Heterotachy and functional shift in protein evolution

IUBMB Life

Volumn 55, Issue 4-5, 2003, Pages 257-265

  Philippe, Hervé ^a   Casane, Didier ^b   Gribaldo, Simonetta ^c   Lopez, Philippe ^d   Meunier, Julien ^e  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b CNRS   (France)

^c UNIVERSITÉ PARIS SACLAY   (France)

^d SORBONNE UNIVERSITÉ   (France)

^e UNIVERSITÉ LYON 1   (France)

Author keywords

Covarian; Evolutionary rate; Hemoglobin; Heterotachy; Protein function; Tertiary structures

Indexed keywords

ALPHA MANNOSIDASE; CASPASE; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE; LEPTIN; MUTANT PROTEIN; MYC PROTEIN; PROSTAGLANDIN SYNTHASE; PROTEIN; PROTEIN TYROSINE KINASE; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; DRUG DESIGN; GENE DUPLICATION; GENETIC VARIABILITY; GENOMICS; IN VITRO STUDY; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MULTIGENE FAMILY; MUTAGENESIS; NONHUMAN; PREDICTION; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

EID: 0037815065     PISSN: 15216543     EISSN: None     Source Type: Journal    
DOI: 10.1080/1521654031000123330     Document Type: Review

References (98)

