Genetic constraints on protein evolution

Critical Reviews in Biochemistry and Molecular Biology

Volumn 42, Issue 5, 2007, Pages 313-326

  Camps, Manel ^a   Herman, Asael ^b   Loh, Ern ^b   Loeb, Lawrence A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Adaptation; Enzyme evolution; Epistasis; Evolvability; Positive selection

Indexed keywords

AZTREONAM; BETA LACTAMASE;

EVOLUTIONARY ADAPTATION; GENE MUTATION; GENETIC EPISTASIS; HUMAN; MISSENSE MUTATION; MOLECULAR EVOLUTION; NEUTRAL GENE THEORY; PHYLOGENY; PLEIOTROPY; PREVALENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; SUPPRESSOR GENE; THERMODYNAMICS; WILD TYPE;

ANIMALS; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; HUMANS; MODELS, BIOLOGICAL; MUTATION; PHYLOGENY; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 35148875679     PISSN: 10409238     EISSN: 15497798     Source Type: Journal    
DOI: 10.1080/10409230701597642     Document Type: Review

References (81)

1. Akanuma, S., Yamagishi, A., Tanaka, N., and Oshima, T. 1998. Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution. Protein Sci 7:698-705.
2. Anderson, J.B., Sirjusingh, C., Parsons, A.B., Boone, C., Wickens, C., Cowen, L.E., and Kohn, L.M. 2003. Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae. Genetics 163:1287-1298.
3. Arjan, J.A., Visser, M., Zeyl, C.W., Gerrish, P.J., Blanchard, J.L., and Lenski, R.E. 1999. Diminishing returns from mutation supply rate in asexual populations. Science 283:404-406.
4. Axe, D.D., Foster, N.W., and Fersht, A.R. 1998. A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease. Biochemistry 37:7157-7166.
5. Barlow, M. and Hall, B.G. 2003. Experimental prediction of the natural evolution of antibiotic resistance Genetics 163:1237-1241.
6. Baroni, T.E., Wang, T., Qian, H., Dearth, L.R., Truong, L.N., Zeng, J., Denes, A.E., Chen, S.W., and Brachmann, R.K. 2004. A global suppressor motif for p53 cancer mutants. Proc Natl Acad Sci USA 101:4930-4935.
7. Bazykin, G.A., Kondrashov, F.A., Ogurtsov, A.Y., Sunyaev, S., and Kondrashov, A.S. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429:558-562.
8. Beltrao, P., and Serrano, L. 2007. Specificity and Evolvability in Eukaryotic Protein Interaction Networks. PLoS Comput Biol 3:e25.
9. Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N., and Tawfik, D. S. 2006. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444:929-932.
10. Besenmatter, W., Kast, P., and Hilvert, D. 2007. Relative tolerance of mesostable and thermostable protein homologs to extensive mutation. Proteins 66:500-506.
11. Bjedov, I., Tenaillon, O., Gerard, B., Souza, V., Denamur, E., Radman, M., Taddei, F., and Matic, I. 2003. Stress-induced mutagenesis in bacteria. Science 300:1404-1409.
12. Blazquez, J., Negri, M.C., Morosini, M.I., Gomez-Gomez, J.M., and Baquero, F. 1998. A237T as a modulating mutation in naturally occurring extended-spectrum TEM-type beta-lactamases. Antimicrob Agents Chemother 42:1042-1044.
13. Blazquez, J., Morosini, M.I., Negri, M.C., and Baquero, F. 2000. Selection of naturally occurring extended-spectrum TEM beta-lactamase variants by fluctuating beta-lactam pressure. Antimicrob Agents Chemother 44:2182-2184.
14. Bloom, J.D., Labthavikul, S.T., Otey, C.R., and Arnold, F.H. 2006. Protein stability promotes evolvability. Proc Natl Acad Sci USA 103:5869-5874.
15. Borman, A.M., Paulous, S., and Clavel, F. 1996. Resistance of human immunodeficiency virus type 1 to protease inhibitors: selection of resistance mutations in the presence and absence of the drug. J Gen Virol 77( Pt 3):419-426.
16. Camps, M., Naukkarinen, J., Johnson, B.P., and Loeb, L.A. 2003. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proc Natl Acad Sci USA 100:9727-9732.
17. Camps, M. and Loeb, L.A. 2005. Critical role of R-loops in processing replication blocks. Front Biosci 10:689-698.
18. Choi, S.S., Li, W. and Lahn, B.T. 2005. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat Genet 37:1367-1371.
19. Counago, R., Chen, S., and Shamoo, Y. 2006. In vivo molecular evolution reveals biophysical origins of organismal fitness. Mol Cell 22:441-449.
