Coevolution, modularity and human disease

Current Opinion in Genetics and Development

Volumn 16, Issue 6, 2006, Pages 637-644

  Fraser, Hunter B ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; COEVOLUTION; GENE EXPRESSION; GENE SEQUENCE; GENERAL ASPECTS OF DISEASE; GENOMICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC DISEASES, INBORN; GENOMICS; HUMANS; MODELS, GENETIC; PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 33750932315     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2006.09.001     Document Type: Review

References (49)

1. Thompson J.N. The coevolutionary process (1994), University Chicago Press
2. Dover G.A., and Flavell R.B. Molecular coevolution: DNA divergence and the maintenance of function. Cell 38 (1984) 623-624
3. Altschuh D., Lesk A.M., Bloomer A.C., and Klug A. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 193 (1987) 693-707
4. Haag E.S., Wang S., and Kimble J. Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Curr Biol 12 (2002) 2035-2041
5. Gildor T., Shemer R., Atir-Lande A., and Kornitzer D. Coevolution of cyclin Pcl5 and its substrate Gcn4. Eukaryot Cell 4 (2005) 310-318
6. Shaw P.J., Wratten N.S., McGregor A.P., and Dover G.A. Coevolution in Bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera. Evol Dev 4 (2002) 265-277
7. Gasch A.P., Moses A.M., Chiang D.Y., Fraser H.B., Berardini M., and Eisen M.B. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2 (2004) e398
8. Pazos F., and Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47 (2002) 219-227
9. Fraser H.B., Hirsh A.E., Wall D.P., and Eisen M.B. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 101 (2004) 9033-9038. This work was the first demonstration of gene expression coevolution, and also made the prediction that the GAL genes of yeast would show coordinated degeneration in some species.
10. Kim W.K., Bolser D.M., and Park J.H. Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics 20 (2004) 1138-1150
11. Lithwick G., and Margalit H. Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res 33 (2005) 1051-1057
12. Shulman A.I., Larson C., Mangelsdorf D.J., and Ranganathan R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116 (2004) 417-429
13. Socolich M., Lockless S.W., Russ W.P., Lee H., Gardner K.H., and Ranganathan R. Evolutionary information for specifying a protein fold. Nature 437 (2005) 512-518
14. Russ W.P., Lowery D.M., Mishra P., Yaffe M.B., and Ranganathan R. Natural-like function in artificial WW domains. Nature 437 (2005) 579-583
15. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
16. von Dassow G., and Munro E. Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo. J Exp Zool 285 (1999) 307-325
17. Keller L.C., Romijn E.P., Zamora I., Yates III J.R., and Marshall W.F. Proteomic analysis of isolated Chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Curr Biol 15 (2005) 1090-1098
18. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636
19. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
20. Ihmels J., Bergmann S., and Barkai N. Defining transcription modules using large-scale gene expression data. Bioinformatics 20 (2004) 1993-2003
21. Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., and Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34 (2003) 166-176
22. Pan X., Ye P., Yuan D.S., Wang X., Bader J.S., and Boeke J.D. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124 (2006) 1069-1081
23. Schuldiner M., Collins S.R., Thompson N.J., Denic V., Bhamidipati A., Punna T., Ihmels J., Andrews B., Boone C., Greenblatt J.F., et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123 (2005) 507-519
24. Han J.D., Bertin N., Hao T., Goldberg D.S., Berriz G.F., Zhang L.V., Dupuy D., Walhout A.J., Cusick M.E., Roth F.P., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430 (2004) 88-93. A good example of how data integration can lead to new insights about the modularity of protein networks.
25. Prinz S., Avila-Campillo I., Aldridge C., Srinivasan A., Dimitrov K., Siegel A.F., and Galitski T. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res 14 (2004) 380-390
26. Tanay A., Sharan R., Kupiec M., and Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci USA 101 (2004) 2981-2986
27. •].
28. Slonim N, Elemento O, Tavazoie S: Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol. 2006, 2:2006.0005.
29. von Mering C., Zdobnov E.M., Tsoka S., Ciccarelli F.D., Pereira-Leal J.B., Ouzounis C.A., and Bork P. Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA 100 (2003) 15428-15433
30. Snel B., and Huynen M.A. Quantifying modularity in the evolution of biomolecular systems. Genome Res 14 (2004) 391-397
31. Hartwell L.H., Hopfield J.J., Leibler S., and Murray A.W. From molecular to modular cell biology. Nature 402 (1999) C47-C52
32. Davidson E.H., and Erwin D.H. Gene regulatory networks and the evolution of animal body plans. Science 311 (2006) 796-800
33. Schlosser G. Modularity and the units of evolution. Theory Biosci 121 (2002) 1-80
34. Fraser H.B. Modularity and evolutionary constraint on proteins. Nat Genet 37 (2005) 351-352
35. Hertveldt K., Dechassa M.L., Robben J., and Volckaert G. Identification of Gal80p-interacting proteins by Saccharomyces cerevisiae whole genome phage display. Gene 307 (2003) 141-149
36. •].
37. •].
38. •].
39. •] combine phylogenetic profiling with other data types to identify cilia-related genes responsible for cases of Bardet-Biedl Syndrome.
40. Lim J., Hao T., Shaw C., Patel A.J., Szabo G., Rual J.F., Fisk C.J., Li N., Smolyar A., Hill D.E., et al. A protein-protein interaction network for human inherited ataxias and disorders of purkinje cell degeneration. Cell 125 (2006) 801-814
41. Krauthammer M., Kaufmann C.A., Gilliam T.C., and Rzhetsky A. Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci USA 101 (2004) 15148-15153
42. Kelley R., and Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23 (2005) 561-566
43. Zhong W., and Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 311 (2006) 1481-1484
44. Hirschhorn J.N., and Daly M.J. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6 (2005) 95-108
45. Marchini J., Donnelly P., and Cardon L.R. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37 (2005) 413-417
46. Storey J.D., Akey J.M., and Kruglyak L. Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3 (2005) e267
47. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., and Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13 (2003) 2498-2504
48. Chen Y., and Dokholyan N.V. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 22 (2006) 416-419. This is the first study to show that genes within modules have coordinated evolutionary rates - and not just correlated phylogenetic profiles.
49. Oti M., Snel B., Huynen M.A., and Brunner H.G. Predicting disease genes using protein-protein interactions. J Med Genet 43 (2006) 691-698. The authors are the first to combine protein interaction data with genetic mapping data to predict genes underlying diverse human diseases.