Evolutionary and physiological importance of hub proteins

PLoS Computational Biology

Volumn 2, Issue 7, 2006, Pages 0748-0756

  Batada, Nizar N ^a   Hurst, Laurence D ^b   Tyers, Mike ^a,c  

^a MOUNT SINAI HOSPITAL   (Canada)

^b University of Bath   (United Kingdom)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; PHYSIOLOGY; PROTEINS;

BINDING-SITES; DECAY RATE; EVOLUTIONARY RATE; HIGH QUALITY; HUB PROTEINS; HYBRID DATUM; LOCAL CONNECTIVITY; PROTEIN EVOLUTION; PROTEIN INTERACTION; YEAST TWO HYBRID;

YEAST;

SACCHAROMYCES CEREVISIAE PROTEIN; MESSENGER RNA;

ARTICLE; BINDING SITE; CONTROLLED STUDY; NONHUMAN; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; YEAST; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; EVOLUTION; GENE EXPRESSION REGULATION; GENETIC DATABASE; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN ANALYSIS; STATISTICAL MODEL;

SACCHAROMYCES CEREVISIAE;

BIOLOGICAL EVOLUTION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; MODELS, STATISTICAL; PROTEIN INTERACTION MAPPING; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33746631391     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020088     Document Type: Article

References (46)

1. Han JDJ, Dupuy D, Bertin N, Cusick ME, Vidal M (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol 23: 839-844.
2. Mintseris J, Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102: 10930-10935.
3. Fraser HB, Wall DP, Hirsh AE (2003) A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 3: 11.
4. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein-interaction network. Science 296: 750-752.
5. Saeed R, Deane CM (2006) Protein-protein interactions, evolutionary rate, abundance, and age. BMC Bioinformatics 7: 128.
6. Makino T, Gojobori T (2006) The evolutionary rate of a protein is influenced by features of the interacting partners. Mol Biol Evol 23: 784-789.
7. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
8. Chen Y, Xu D (2005) Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics 21: 575-581.
9. Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22: 803-806.
10. Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA (2005) An exponential core in the heart of the yeast protein-interaction network. Mol Biol Evol 22: 421-425.
11. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale datasets of protein-protein interactions. Nature 417: 399-403.
12. Bader GD, Hogue CW (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20: 991-997.
13. Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon G, et al. (2006) Comprehensive curation and analysis of global interaction networks of Saccharomyces cerevisiae. J Biol. 5: 11.
14. Coulomb S, Bauer M, Bernard D, Marsolier-Kergoat MC (2005) Gene essentiality and the topology of protein-interaction networks. Proc R Soc Lond Ser Biol Sci 272: 1721-1725.
15. Bloom J, Adami C (2003) Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions datasets. BMC Evol Biol 3: 21.
16. Jordan IK, Wolf YI, Koonin EV (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.
17. Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
18. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH (2005) Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 102: 14338-14343.
19. Bloom JD, Adami C (2004) Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response. BMC Evol Biol 4: 14.
20. Drummond DA, Raval A, Wilke CO (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23: 327-337.
21. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
22. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
23. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
24. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98: 4569-4574.
25. Papp B, Pal C, Hurst LD (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664.
26. Gibbons JD (1993) Nonparametric measures of association. Newbury Park (California): Sage. 104 p.
27. Sharp PM, Li WH (1987) The codon adaptation index - a measure of directional synonymous codon usage bias and its potential applications. Nucl Acid Res 15: 1281-1295.
28. Fares MA, Byrne KP, Wolfe KH (2005) Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol Biol Evol 23: 245-254.
29. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
30. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
31. Teichmann SA, Murzin AG, Chothia C (2001) Determination of protein function, evolution, and interactions by structural genomics. Curr Opin Struct Biol 11: 354-363.
32. Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A (2005) PRISM: Protein interactions by structural matching. Nucl Acid Res 33: W331-W336.
33. Aytuna AS, Gursoy A, Keskin O (2005) Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21: 2850-2855.
34. Pawson T, Scott JD (2005) Protein phosphorylation in signaling - 50 years and counting. Trends Biochem Sci 30: 286-290.
35. Willems AR, Schwab M, Tyers M (2004) A hitchhiker's guide to the cullin ubiquitin ligases: SCF and its kin. Biochim Biophys Acta 1695: 133-170.
36. Kirschner M, Gerhart J (1998) Evolvability. Proc Natl Acad Sci U S A 95: 8420-8427.
37. Johnson ES, Gonda DK, Varshavsky A (1990) cis-trans recognition and subunit-specific degradation of short-lived proteins. Nature 346: 287-291.
38. Verma R, McDonald H, Yates JR, Deshaies RJ (2001) Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields active S phase cyclin-Cdk. Mol Cell 8: 439-448.
39. Hirsh AE, Fraser HB, Wall DP (2005) Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22: 174-177.
40. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741.
41. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A 99: 5860-5865.
42. Arava Y, Wang YL, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 100: 3889-3894.
43. Obenauer JC, Cantley LC, Yaffe MB (2003) Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucl Acid Res 31: 3635-3641.
44. Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, et al. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucl Acid Res 30: 69-72.
45. Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31: 400-404.
46. Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, et al. (2005) Mechanisms of haplo-insufficiency revealed by genome-wide profiling in yeast. Genetics 169: 1915-1925.