1. Nixon, A. E., and Firestine, S. M. (2000) Rational and 'irrational' design of proteins and their use in biotechnology. IUBMB Life 49, 181-187.
2. Dahiyat, B. I., and Mayo, S. L. (1997) De novo protein design: fully automated sequence selection. Science 278, 82-87.
3. Nixon, A. E., Ostermeier, M., and Benkovic, S. J. (1998) Hybrid enzymes: manipulating enzyme design. Trends Biotechnol. 16, 258-264.
4. Getzoff, E. D., Cabelli, D. E., Fisher, C. L., Parge, H. E., Viezzoli, M. S., Banci, L., and Hallewell, R. A. (1992) Faster superoxide dismutase mutants designed by enhancing electrostatic guidance. Nature 358, 347-351.
5. Chen, R., Greer, A., and Dean, A. M. (1995) A highly active decarboxylating dehydrogenase with rationally inverted coenzyme specificity. Proc. Natl. Acad. Sci. U.S.A. 92, 11666-11670.
6. Lockridge, O., Blong, R. M., Masson, P., Froment, M. T., Millard, C. B., and Broomfield, C. A. (1997) A single amino acid substitution, Gly117His, confers phosphotriesterase (organophosphorus acid anhydride hydrolase) activity on human butyrylcholinesterase. Biochemistry 36, 786-795.
7. Spector, S., Wang, M., Carp, S. A., Robblee, J., Hendsch, Z. S., Fairman, R., Tidor, B., and Raleigh, D. P. (2000) Rational modification of protein stability by the mutation of charged surface residues. Biochemistry 39, 872-879.
8. Tobin, M. B., Gustafsson, C., and Huisman, G. W. (2000) Directed evolution: the 'rational' basis for 'irrational' design. Curr. Opin. Struct. Biol. 10, 421-427.
9. Malakauskas, S. M., and Mayo, S. L. (1998) Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5, 470-475.
10. Vasserot, A. P., Dickinson, C. D., Tang, Y., Huse, W. D., Manchester, K. S., and Watkins, J. D. (2003) Optimization of protein therapeutics by directed evolution. Drug Discov. Today 8, 118-126.
11. Waldo, G. S. (2003) Genetic screens and directed evolution for protein solubility. Curr. Opin. Chem. Biol. 7, 33-38.
12. Arnold, F. H. (2001) Evolutionary protein design. Academic Press, New York.
13. Schober, A., Thuerk, M., and Eigen, M. (1993) Optimization by hierarchical mutant production. Biol. Cybern. 69, 493-501.
14. Arnold, F. H. (1998) Design by directed evolution. Acc. Chem. Res. 31, 125-131.
15. Miyazaki, K., and Arnold, F. H. (1999) Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J. Mol. Evol. 49, 716-720.
16. Zaccolo, M., and Gherardi, E. (1999) The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase. J. Mol. Biol. 285, 775-783.
17. Black, M. E., Newcomb, T. G., Wilson, H. M., and Loeb, L. A. (1996) Creation of drug-specific herpes simplex virus type 1 thymidine kinase mutants for gene therapy. Proc. Natl. Acad. Sci. U.S.A. 93, 3525-3529.
18. Stemmer, W. P. (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391.
19. Burt, A. (2000) Perspective: sex, recombination, and the efficacy of selection - was Weismann right? Evolution Int. J. Org. Evolution 54, 337-351.
20. Barton, N. H., and Charlesworth, B. (1998) Why sex and recombination? Science 281, 1986-1990.
21. Crameri, A., Raillard, S. A., Bermudez, E., and Stemmer, W. P. (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291.
22. Moore, J. C., Jin, H. M., Kuchner, O., and Arnold, F. H. (1997) Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J. Mol. Biol. 272, 336-347.
23. Liu, D. R., Magliery, T. J., Pastrnak, M., and Schultz, P. G. (1997) Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo. Proc. Natl. Acad. Sci. U.S.A. 94, 10092-10097.
24. Chen, R. (2001) Enzyme engineering: rational redesign versus directed evolution. Trends Biotechnol. 19, 13-14.
25. Oue, S., Okamoto, A., Yano, T., and Kagamiyama, H. (1999) Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J. Biol. Chem. 274, 2344-2349.
26. Philippe, H., and Lopez, P. (2001) On the conservation of protein sequences in evolution. Trends in Biochemical Sciences 26, 414-416.
27. Honig, B., and Nicholls, A. (1995) Classical electrostatics in biology and chemistry. Science 268, 1144-1149.
28. Voigt, C. A., Martinez, C., Wang, Z. G., Mayo, S. L., and Arnold, F. H. (2002) Protein building blocks preserved by recombination. Nat. Struct. Biol. 9, 553-558.
29. Voigt, C. A., Mayo, S. L., Arnold, F. H., and Wang, Z. G. (2001) Computational method to reduce the search space for directed protein evolution. Proc. Natl. Acad. Sci. U.S.A. 98, 3778-3783.
30. Pokala, N., and Handel, T. M. (2001) Review: protein design-where we were, where we are, where we're going. J. Struct. Biol. 134, 269-281.
31. Lecompte, O., Thompson, J. D., Plewniak, F., Thierry, J., and Poch, O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 270, 17-30.