20. DePristo, M.A., Weinreich, D.M., and Hartl, D.L. 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6:678-687.
21. Ellis, R.J. 2007. Protein misassembly: macromolecular crowding and molecular chaperones. Adv Exp Med Biol 594:1-13.
22. Fay, J.C., Wyckoff, G.J., and Wu, C.I. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415:1024-1026.
23. Forrer, P., Binz, H.K., Stumpp, M.T., and Pluckthun, A. 2004. Consensus design of repeat proteins. Chembiochem 5:183-189.
24. Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C., and Feldman, M.W. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752.
25. Gillespie, S.H. 2001. Antibiotic resistance in the absence of selective pressure. Int J Antimicrob Agents 17:171-176.
26. Goldman, N., Thorne, J.L., and Jones, D.T. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
27. Greenman, C., Stephens, P., Smith, R., and other authors 2007. Patterns of somatic mutation in human cancer genomes. Nature 446:153-158.
28. Guo, H.H., Choe, J., and Loeb, L.A. 2004. Protein tolerance to random amino acid change. Proc Natl Acad Sci U S A 101:9205-9210.
29. Hahn, M.W., Conant, G.C., and Wagner, A. 2004. Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 58:203-211.
30. Hall, B.G. 2004. Predicting the evolution of antibiotic resistance genes. Nat Rev Microbiol 2:430-435.
31. Herring, C.D., Raghunathan, A., Honisch, C., et al. 2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38:1406-1412.
32. Huang, W. and Palzkill, T. 1997. A natural polymorphism in beta-lactamase is a global suppressor. Proc Natl Acad Sci USA 94:8801-8806.
33. Hurst, L.D. and Smith, N.G. 1999. Do essential genes evolve slowly? Curr Biol 9:747-750.
34. James, L.C. and Tawfik, D.S. 2003. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem Sci 28:361-368.
35. Jordan, I.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S., and Sunyaev, S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature 433:633-638.
36. Khersonsky, O., Roodveldt, C., and Tawfik, D.S. 2006. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr Opin Chem Biol 10:498-508.
37. Kim, P.M., Lu, L.J., Xia, Y., and Gerstein, M.B. 2006. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938-1941.
38. Kondrashov, A.S., Sunyaev, S., and Kondrashov, F.A. 2002. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA 99:14878-14883.
39. Kulathinal, R.J., Bettencourt, B.R., and Hartl, D. L. 2004. Compensated deleterious mutations in insect genomes. Science 306:1553-1554.
40. Lenski, R.E., Barrick, J.E., and Ofria, C. 2006. Balancing robustness and evolvability. PLoS Biol 4:e428.
41. Levin, B.R., Perrot, V., and Walker, N. 2000. Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics 154:985-997.
42. Loeb, D.D., Swanstrom, R., Everitt, L., Manchester, M., Stamper, S.E., and Hutchison, C.A., 3rd 1989. Complete mutagenesis of the HIV-1 protease. Nature 340:397-400.
43. Loh, E., Choe, J., and Loeb, L.A. 2007. Highly tolerated amino acid substitutions increase the fidelity of E. coli DNA polymerase I. J Biol Chem 282:12201-12209.
44. Maisnier-Patin, S., Berg, O.G., Liljas, L., and Andersson, D.I. 2002. Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol 46:355-366.
45. Mao, E.F., Lane, L., Lee, J., and Miller, J.H. 1997. Proliferation of mutators in A cell population. J Bacteriol 179:417-422.
46. Markiewicz, P., Kleina, L.G., Cruz, C., Ehret, S., and Miller, J.H. 1994. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J Mol Biol 240:421-433.
47. Merlo, L.M., Pepper, J.W., Reid, B.J., and Maley, C.C. 2006. Cancer as an evolutionary and ecological process. Nat Rev Cancer 6:924-935.
48. Nagaev, I., Bjorkman, J., Andersson, D.I, and Hughes, D. 2001. Biological cost and compensatory evolution in fusidic acid-resistant Staphylococcus aureus. Mol Microbiol 40:433-439.
49. Neduva, V. and Russell, R.B. 2005. Linear motifs: evolutionary interaction switches. FEBS Lett 579:3342-3345.
50. Ng, P.C. and Henikoff, S. 2006. Predicting the effects of amino Acid substitutions on protein function. Annu Rev Genomics Hum Genet 7:61-80.
51. O'Loughlin, T.L., Patrick, W.M., and Matsumura, I. 2006. Natural history as a predictor of protein evolvability. Protein Eng Des Sel 19:439-442.
