding specificity in the steroid receptors. It then follows up with detailed biophysical investigations of the mechanism of the transition.

  52. 52.

    Downhill protein folding: evolution meets physics. Comp. Rend. Biol. 328, 701–712 (2005).

  53. 53.

    , , & A backbone-based theory of protein folding. Proc. Natl Acad. Sci. USA 103, 16623 (2006).

  54. 54.

    , , , & Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 102, 14338–14343 (2005).

  55. 55.

    et al. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc. Natl Acad. Sci. USA 108, 680–685 (2011).

  56. 56.

    , & Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep. 2, 249–256 (2012).

  57. 57.

    Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99, 364–373 (2007).

  58. 58.

    & Molecular spandrels: tests of adaptation at the genetic level. Nature Rev. Genet. 12, 767–780 (2011).

  59. 59.

    Genetic Basis of Evolutionary Change (Columbia Univ. Press, 1974).

  60. 60.

    Changing effective population size and the McDonald-Kreitman test. Genetics 162, 2017–2024 (2002).

  61. 61.

    Molecular signatures of natural selection. Annu. Rev. Genet. 39, 197–218 (2005).

  62. 62.

    , , & Comment on papers by Evans et al. and Mekel-Bobrov et al. on evidence for positive selection of MCPH1 and ASPM. Science 317, 1036–1036 (2007).

  63. 63.

    , & Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. Proc. Natl Acad. Sci. USA 106, 21247–21251 (2009).

  64. 64.

    , & Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii. Evolution 66, 469–485 (2012).

  65. 65.

    The stability of globular proteins. Crit. Rev. Biochem. 3, 1–43 (1975).

  66. 66.

    & Principles of protein stability derived from protein engineering experiments. Curr. Opin. Struct. Biol. 3, 75–75 (1993).

  67. 67.

    & Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. J. Biomol. Struct. Dynam. 16, 397–411 (1998).

  68. 68.

    & The protein trinity—linking function and disorder. Nature Biotech. 19, 805–806 (2001).

  69. 69.

    , & Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Rev. Genet. 6, 678–687 (2005).

  70. 70.

    , , & Directed evolution of a thermostable esterase. Proc. Natl Acad. Sci. USA 95, 12809–12813 (1998).

  71. 71.

    , , & How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 26, 100–106 (2001).

  72. 72.

    & Why are proteins marginally stable? Proteins Struct. Function Genet. 46, 105–109 (2002).

  73. 73.

    in Computational Science — ICCS 2004 718–727 (2004).

  74. 74.

    , & Thermodynamics of neutral protein evolution. Genetics 175, 255–266 (2007).

  75. 75.

    , , & Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations. J. Mol. Biol. 336, 313–318 (2004).

  76. 76.

    , , & Protein stability promotes evolvability. Proc. Natl Acad. Sci. USA 103, 5869–5874 (2006). A directed evolution experiment is presented here that shows how increasing the stability of a protein makes it more 'evolvable' by offsetting the destabilizing effects of function-switching mutations.

  77. 77.

    , , , & Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444, 929–932 (2006). This is a direct demonstration in a laboratory evolution experiment that epistasis can arise directly from stability thresholds.

  78. 78.

    , , , & An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability–activity trade-offs. Protein Eng. Des. Sel. 21, 19–27 (2008).

  79. 79.

    , , & How protein stability and new functions trade off. PLoS Comput. Biol. 4, e1000002 (2008).

  80. 80.

    & Signatures of protein biophysics in coding sequence evolution. Curr. Opin. Struct. Biol. 20, 385–389 (2010).

  81. 81.

    et al. Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments. J. Mol. Biol. 362, 966–978 (2006).

  82. 82.

    , & Structural and functional constraints in the evolution of protein families. Nature Rev. Mol. Cell Biol. 10, 709–720 (2009).

  83. 83.

    , & Stability and function: two constraints in the evolution of barstar and other proteins. Structure 2, 945–951 (1994).

  84. 84.

    , & Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Natl Acad. Sci. USA 104, 16152–16157 (2007).

  85. 85.

    Wonderful Life: The Burgess Shale and the Nature of History (W. W. Norton & Company, 1990).

  86. 86.

    , , , de & Contingency and determinism in replicated adaptive radiations of island lizards. Science 279, 2115–2118 (1998).

  87. 87.

    , & Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl Acad. Sci. USA 105, 7899–7906 (2008).

  88. 88.

    & Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol. 25, 1943–1953 (2008).

  89. 89.

    et al. Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl. Mol. Ecol. 18, 3992–4005 (2009).

  90. 90.

    et al. The genetic basis of resistance to anticoagulants in rodents. Genetics 170, 1839–1847 (2005).

  91. 91.

    Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res. 85, 210–231 (2010).

  92. 92.

    et al. Chloroquine transport via the malaria parasite's chloroquine resistance transporter. Science 325, 1680–1682 (2009).

  93. 93.

    & Evolution in action: plants resistant to herbicides. Annu. Rev. Plant Biol. 61, 317–347 (2010).

  94. 94.

    , , & Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111–114 (2006).

  95. 95.

    et al. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc. Natl Acad. Sci. USA 106, 12025–12030 (2009).

  96. 96.

    et al. Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. Mol. Biol. Evol. 27, 2682–2690 (2010).

  97. 97.

    , & Fitness trade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falciparum. PLoS ONE 6, e19636 (2011).

  98. 98.

    , & In vivo molecular evolution reveals biophysical origins of organismal fitness. Mol. Cell 22, 441–449 (2006). This is a laboratory demonstration of the capacity of biophysical constraints to cause the parallel accumulation of identical mutations in independent lineages.

  99. 99.

    et al. Experimental evolution of adenylate kinase reveals contrasting strategies toward protein thermostability. Biophys. J. 99, 887–896 (2010).

  100. 100.

    , & Compensatory mutations are repeatable and clustered within proteins. Proc. R. Soc. B 276, 1823–1827 (2009).

  101. 101.

    , & Know your enemy: understanding the role of PfCRT in drug resistance could lead to new antimalarial tactics. Cell. Mol. Life Sci. (2012).

  102. 102.

    & Retracing evolution of red fluorescence in GFP-like proteins from faviina corals. Mol. Biol. Evol. 27, 225–233 (2010).

  103. 103.

    et al. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nature Commun. 3, 1257 (2012).

  104. 104.

    et al. Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. AIDS 13, 2349–2359 (1999).

  105. 105.

    & Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res. Microbiol. 155, 360–369 (2004).

  106. 106.

    , , , & A minimal sequence code for switching protein structure and function. Proc. Natl Acad. Sci. USA 106, 21149–21154 (2009). This is an amazing demonstration of epistasis in protein folding, in which a mutation that is merely destabilizing in some genetic backgrounds drives a transition to an entirely different fold in another background.

  107. 107.

    , & Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature 480, 383–386 (2011).

  108. 108.

    & Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease. Biochemistry 32, 10131–10139 (1993).

  109. 109.

    & Long-range, small magnitude nonadditivity of mutational effects in proteins. Biochemistry 34, 3133–3139 (1995).

  110. 110.

    et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nature Chem. Biol. 4, 617–623 (2008).

  111. 111.

    , , & Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Struct. Mol. Biol. 10, 59–69 (2002).

  112. 112.

    et al. Surface sites for engineering allosteric control in proteins. Science 322, 438–442 (2008).

  113. 113.

    , & Tradeoffs and optimality in the evolution of gene regulation. Cell 146, 462–470 (2011).

  114. 114.

    , & Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328, 1272–1275 (2010). This analysis of historical viral evolution data unequivocally identifies permissive mutations that preceded function-switching mutations.

  115. 115.

    , & Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J. Mol. Biol. 395, 785–802 (2010).

  116. 116.

    et al. Rewiring the specificity of two-component signal transduction systems. Cell 133, 1043–1054 (2008).

  117. 117.

    , , & Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol. Direct 2, 17 (2007).

  118. 118.

    et al. The 'evolvability' of promiscuous protein functions. Nature Genet. 37, 73–76 (2005).

  119. 119.

    , & Structural bases for stability-function tradeoffs in antibiotic resistance. J. Mol. Biol. 396, 47–59 (2010).

  120. 120.

    , & Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3, 76 (2007).

  121. 121.

    , , & Relationship between protein stability and protein function. Proc. Natl Acad. Sci. USA 92, 452–456 (1995).

  122. 122.

    & Structural bases of stability-function tradeoffs in enzymes. J. Mol. Biol. 321, 285–296 (2002).

  123. 123.

    , , , & Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection. Mol. Syst. Biol. 6, 387 (2010).

  124. 124.

    et al. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 443, 45–49 (2006).

  125. 125.

    et al. The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. Antiviral Res. 55, 307–317 (2002).

  126. 126.

    , & Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2, e00631 (2013).

  127. 127.

    & Genetic analysis of staphylococcal nuclease: identification of three intragenic 'global' suppressors of nuclease-minus mutations. Genetics 110, 539–555 (1985).

  128. 128.

    & Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins 1, 81–89 (1986).

  129. 129.

    Neutralism and selectionism: a network-based reconciliation. Nature Rev. Genet. 9, 965–974 (2008). This is a thoughtful Review of how the vast neutral networks accessible to evolving biological molecules shape the mode and tempo of molecular evolution.

  130. 130.

    , & Goose lysozyme structure: an evolutionary link between hen and bacteriophage lysozymes? Nature 303, 828–831 (1983).

  131. 131.

    , , & Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous. Nature 347, 692–694 (1990).

  132. 132.

    , & One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321, 741–765 (2002).

  133. 133.

    , & Mycobacterium tuberculosis vitamin K epoxide reductase homologue supports vitamin K–dependent carboxylation in mammalian cells. Antioxid. Redox Signal. 16, 329–338 (2012).

  134. 134.

    et al. Complete mutagenesis of the HIV-1 protease. Nature 340, 397–400 (1989).

  135. 135.

    , & Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 29, 8033–8041 (1990).

  136. 136.

    et al. Cumulative site-directed charge-change replacements in bacteriophage T4 lysozyme suggest that long-range electrostatic interactions contribute little to protein stability. J. Mol. Biol. 221, 873–887 (1991).

  137. 137.

    , & Contributions of the ionizable amino acids to the stability of staphylococcal nuclease. Biochemistry 35, 6443–6449 (1996).

  138. 138.

    , & Protein tolerance to random amino acid change. Proc. Natl Acad. Sci. USA 101, 9205–9210 (2004).

  139. 139.

    et al. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature 463, 507–512 (2010).

  140. 140.

    et al. Inhibition of bacterial disulfide bond formation by the anticoagulant warfarin. Proc. Natl Acad. Sci. USA 107, 297–301 (2010).

  141. 141.

    et al. Patterns of point mutations associated with antiretroviral drug treatment failure in CRF01_AE (subtype E) infection differ from subtype B infection. J. Acquir. Immune Def. Syndr. 33, 335–342 (2003).

  142. 142.

    et al. The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways. J. Virol. 84, 9995–10003 (2010).

  143. 143.

    , , , & Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering. Proc. Natl Acad. Sci. USA 88, 6519–6522 (1991).

  144. 144.

    , , & Natural engineering principles of electron tunnelling in biological oxidation–reduction. Nature 402, 47–52 (1999).

  145. 145.

    , , , & Design principles of a bacterial signalling network. Nature 438, 504–507 (2005).

  146. 146.

    & Ädelroth, P. Design principles of proton-pumping haem-copper oxidases. Curr. Opin. Struct. Biol. 16, 465–472 (2006).

  147. 147.

    Evolution and tinkering. Science 196, 1161–1166 (1977).

  148. 148.

    et al. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307, 1928–1933 (2005).

  149. 149.