32. Heringa, J. (2000) Computational methods for protein secondary structure prediction using multiple sequence alignments. Curr. Protein. Pept. Sci. 1, 273-301.
33. Hofacker, I. L., Fekete, M., and Stadler, P. F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059-1066.
34. Lehmann, M., Loch, C., Middendorf, A., Studer, D., Lassen, S. F., Pasamontes, L., van Loon, A. P., and Wyss, M. (2002) The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15, 403-411.
35. Li, W.-H. (1997) Molecular evolution. Sinauer Associates, Sunderland, Massachusetts.
36. Kimura, M. (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
37. Ota, T. (1973) Slightly deleterious mutant substitutions in evolution. Nature 246, 96-98.
38. del Sol Mesa, A., Pazos, F., and Valencia, A. (2003) Automatic methods for predicting functionally important residues. J. Mol. Biol. 326, 1289-1302.
39. Casari, G., Sander, C., and Valencia, A. (1995) A method to predict functional residues in proteins. Nat. Struct. Biol. 2, 171-178.
40. Pupko, T., Bell, R. E., Mayrose, I., Glaser, F., and Ben-Tal, N. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71-S77.
41. Simon, A. L., Stone, E. A., and Sidow, A. (2002) Inference of functional regions in proteins by quantification of evolutionary constraints. Proc. Natl. Acad. Sci. U.S.A. 99, 2912-2917.
42. Madabushi, S., Yao, H., Marsh, M., Kristensen, D. M., Philippi, A., Sowa, M. E., and Lichtarge, O. (2002) Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol. 316, 139-154.
43. Lichtarge, O., Bourne, H. R., and Cohen, F. E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257, 342-358.
44. Livingstone, C. D., and Barton, G. J. (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci. 9, 745-756.
45. Sumiyama, K., Kim, C. B., and Ruddle, F. H. (2001) An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71, 260-262.
46. Bickel, P. J., Kechris, K. J., Spector, P. C., Wedemayer, G. J., and Glazer, A. N. (2002) Finding important sites in protein sequences. Proc. Natl. Acad. Sci. U.S.A. 99, 14764-14771.
47. Bauer, B., Mirey, G., Vetter, I. R., Garcia-Ranea, J. A., Valencia, A., Wittinghofer, A., Camonis, J. H., and Cool, R. H. (1999) Effector recognition by the small GTP-binding proteins Ras and Ral. J. Biol. Chem. 274, 17763-17770.
48. Yang, Z. (2002) Inference of selection from multiple species alignments. Curr. Opin. Genet. Dev. 12, 688-694.
49. Sharp, P. M. (1997) In search of molecular darwinism. Nature 385, 111-112.
50. Gaucher, E., A., Gu, X., Miyamoto, M. M., and Benner, S. A. (2002) Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem. Sci. 27, 315-321.
51. Ohno, S., Wolf, U., and Atkin, N. B. (1968) Evolution from fish to mammals by gene duplication. Hereditas 59, 169-187.
52. Gaucher, E. A., Miyamoto, M. M., and Benner, S. A. (2001) Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc. Natl. Acad. Sci. U.S.A. 98, 548-552.
53. Gaucher, E. A., Das, U. K., Miyamoto, M. M., and Benner, S. A. (2002) The Crystal Structure of eEF1A Refines the Functional Predictions of an Evolutionary Analysis of Rate Changes Among Elongation Factors. Mol. Biol. Evol. 19, 569-573.
54. Gu, X. (1999) Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16, 1664-1674.
55. Gu, X. (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18, 453-464.
56. Knudsen, B., and Miyamoto, M. M. (2001) A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. U.S.A. 98, 14512-14517.
57. Naylor, G. J., and Gerstein, M. (2000) Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. J. Mol. Evol. 51, 223-233.
58. Susko, E., Inagaki, Y., Field, C., Holder, M. E., and Roger, A. J. (2002) Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol. Biol. Evol. 19, 1514-1523.
59. Lopez, P., Casane, D., and Philippe, H. (2002) Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19, 1-7.
60. Lopez, P., Forterre, P., and Philippe, H. (1999) The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49, 496-508.
61. Pupko, T., and Galtier, N. (2002) A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc. R. Soc. Lond. B. Biol. Sci. 269, 1313-1316.
62. Blouin, C., Boucher, Y., and Roger, A. J. (2003) Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31, 790-797.
63. Gu, J., Wang, Y., and Gu, X. (2002) Evolutionary analysis for functional divergence of jak protein kinase domains and tissue-specific genes. J. Mol. Evol. 54, 725-733.
64. Siltberg, J., and Liberles, D. A. (2002) A simple covarion-based approach to analyse nucleotide substitution rates. J. Evol. Biol. 15, 588-594.
65. Jordan, I. K., Bishop, G. R., and Gonzalez, D. S. (2001) Sequence and structural aspects of functional diversification in class I alphamannosidase evolution. Bioinformatics 17, 965-976.