52. Orencia, M.C., Yoon, J.S., Ness, J.E., Stemmer, W.P., and Stevens, R.C. 2001. Predicting the emergence of antibiotic resistance by directed evolution and structural analysis. Nat Struct Biol 8:238-242.
53. Orr, H.A. 2005. The genetic theory of adaptation: a brief history. Nat Rev Genet 6:119-127.
54. Pagel, M., Venditti, C., and Meade, A. 2006. Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314:119-121.
55. Pakula, A.A., Young, V.B., and Sauer, R.T. 1986. Bacteriophage lambda cro mutations: effects on activity and intracellular degradation. Proc Natl Acad Sci USA 83:8829-8833.
56. Parisi, G. and Echave, J. 2005. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene 345:45-53.
57. Poon, A. and Chao, L. 2005. The rate of compensatory mutation in the DNA bacteriophage phiX174. Genetics 170:989-999.
58. Poon, A., Davis, B.H., and Chao, L. 2005. The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood. Genetics 170:1323-1332.
59. Queitsch, C., Sangster, T.A., and Lindquist, S. 2002. Hsp90 as a capacitor of phenotypic variation. Nature 417:618-624.
60. Rennell, D., Bouvier, S.E., Hardy, L.W., and Poteete, A.R. 1991. Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol 222:67-88.
61. Rutherford, S.L. and Lindquist, S. 1998. Hsp90 as a capacitor for morphological evolution. Nature 396:336-342.
62. Salathe, M., Ackermann, M., and Bonhoeffer, S. 2006. The effect of multi-functionality on the rate of evolution in yeast. Mol Biol Evol 23:721-722.
63. Schrag, S.J., Perrot, V., and Levin, B.R. 1997. Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc Biol Sci 264:1287-1291.
64. Sjoblom, T., Jones, S., Wood, L.D., and other authors 2006. The consensus coding sequences of human breast and colorectal cancers. Science 314:268-274.
65. Smith, N.G. and Eyre-Walker, A. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024.
66. Sniegowski, P.D. and Murphy, H.A. 2006. Evolvability. Curr Biol 16:R831-834.
67. Stone, E.A. and Sidow, A. 2005. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 15:978-986.
68. Suckow, J., Markiewicz, P., Kleina, L.G., Miller, J., Kisters-Woike, B., and Muller-Hill, B. 1996. Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J Mol Biol 261:509-523.
69. Thomas, R.K., Baker, A.C., Debiasi, R.M., and other authors 2007. High-throughput oncogene mutation profiling in human cancer. Nat Genet 39:347-351.
70. Wall, D.P., Hirsh, A.E., Fraser, H.B., Kumm, J., Giaever, G., Eisen, M.B., and Feldman, M.W. 2005. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A 102:5483-5488.
71. Wang, T.W., Zhu, H., Ma, X.Y., Zhang, T., Ma, Y.S., and Wei, D.Z. 2006. Mutant library construction in directed molecular evolution: casting a wider net. Mol Biotechnol 34:55-68.
72. Wang, X., Minasov, G., and Shoichet, B.K. 2002. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320:85-95.
73. Watanabe, K., Ohkuri, T., Yokobori, S., and Yamagishi, A. 2006. Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree. J Mol Biol 355:664-674.
74. Weinreich, D.M. and Chao, L. 2005. Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution Int J Org Evolution 59:1175-1182.
75. Weinreich, D.M., Delaney, N.F., Depristo, M.A., and Hartl, D.L. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114.
76. Wichman, H.A., Badgett, M.R., Scott, L.A., Boulianne, C.M., and Bull, J.J. 1999. Different trajectories of parallel evolution during viral adaptation. Science 285:422-424.
77. Wichman, H.A., Scott, L.A., Yarber, C.D., and Bull, J.J. 2000. Experimental evolution recapitulates natural evolution. Philos Trans R Soc Lond B Biol Sci 355:1677-1684.
78. Wichman, H.A., Millstein, J., and Bull, J.J. 2005. Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170:19-31.
79. Wintrode, P.L. and Arnold, F.H. 2000. Temperature adaptation of enzymes: lessons from laboratory evolution. Adv Protein Chem 55:161-225.
80. Woods, R., Schneider, D., Winkworth, C.L., Riley, M.A., and Lenski, R.E. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A 103:9107-9112.
81. Yue, P. and Moult, J. 2006. Identification and analysis of deleterious human SNPs. J Mol Biol 356:1263-1274.