Molecular evolution in the yeast transcriptionial regulation network

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 302, Issue 4, 2004, Pages 392-411

  Evangelisti, Annette M ^a   Wagner, Andreas ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 4344624948     PISSN: 0022104X     EISSN: None     Source Type: Journal    
DOI: 10.1002/jez.b.20027     Document Type: Article

References (63)

1. Albert R, Jeong H, Barabasi A. 2000. Error and attack tolerance of complex networks. Nature 406:378-382.
2. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. 1997. Gapped Blast and Psi - Blast: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
3. Ashbuner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, Harris M, Hill D, Issel-Tarver L, Kasarskis A, Lewis S, Matese J, Richardson J, Ringwald M, Rubin G, Sherlock G. 2000. Gene ontology: Tool for the unification of biology. Nat Genet 25:25-29.
4. Bhan A, Galas D, Dewey T. 2002. A duplication growth model of gene expression networks. Bioinformatics 18:1486-1493.
5. Briscoe A. 2001. Functional diversification of lepidopteran opsins following gene duplication. Mol Cell Biol 18:2270-2279.
6. Bussemaker H, Li H, Siggia E. 2001. Regulatory element detection using correlation with expression. Nat Genet 27:167-171.
7. Chaput M, Claes V, Portetelle D, Cludts I, Cravador A, Aburny A, Gras H, Tartar A. 1988. The neurotrophic factor neuroleukin is 90 percent homologous with phosphohexose isomerase. Nature 332:454-455.
8. Chung F, Lu L, Dewey T, Galas D. 2003. Duplication models for biological networks. J Comput Biol 10:677-687.
9. Conant G, Wagner A. 2002. GenomeHistory: A software tool and its application to fully sequenced genomes. Nucleic Acids Res 30:3378-3386.
10. Conant G, Wagner A. 2003. Convergent evolution in gene circuits. Nat Genet 34:264-266.
11. Conant G, Wagner A. 2004. Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. P Roy Soc Ser B-Bio 271:89-96.
12. Costanzo M, Hogan J, Cusick M, Davis B, Fancher A, Hodges P, Kondu P, Lengieza C, Lew-Smith J, Lingner C, Roberg-Perez K, Tillberg M, Brooks J, Garrels J. 2000. The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28:73-76.
13. Faik P, Walker J, Redmill A, Morgan M. 1988. Mouse glucose-6-phosphate isomerase and neuroleukin have identical 3' sequences. Nature 332:455-456.
14. Featherstone D, Broadie K. 2002. Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network. BioEssays 24:267-274.
15. Force A, Lynch M, Pickett F, Amores A, Yan Y, Postlethwait J. 1999a. Preservation of duplicate genes by complementary degenerative mutations. Genetics 151:1531-1545.
16. Force A, Lynch M, Postlethwait J. 1999b. Preservation of duplicate genes by subfunctionalization. Am Zool 39:78A.
17. Fraser H, Hirsh A, Steinmetz L, Scharfe C, Feldman M. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752.
18. Fraser H, Wall D, Hirsh A. 2003. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 3:11.
19. Furukawa T, Yoshimura A, Sumizawa T, Haraguchi M, Akiyama S, Fukui K, Ishizawa M, Yamada Y. 1992. Angiogenic factor. Nature 356:668.
20. Gilchrist M, Salter L, Wagner A. 2004. A statistical framework for combining and interpreting proteomic data sets. Bioinformatics (in press).
21. Gonzalez-Gaitan M, Rothe M, Wimmer E, Taubert H, Jackle H. 1994. Redundant functions of the genes knirps and knirps-related for the establishment of anterior Drosophila head structures. Proc Natl Acad Sci USA 91:8567-8571.
22. Gu Z, Nicolae D, Lu H, Li W. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 18:609-613.
23. Gu Z, Steinmetz L, Gu X, Scharfe C, Davis R, Li W. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
24. Guelzim N, Bottani S, Bourgine P, Kepes F. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31(1):60-63.
25. Hahn M, Conant G, Wagner A. 2004. Molecular evolution in large genetic networks: Does connectivity equal constraint? J Mol Biol 58:203-211.
26. Haraguchi M, Miyadera K, Uemura K, Sumizawa T, Furukawa T, Yamada K, Akiyama S, Yamada Y. 1994. Angiogenic activity of enzymes. Nature 368:198.
27. Hughes A. 1994. The evolution of functionally novel proteins after gene duplication. P Roy Soc Ser B-Bio 256:119-124.
28. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574.
29. Jeffery C. 1999. Moonlighting proteins. Trends Biochem Sci 24:8-11.