    , , , & Single amino acid. mutation contributes to adaptive beach mouse color pattern. Science 313, 101–104 (2006).

  150. 150.

    et al. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132, 783–793 (2008).

  151. 151.

    , , & The developmental role of agouti in color pattern evolution. Science 331, 1062–1065 (2011).

  152. 152.

    & Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. Nature 469, 411–414 (2011).

  153. 153.

    , , & Lineage-specific patterns of functional diversification in the α- and β-globin gene families of tetrapod vertebrates. Mol. Biol. Evol. 27, 1126–1138 (2010).

  154. 154.

    Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366–375 (2004).

  155. 155.

    , & Intense neutral drifts yield robust and evolvable consensus proteins. J. Mol. Biol. 379, 1029–1044 (2008).

  156. 156.

    , & A system for the continuous directed evolution of biomolecules. Nature 472, 499–503 (2011).

  157. 157.

    , , , & Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc. Natl Acad. Sci. USA 110, 9007–9012 (2013). An ultra-high-throughput directed evolution study is discussed here that reveals how epistasis can lead to stochastic and irreproducible outcomes in protein evolution.

  158. 158.

    , , & Fitness analyses of all possible point mutations for regions of genes in yeast. Nature Protoc. 7, 1382–1396 (2012).

  159. 159.

    , , , & The spatial architecture of protein function and adaptation. Nature (2012).

  160. 160.

    , , , & Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J. Mol. Biol. 425, 1363–1377 (2013).

  161. 161.

    , , & Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des. 2, 261–269 (1997).

  162. 162.

    et al. Structural basis of cyanobacterial photosystem II inhibition by the herbicide terbutryn. J. Biol. Chem. 286, 15964–15972 (2011).

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Acknowledgements

This work was supported by US National Institutes of Health Grants R01-GM081592, R01-GM104397 and F32-GM090650, as well as by the Howard Hughes Medical Institute. The authors thank A. Drummond, T. Dean and members of the Thornton laboratory for helpful comments.

Author information

Affiliations

  1. Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA.

    • Michael J. Harms
    •  & Joseph W. Thornton
  2. Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA.

    • Michael J. Harms
  3. Departments of Human Genetics and Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

    • Joseph W. Thornton

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph W. Thornton.

Glossary

Biochemistry

The study of the chemical and physical properties of biological molecules and how those properties determine the functions of each molecule. Defined this way, biochemistry also includes structural biology, biophysics and some areas of molecular and computational biology.

Molecular clock

The hypothesis that, over long timescales, mutations accumulate at a characteristic rate for each gene. For genes with clock-like evolution, the proportion of sequence differences between related genes can be used to estimate the time since they diverged.

Ancestral protein reconstruction

The use of statistical phylogenetic methods to infer ancestral protein sequences from large alignments of present-day proteins, followed by synthesis, expression and experimental characterization of the 'resurrected' ancestral proteins.

Homology

Similarity due to descent from a shared common ancestral form.

Protein stability

A thermodynamic description of the difference in free energy between the folded and unfolded states of a protein.

Parallel evolution

The repeated acquisition of the same phenotype on different lineages under similar forms of selection.

Epistasis

Dependency of the phenotypic effects of a mutation on the genetic state at other sites in the same or other loci.

Sequence signatures

Patterns in groups of protein or DNA sequences — such as the relative frequency of synonymous and nonsynonymous mutations or the degree of genetic diversity within and between populations — that are interpreted as reflecting specific evolutionary processes.

Directed evolution

A laboratory procedure for identifying genotypes with a desired property by iteratively introducing random mutations into a protein and using chemical or biological means to select for variants in which the property is improved.

Mutation–selection balance

Equilibrium between the accumulation of variation in a population due to ongoing mutation and the removal of variation due to purifying selection.

Genetic drift

Changes in the frequency across generations of genotypes in populations due to stochastic factors.

Neutral network

A set of protein sequences that are connected to each other by single amino acid replacements and have similar enough functions and physical properties that selection does not distinguish among them.

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