Evolution of protein-protein interaction network

Genome Dynamics

Volumn 3, Issue , 2007, Pages 13-29

  Makino, T ^a,b,c   Gojobori, T ^a,d  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b SHIZUOKA CANCER CENTER   (Japan)

^c TRINITY COLLEGE DUBLIN   (Ireland)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN;

GENE DUPLICATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN LIPID INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REVIEW; ANIMAL; DUPLICATE GENE; HUMAN; METABOLISM; PROTEIN BINDING;

ANIMALS; EVOLUTION, MOLECULAR; GENES, DUPLICATE; HUMANS; PROTEIN BINDING; PROTEINS;

EID: 58149200211     PISSN: 16609263     EISSN: None     Source Type: Book Series    
DOI: 10.1159/000107601     Document Type: Review

References (48)

1. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, et al: Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001;292:929-934.
2. Odorizzi G, Babst M, Emr SD: Phosphoinositide signaling and the regulation of membrane trafficking in yeast. Trends Biochem Sci 2000;25:229-235.
3. Wera S, Bergsma JC, Thevelein JM: Phosphoinositides in yeast: genetically tractable signalling. FEMS Yeast Res 2001;1:9-13.
4. Tsai MJ, O'Malley BW: Molecular mechanisms of action of steroid/thyroid receptor superfamily members. Annu Rev Biochem 1994;63:451-486.
5. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, et al: The protein-protein interaction map of Helicobacter pylori. Nature 2001;409:211-215.
6. Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al: Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005;433:531-537.
7. LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, et al: A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 2005;438:103-107.
8. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al: A map of the interactome network of the metazoan C. elegans. Science 2004;303:540-543.
9. Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, et al: Protein interaction mapping: a Drosophila case study. Genome Res 2005;15:376-384.
10. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al: A protein interaction map of Drosophila melanogaster. Science 2003;302:1727-1736.
11. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005;437:1173-1178.
12. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005;122:957-968.
13. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, et al: Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 2000;97:1143-1147.
14. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-627.
15. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002;415:141-147.
16. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002;415:180-183.
17. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006;440:637-643
18. Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002;20:991-997.
19. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004;22:78-85.
20. Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002;1:349-356.
21. Wagner A: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 2001;18:1283-1292.
22. Makino T, Suzuki Y, Gojobori T: Differential evolutionary rates of duplicated genes in protein interaction network. Gene 2006;385:57-63.
23. Ge H, Liu Z, Church GM, Vidal M: Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001;29:482-486.
24. Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000;18:1257-1261.
25. Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks. Proteomics 2004;4:928-942.
26. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al: Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004;430:88-93.
27. Makino T, Gojobori T: The evolutionary rate of a protein is influenced by features of the interacting partners. Mol Biol Evol 2006;23:784-789.
28. Hirsh AE, Fraser HB: Protein dispensability and rate of evolution. Nature 2001;411:1046-1049.
29. Jordan IK, Rogozin IB, Wolf YI, Koonin EV: Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002;12:962-968.
30. Pal C, Papp B, Hurst LD: Highly expressed genes in yeast evolve slowly. Genetics 2001;158:927-931.
31. Wilson AC, Carlson SS, White TJ: Biochemical evolution. Annu Rev Biochem 1977;46:573-639.
32. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science 2002;296:750-752.
33. Fraser HB, Wall DP, Hirsh AE: A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 2003;3:11.
34. Wagner A: Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 2002;19:1760-1768.
35. Ohno S: Evolution by Gene Duplication. Springer, Berlin, 1970.
36. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J: Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999;151:1531-1545.
37. Li WH, Gojobori T: Rapid evolution of goat and sheep globin genes following gene duplication. Mol Biol Evol 1983;1:94-108.
38. Baudot A, Jacq B, Brun C: A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol 2004;5:R76.
39. Kellis M, Birren BW, Lander ES: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004;428:617-624.
40. Wolfe KH, Shields DC: Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997;387:708-713.
41. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, et al: MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002;30:31-34.
42. Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, et al: RSC, an essential, abundant chromatin-remodeling complex. Cell 1996;87:1249-1260.
43. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003;100:12123-12128.
44. Davis TN, Urdea MS, Masiarz FR, Thorner J: Isolation of the yeast calmodulin gene: calmodulin is an essential protein. Cell 1986;47:423-431.
45. Hahn MW, Kern AD: Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005;22:803-806.
46. Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 1998;393:440-442.
47. Wuchty S, Oltvai ZN, Barabasi AL: Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 2003;35:176-179.
48. Teichmann SA: The constraints protein-protein interactions place on sequence divergence. J Mol Biol 2002;324:399-407.