30. Jeong H, Mason S, Barabasi A, Oltvai Z. 2001. Lethality and centrality in protein networks. Nature 411:41-42.
31. Jordan I, Wolf Y, Koonin E. 2003a. Correction: no simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors evolve slowly. BMC Evol Biol 3:5.
32. Jordan I, Wolf Y, Koonin E. 2003b. 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 3:5.
33. Kellis M, Patterson N, Endrizzi M, Birren B, Lander E. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
34. Kennedy M, Mendemueller L, Blondin G, Beinert H. 1992. Purification and characterization of cytosolic aconitase from beef-liver and its relationship to the iron-responsive element binding-protein. Proc Natl Acad Sci USA 89:11730-11734.
35. Knop M, Siegers K, Pereira G, Zachariae W, Winsor B, Nasmyth K, Schiebel E. 1999. Epitope tagging of yeast genes using a PCR-based strategy: More tags and improved practical routines. Yeast 15:963-972.
36. Lee T, Rinaldi N, Robert F, Odom D, Bar-Joseph Z, Gerber G, Hannett N, Harbison C, Thompson C, Simon I, Zeitlinger J, Jennings E, Murray H, Gordon D, Ren B, Wyrick J, Tagne J, Volkert T, Fraenkel E, Gifford D, Young R. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
37. Li W-H. 1997. Molecular Evolution. Massachusetts: Sinauer.
38. Lynch M, Force A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
39. Maslov S, Sneppen K, Eriksen K, Yan K-K. 2004. Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks. BMC Evol Biol 4:9.
40. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. 2002. Network motifs: Simple building blocks of complex networks. Science 298:824-827.
41. Nowak MA, Boerlijst MC, Cooke J, Maynard-Smith J. 1997. Evolution of genetic redundancy. Nature 388:167-171.
42. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 28:1838-1847.
43. Prince V, Pickett F. 2002. Splitting pairs: The diverging fates of duplicated genes. Nat Rev Genet 3:827-837.
44. Ptashne M. 1988. How eukaryotic transcriptional activators work. Nature 335:683-689.
45. Ptashne M, Gann A. 2002. Genes and Signals. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
46. Ren B, Robert F, Wyrick J, Aparicio O, Jennings E, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert T, Wilson C, Bell S, Young R. 2000. Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
47. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J. 2004. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 32:D303-D306.
48. Shen-Orr S, Milo R, Mangan S, Alon U. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64-68.
49. Smith T, Waterman M. 1981. Identification of common molecular subsequences. J Mol Biol 147:195-197.
50. Sokal R, Rohlf F. 1981. Biometry. New York: Freeman.
51. Sole R, Pastor-Satorras R, Smith ED, Kepler T. 2002. A model of large-scale proteome evolution. Adv Complex Syst 5:43-54.
52. Steinmetz L, Scharfe C, Deutschbauer A, Mokranjac D, Herman Z, Jones T, Chu A, Giaever G, Prokisch H, Oefner P, Davis R. 2002. Systematic screen for human disease genes in yeast. Nat Genet 31:400-404.
53. Stone J, Wray G. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18:1764-1770.
54. Uetz P, Giot L, Cagney G, Mansfield T, Judson R, Knight J, Lockshon D, Narayan V, Srinivasan M, Pochart P, QureshiEmili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg J. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
55. van Noort V, Snel B, Huynen M. 2004. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. Embo reports (in press).
56. von Mering C, Krause R, Snel B, Cornell M, Oliver S, Fields S, Bork P. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403.
57. Wagner A. 1999. Redundant gene functions and natural selection. J Evol Biol 12:1-16.
58. Wagner A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate. Proc Natl Acad Sci USA 97(12):6579-6584.
59. Wagner A. 2001. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18:1283-1292.
60. Wagner A. 2003. How the global structure of protein interaction networks evolves. Proc Roy Soc Ser B-Bio 270:457-466.
61. Wang Y, Schnegelsberg P, Dausman J, Jaenisch R. 1996. Functional redundancy of the muscle-specific transcription factors Myf5 and myogenin. Nature 379:823-825.
62. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43.
63. Zhang J, Rosenberg H, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA 95:3708-3713.