Evolution in protein interaction networks: Co-evolution, rewiring and the role of duplication

Biochemical Society Transactions

Volumn 37, Issue 4, 2009, Pages 768-771

  Robertson, David L ^a   Lovell, Simon C ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Co evolution; Duplication; Protein interaction network; Protein protein interaction; Rewiring

Indexed keywords

AMINO ACID SEQUENCE; CONFERENCE PAPER; GENE DUPLICATION; GENE MUTATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; CHEMISTRY; GENETICS; METABOLISM; PROTEIN ANALYSIS; REVIEW;

PROTEIN;

EVOLUTION, MOLECULAR; GENE DUPLICATION; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 70349314254     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370768     Document Type: Conference Paper

References (47)

1. Graur, D. and Wen-Hsiung, L. (2000) Fundamentals of Molecular Evolution, Sinauer Associates Inc., Sunderland, MA, U.S.A.
2. Hartl, D.L. and Clark, A.G. (2007) Principles of Population Genetics, Sinauer Associates Inc., Sunderland, MA, U.S.A.
3. Nooren, I.M. and Thornton, J.M. (2003) Diversity of protein-protein interactions. EMBO J. 22, 3486-3492
4. Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W. (1999) From molecular to modular cell biology. Nature 402, C47-C52
5. Mintseris, J. and Weng, Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 102, 10930-10935
6. Pollock, D.D., Taylor, W.R. and Goldman, N. (1999) Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 287, 187-198
7. Dutheil, J., Pupko, T., Jean-Marie, A. and Galtier, N. (2005) A model-based approach for detecting coevolving positions in a molecule. Mol. Biol. Evol. 22, 1919-1928
8. Wang, Z.O. and Pollock, D.D. (2007) Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J. Mol. Evol. 65, 485-495
9. Socolich, M., Lockless, S.W., Russ, W.P., Lee, H., Gardner, K.H. and Ranganathan, R. (2005) Evolutionary information for specifying a protein fold. Nature 437, 512-518
10. Gloor, G.B., Martin, L.C., Wahl, L.M. and Dunn, S.D. (2005) Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 44, 7156-7165
11. Moyle, W.R., Campbell, R.K., Myers, R.V., Bernard, M.P., Han, Y. and Wang, X. (1994) Co-evolution of ligand-receptor pairs. Nature 368, 251-255
12. Atchley, W.R., Wollenberg, K.R., Fitch, W.M., Terhalle, W. and Dress, A.W. (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol. 17, 164-178
13. Chao, J.A., Patskovsky, Y., Almo, S.C. and Singer, R.H. (2008) Structural basis for the coevolution of a viral RNA-protein complex. Nat. Struct. Mol. Biol. 15, 103-105
14. Yeang, C.H. and Haussler, D. (2007) Detecting coevolution in and among protein domains. PLoS Comput. Biol. 3, e211
15. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
16. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
17. Kim, W.K., Krumpelman, C. and Marcotte, E.M. (2008) Inferring mouse gene functions from genomic-scale data using a combined functional network/ classification strategy. Genome Biol. 9, (Suppl. 1), S5
18. Sharan, R. and Ideker, T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechnol. 24, 427-433
19. Pinney, J.W., Amoutzias, G.D., Rattray, M. and Robertson, D.L. (2007) Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc. Natl. Acad. Sci. U.S.A. 104, 20449-20453
20. Hakes, L., Pinney, J.W., Lovell, S.C., Oliver, S.G. and Robertson, D.L. (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol. 8, R209
21. Hakes, L., Lovell, S.C., Oliver, S.G. and Robertson, D.L. (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc. Natl. Acad. Sci. U.S.A. 104, 7999-8004
22. Wagner, A. (2002) Asymmetric functional divergence of duplicate genes in yeast. Mol. Biol. Evol. 19, 1760-1768
23. Baudot, A., Jacq, B. and Brun, C. (2004) A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol. 5, R76
24. Conant, G.C. and Wolfe, K.H. (2006) Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol. 4, e109
25. Guan, Y., Dunham, M.J. and Troyanskaya, O.G. (2007) Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175, 933-943
26. Conant, G.C. and Wagner, A. (2003) Asymmetric sequence divergence of duplicate genes. Genome Res. 13, 2052-2058
27. Kellis, M., Birren, B.W. and Lander, E.S. (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617-624
28. Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14, 609-614
29. Valencia, A. and Pazos, F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12, 368-373
30. Pal, C., Papp, B. and Lercher, M.J. (2006) An integrated view of protein evolution. Nat. Rev. Genet. 7, 337-348
31. Agrafioti, I., Swire, J., Abbott, J., Huntley, D., Butcher, S. and Stumpf, M.P. (2005) Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol. Biol. 5, 23
32. Drummond, D.A., Raval, A. and Wilke, C.O. (2006) A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23, 327-337
33. Chen, Y. and Dokholyan, N.V. (2006) The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet. 22, 416-419
34. Juan, D., Pazos, F. and Valencia, A. (2008) High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc. Natl. Acad. Sci. U.S.A. 105, 934-939
35. DeLano, W.L. (2002) Unraveling hot spots in binding interfaces: progress and challenges. Curr. Opin. Struct. Biol. 12, 14-20
36. Maddison, W.P. (1997) Gene trees in species trees. Syst. Biol. 46, 523-536
37. Pazos, F., Ranea, J.A., Juan, D. and Sternberg, M.J. (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J. Mol. Biol. 352, 1002-1015
38. Pazos, F. and Valencia, A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J. 27, 2648-2655
39. Kann, M.G., Jothi, R., Cherukuri, P.F. and Przytycka, T.M. (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins 67, 811-820
40. Williams, S.G. and Lovell, S.C. (2009) The effect of sequence evolution on protein structural divergence. Mol. Biol. Evol. 26, 1055-1065
41. Orengo, C.A. and Thornton, J.M. (2005) Protein families and their evolution: a structural perspective. Annu. Rev. Biochem. 74, 867-900
42. Conant, G.C. and Wolfe, K.H. (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 9, 938-950
43. Stumpf, M.P., Kelly, W.P., Thorne, T. and Wiuf, C. (2007) Evolution at the system level: the natural history of protein interaction networks. Trends Ecol. Evol. 22, 366-373
44. Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. and Teichmann, S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283-291
45. Papp, B., Pal, C. and Hurst, L.D. (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424, 194-197
46. Hakes, L., Pinney, J.W., Robertson, D.L. and Lovell, S.C. (2008) Protein-protein interaction networks and biology: what's the connection? Nat. Biotechnol. 26, 69-72
47. Hou, Z., Bernstein, D.A., Fox, C.A. and Keck, J.L. (2005) Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc. Natl. Acad. Sci. U.S.A. 102, 8489-8494