Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

Genome Biology

Volumn 2, Issue 12, 2001, Pages

  Jordan, I King ^a   Kondrashov, Fyodor A ^a   Rogozin, Igor B ^a   Tatusov, Roman L ^a   Wolf, Yuri I ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Chlamydia Trachomatis; Diversify Protein; Functional Diversification; Orthologous Protein; Relative Rate Test

Indexed keywords

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; PROTEIN;

ANIMAL; ARTICLE; BACTERIAL GENOME; CHEMISTRY; EUKARYOTIC CELL; FORECASTING; GENETICS; GENOME; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MOUSE; MUTATION; PHYLOGENY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; RAT; SEQUENCE ANALYSIS;

ANIMALS; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FORECASTING; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, HUMAN; HUMANS; MICE; MUTATION; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RATS; SEQUENCE ANALYSIS, PROTEIN;

EID: 0035748444     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2001-2-12-research0053     Document Type: Article

References (43)

1. Kimura M, Ohta T: On some principles governing molecular evolution. Proc Natl Acad Sci USA. 1974, 71: 2848-2852. DOI: 10.1073/pnas.71.7.2848
2. Kimura M: The Neutral Theory of Molecular Evolution, New York: Cambridge University Press;. 1983 DOI: 10.1017/CBO9780511623486
3. Hughes AL: Adaptive Evolution of Genes and Genomes, Oxford: Oxford University Press;. 1999
4. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science. 1997, 278: 631-637. 10.1126/science.278.5338.631. DOI: 10.1126/science.278.5338.631
5. Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28: 33-36. 10.1093/nar/28.1.33. DOI: 10.1093/nar/28.1.33
6. Messier W, Stewart CB: Episodic adaptive evolution of primate lysozymes. Nature. 1997, 385: 151-154. 10.1038/385151a0. DOI: 10.1038/385151a0
7. Zhang J, Rosenberg HF, Nei M: Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA. 1998, 95: 3708-3713. 10.1073/pnas.95.7.3708. DOI: 10.1073/pnas.95.7.3708
8. Goodman M, Moore GW, Matsuda G: Darwinian evolution in the genealogy of haemoglobin. Nature. 1975, 253: 603-608. DOI: 10.1038/253603a0
9. Gonzalez DS, Jordan IK: The alpha-mannosidases: phylogeny and adaptive diversification. Mol Biol Evol. 2000, 17: 292-300. DOI: 10.1093/oxfordjournals.molbev.a026309
10. Wolfe KH, Sharp PM: Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol. 1993, 37: 441-456. DOI: 10.1007/BF00178874
11. Endo T, Ikeo K, Gojobori T: Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 1996, 13: 685-690. DOI: 10.1093/oxfordjournals.molbev.a025629
12. Sharp PM: In search of molecular Darwinism. Nature. 1997, 385: 111-112. 10.1038/385111a0. DOI: 10.1038/385111a0
13. Yang Z, Bielawski JP: Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000, 15: 496-503. 10.1016/S0169-5347(00)01994-7. DOI: 10.1016/S0169-5347(00)01994-7
14. Graur D: Amino acid composition and the evolutionary rates of protein-coding genes. J Mol Evol. 1985, 22: 53-62. DOI: 10.1007/BF02105805
15. Mouchiroud D, Gautier C, Bernardi G: Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J Mol Evol. 1995, 40: 107-113. DOI: 10.1007/BF00166602
16. Ohta T, Ina Y: Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences. J Mol Evol. 1995, 41: 717-720.
17. Makalowski W, Boguski MS: Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA. 1998, 95: 9407-9412. 10.1073/pnas.95.16.9407. DOI: 10.1073/pnas.95.16.9407
18. Averof M, Rokas A, Wolfe KH, Sharp PM: Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science. 2000, 287: 1283-1286. 10.1126/science.287.5456.1283. DOI: 10.1126/science.287.5456.1283
19. Williams EJ, Hurst LD: The proteins of linked genes evolve at similar rates. Nature. 2000, 407: 900-903. 10.1038/35038066. DOI: 10.1038/35038066
20. Miyata T, Hayashida H: Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons. Proc Natl Acad Sci USA. 1981, 78: 5739-5743. DOI: 10.1073/pnas.78.9.5739
21. Lipman DJ, Wilbur WJ: Interaction of silent and replacement changes in eukaryotic coding sequences. J Mol Evol. 1984, 21: 161-167. DOI: 10.1007/BF02100090
22. Ticher A, Graur D: Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J Mol Evol. 1989, 28: 286-298. DOI: 10.1007/BF02103424
23. Akashi H: Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 1994, 136: 927-935.
24. Grishin NV, Wolf YI, Koonin EV: From complete genomes to measures of substitution rate variability within and between proteins. Genome Res. 2000, 10: 991-1000. 10.1101/gr.10.7.991. DOI: 10.1101/gr.10.7.991
25. Li WH: Molecular Evolution, Sunderland, MA: Sinauer Associates;. 1997
26. National Center for Biotechnology Information Bacterial Genomes. [ftp://ncbi.nlm.nih.gov/genomes/Bacteria/]
27. Utah Genome Center: P. furiosus ORF sequences. [http://www.genome.utah.edu/pfu599.pep]
28. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389. DOI: 10.1093/nar/25.17.3389
29. Batch Entrez. [http://www.ncbi.nlm.nih.gov:80/Entrez/batch.html]
30. NCBI BLAST download. [ftp://ncbi.nlm.nih.gov/blast/executables/]
31. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. DOI: 10.1093/nar/22.22.4673
32. Ota T, Nei M: Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J Mol Evol. 1994, 38: 469-482. DOI: 10.1007/BF00175885
33. Grishin NV: Estimation of the number of amino-acid substitutions per site when the substitution rate varies among sites. J Mol Evol. 1995, 41: 675-679. DOI: 10.1007/BF00175826
34. Li WH: Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol. 1993, 36: 96-99. DOI: 10.1007/BF02407308
35. Pamilo P, Bianchi NO: Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol. 1993, 10: 271-281.
36. Schultz J, Copley RR, Doerks T, Ponting CP, Bork P: SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 2000, 28: 231-234. 10.1093/nar/28.1.231. DOI: 10.1093/nar/28.1.231
37. SMART. [http://smart.embl-heidelberg.de/]
38. CD-search. [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi]
39. Entrez protein. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein]
40. COGs: Phylogenetic classification of proteins encoded in complete genomes database. [http://www.ncbi.nlm.nih.gov/COG/]
41. Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol. 1997, 5: 333-339.
42. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406-425.
43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25: 4876-4882. 10.1093/nar/25.24.4876. DOI: 10.1093/nar/25.24.4876