Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae

Molecular Biology and Evolution

Volumn 23, Issue 5, 2006, Pages 1068-1075

  Kim, Seong Ho ^a   Yi, Soojin V ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Functional divergence; Gene duplication; Saccharomyces cerevisiae; Sequence divergence; Whole genome duplication

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CORRELATION ANALYSIS; GENE DUPLICATION; GENE FUNCTION; GENOME ANALYSIS; NATURAL SELECTION; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION;

AMINO ACIDS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENETICS; GENOME, FUNGAL; GENOMICS; KLUYVEROMYCES; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; SPECIES SPECIFICITY; VARIATION (GENETICS);

SACCHAROMYCES CEREVISIAE;

EID: 33646588998     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj115     Document Type: Article

References (48)

1. Adams, K. L., and J. F. Wendel. 2005. Novel patterns of gene expression in polyploid plants. Trends Genet. 10:539-543.
2. Batagelj, V., and A. Mrvar. 2003. Pajek - analysis and visualization of large networks. Pp. 77-103 in M. Junger and P. Mutzel, eds. Graph Drawing Software, Springer, Berlin.
3. Bloom, J. D., and C. Adami. 2003. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interaction data sets. BMC Evol. Biol. 3:21.
4. Breitkreutz, B. J., C. Stark, and M. Tyers. 2003. The GRID: the general repository for interaction datasets. Genome Biol. 4:R23.
5. Casella, G., and R. L. Berger. 1990. Statistical inference. Duxbury Press, Belmont, Calif.
6. Conant, G. C., and A. Wagner. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res. 13:2052-2058.
7. Davis, J. C., and D. A. Petrov. 2004. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2:e55.
8. Drummond, D. A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnod. 2005. Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338-14343.
9. Drummond, D. A., A. Raval, and C. O. Wilke. 2006. A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23:327-337.
10. Duret, L., and D. Mouchiroud. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17:68-70.
11. Enright, A. J., S. Van Dongen, and C. A. Ouzounis. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584.
12. Fraser, H. B., A. E. Hirsh, L. M. Steinmetz, C. Scharfe, and M. W. Feldman. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752.
13. Ghaemmaghami, S., W.-K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, and J. S. Weissman. 2003. Global analysis of protein expression in yeast. Nature 425:737-741.
14. Gibbons, J. D., and S. Chakraborti. 2003. Nonparametric statistical inference. 4th edition. Marcel Dekker, New York.
15. Gu, X., Z. Zhang, and W. Huang. 2005. Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. USA 102:707-712.
16. Gu, Z., D. Nicolae, H. H.-S. Lu, and W.-H. Li. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:609-613.
17. Gu, Z., L. M. Steinemann, X. Gu, C. Scharfe, R. W. Davis, and W.-H. Li. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
18. Hahn, M. W., G. C. Conant, and A. Wagner. 2004. Molecular evolution in large genetic networks: does connectivity equal constraint? J. Mol. Evol. 58:203-211.
19. Hahn, M. W., and A. D. Kern. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22:803-806.
20. Ito, T., T. Chiba, T. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98:4569-4574.
21. Johnson, R. A., and D. W. Wichern. 2002. Applied multivariate statistical analysis. 5th edition. Prentice Hall, Upper Saddle River, N.J.
22. Jordan, I. K., Y. I. Wolf, and E. V. Koonin. 2003. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3:1.
23. _. 2004. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol. Biol. 4:22.
24. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
25. Krylov, D. M., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13:2229-2235.
26. Lemos, B., B. R. Bettencourt, C. D. Meiklejohn, and D. L. Hartl. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol. Biol. Evol. 22:1345-1354.
27. Li, L., C. J. Stoeckert Jr, and D. S. Roos. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
28. Li, W.-H., J. Yang, and X. Gu. 2005. Expression divergence between duplicate genes. Trends Genet. 21:602-607.
29. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
30. Makova, K. D., and W.-H. Li. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13:1638-1645.
31. Nuzhdin, S. V., M. L. Wayne, K. L. Harmon, and L. M. McIntyre. 2004. Common pattern of evolution of gene expression leveland protein sequence in Drosophila. Mol. Biol. Evol. 21:1308-1317.
32. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Berlin.
33. Pál, C., B. Papp, and L. D. Hurst. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
34. Sokal, R. R., and F. J. Rohlf. 1995. Biometry: the principles and practice of statistics in biological research. 3rd edition. W. H. Freeman and Company, New York.
35. Steinmetz, L. M., C. Scharfe, A. M. Deutschbauer et al. (11 co-authors). 2002. Systematic screen for human disease genes in yeast. Nat. Genet. 31:400-404.
36. Subramanian, S., and S. Kumar. 2004. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381.
37. Uetz, P., L. Giot, G. Cagney et al. (20 co-authors). 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
38. Wagner, A. 2000. Robustness against mutations in genetic networks of yeast. Nat. Genet. 24:355-361.
39. _. 2001. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18:1283-1292.
40. _. 2002. Asymmetric functional divergence of duplicate genes in yeast. Mol. Biol. Evol. 19:1760-1768.
41. Wasserman, S., and K. Faust. 1994. Social network analysis. Cambridge University Press, Cambridge.
42. Whittaker, J. 1996. Graphical models in applied multivariate statistics. John Wiley and Sons, New York.
43. Wolfe, K. H., and D. C. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
44. Yang, J., Z. Gu, and W.-H. Li. 2003. Rate of protein evolution versus fitness effect of gene deletion. Mol. Biol. Evol. 20:772-774.
45. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
46. Yang, Z., and R. Nielsen. 2000. Estimating synonymous and non-synonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
47. Zhang, J. G., and X. He. 2005. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol. Biol. Evol. 22:1147-1155.
48. Zhang, P., Z. Gu, and W.-H. Li. 2003. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol. 4:R56.