66. Wang, Y., and Gu, X. (2001) Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics 158, 1311-1320.
67. Inagaki, Y., Blouin, C., Doolittle, W. F., and Roger, A. J. (2002) Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity. Nucleic Acid Res. 30, 532-544.
68. Gribaldo, S., Casane, D., Lopez, P., and Philippe, H. (in press) Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol. Biol. Evol.
69. Fitch, W. M., and Markowitz, E. (1970) An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4, 579-593.
70. Fitch, W. M. (1971) The nonidentity of invariable positions in the cytochromes c of different species. Biochem. Genet. 5, 231-241.
71. Philippe, H., Lecointre, G., Lê. H. L. V., and Le Guyader, H. (1996) A critical study of homoplasy in molecular data with the use of a morphologically based cladogram. Mol. Biol. Evol. 13, 1174-1186.
72. Fitch, W. M. (1971) Rate of change of concomitantly variable codons. J. Mol. Evol. 1, 84-96.
73. Go, M., and Miyazawa, S. (1978) Volume and polarity changes accompanied by amino acid substitutions in protein evolution. Int. J. Pept. Protein Res. 12, 237-241.
74. Zuckerkandl, E. (1976) Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. J. Mol. Evol. 7, 167-183.
75. Schlusselberg, J., and Debouverie, D. (1975) Study of double and triple simultaneous substitutions of amino acids in cytochromes C. J. Mol. Evol. 5, 187-197.
76. Milkman, R. (1974) How many covarions per species? Biochem. Genet. 11, 181-182.
77. Karon, J. M. (1979) The covarion model for the evolution of proteins: parameter estimates and comparison with Holmquist, Cantor, and Jukes' stochastic model. J. Mol. Evol. 12, 197-218.
78. Uzzell, T., and Corbin, K. W. (1971) Fitting discrete probability distributions to evolutionary events. Science 172, 1089-1096.
79. Fitch, W. M. (1973) Is the fixation of observable mutations distributed randomly among the three nucleotide positions of the codon? J. Mol. Evol. 2, 123-136.
80. Fitch, W. M. (1976) The molecular evolution of cytochrome c in eukaryotes. J. Mol. Evol. 8, 13-40.
81. Fitch, W. M., and Ayala, F. J. (1994) The superoxide dismutase molecular clock revisited. Proc. Natl. Acad. Sci. U.S.A. 91, 6802-6807.
82. Lockhart, P. J., Larkum, A. W., Steel, M., Waddell, P. J., and Penny, D. (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. U.S.A. 93, 1930-1934.
83. Tuffley, C., and Steel, M. (1998) Modeling the covarion hypothesis of nucleotide substitution. Mol. Biosci. 147, 63-91.
84. Galtier, N. (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18, 866-873.
85. Penny, D., McComish, B. J., Charleston, M. A., and Hendy, M. D. (2001) Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53, 711-723.
86. Huelsenbeck, J. P. (2002) Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19, 698-707.
87. Philippe, H., and Germot, A. (2000) Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17, 830-834.
88. Misof, B., Anderson, C. L., Buckley, T. R., Erpenbeck, D., Rickert, A., and Misof, K. (2002) An empirical analysis of mt 16S rRNA covarion-like evolution in insects: site-specific rate variation is clustered and frequently detected. J. Mol. Evol. 55, 460-469.
89. Lockhart, P. J., Huson, D., Maier, U., Fraunholz, M. J., Van De Peer, Y., Barbrook, A. C., Howe, C. J., and Steel, M. A. (2000) How molecules evolve in Eubacteria. Mol. Biol. Evol. 17, 835-838.
90. Germot, A., and Philippe, H. (1999) Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family. J. Eukaryot. Microbiol. 46, 116-124.
91. Miyamoto, M. M., and Fitch, W. M. (1995) Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12, 503-513.
92. Moreira, D., Le Guyader, H., and Philippe, H. (1999) Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes. Mol. Biol. Evol. 16, 234-245.
93. Lockhart, P. J., Steel, M. A., Barbrook, A. C., Huson, D., Charleston, M. A., and Howe, C. J. (1998) A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15, 1183-1188.
94. Sueoka, N. (1999) Two aspects of DNA base composition: G + C content and translation-coupled deviation from intra-strand rule of A = T and G = C. J. Mol. Evol. 49, 49-62.
95. McInerney, J. O. (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. U.S.A. 95, 10698-10703.
96. Bastolla, U., Porto, M., Eduardo Roman, M. H., and Vendruscolo, M. H. (2003) Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. J. Mol. Evol. 56, 243-254.
97. Perutz, M. F. (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228, 726-739.
98. Seoighe, C., Johnston, C. R., and Shields, D. C. (2003) Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Molecular Biology and Evolution 20, 484-490.