Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication

Journal of Proteomics

Volumn 81, Issue , 2013, Pages 112-125

  Gagnon Arsenault, Isabelle ^a   Marois Blanchet, François Christophe ^a   Rochette, Samuel ^a   Diss, Guillaume ^a   Dubé, Alexandre K ^a   Landry, Christian R ^a  

^a UNIVERSITÉ LAVAL   (Canada)

Author keywords

Evolution; Gene duplication; Network rewiring; Protein interaction network; Transcriptional regulation

Indexed keywords

MESSENGER RNA;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; EXON; GENE DUPLICATION; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENETIC PARAMETERS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; REGULATORY SEQUENCE; TRANSCRIPTION REGULATION; TRANSCRIPTIONAL DIVERGENCE;

DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION, FUNGAL; MUTATION; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84877819731     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.09.038     Document Type: Article

References (45)

1. Vidal M., Cusick M.E., Barabasi A.L. Interactome networks and human disease. Cell 2011, 144:986-998.
2. Scott J.D., Pawson T. Cell signaling in space and time: where proteins come together and when they're apart. Science 2009, 326:1220-1224.
3. Zhang J.Z. Evolution by gene duplication: an update. Trends Ecol Evol 2003, 18:292-298.
4. Pereira-Leal J.B., Levy E.D., Kamp C., Teichmann S.A. Evolution of protein complexes by duplication of homomeric interactions. Genome Biol 2007, 8:R51.
5. Amoutzias G.D., Van de Peer Y. Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks. Evolutionary genomics and systems biology 2010, 413-429. G. Caetano-Anollés (Ed.).
6. Guan Y., Dunham M.J., Troyanskaya O.G. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 2007, 175:933-943.
7. Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map. Science 2011, 333:601-607.
8. Wagner A. Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 2002, 19:1760-1768.
9. Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 2001, 18:1283-1292.
10. Freschi L., Courcelles M., Thibault P., Michnick S.W., Landry C.R. Phosphorylation network rewiring by gene duplication. Mol Syst Biol 2011, 7.
11. Bloom J., Cross F.R. Multiple levels of cyclin specificity in cell-cycle control. Nat Rev Mol Cell Biol 2007, 8:149-160.
12. Archambault V., Buchler N.E., Wilmes G.M., Jacobson M.D., Cross F.R. Two-faced cyclins with eyes on the targets. Cell Cycle 2005, 4:125-130.
13. Miller M.E., Cross F.R. Distinct subcellular localization patterns contribute to functional specificity of the Cln2 and Cln3 cyclins of Saccharomyces cerevisiae. Mol Cell Biol 2000, 20:542-555.
14. Miller M.E., Cross F.R. Cyclin specificity: how many wheels do you need on a unicycle?. J Cell Sci 2001, 114:1811-1820.
15. Vogel C., de Sousa Abreu R., Ko D., Le S.Y., Shapiro B.A., Burns S.C., et al. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 2010, 6:400.
16. Levy E.D. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 2010, 403:660-670.
17. Grueninger D., Treiber N., Ziegler M.O., Koetter J.W., Schulze M.S., Schulz G.E. Designed protein-protein association. Science 2008, 319:206-209.
18. Zhong Q., Simonis N., Li Q.R., Charloteaux B., Heuze F., Klitgord N., et al. Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009, 5:321.
19. Moreira I.S., Fernandes P.A., Ramos M.J. Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 2007, 68:803-812.
20. Beltrao P., Serrano L. Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 2007, 3:e25.
21. Katju V., Lynch M. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 2003, 165:1793-1803.
22. Lynch M., Katju V. The altered evolutionary trajectories of gene duplicates. Trends Genet 2004, 20:544-549.
23. Dekker J. Gene regulation in the third dimension. Science 2008, 319:1793-1794.
24. Jansen A., van der Zande E., Meert W., Fink G.R., Verstrepen K.J. Distal chromatin structure influences local nucleosome positions and gene expression. Nucleic Acids Res 2012, 40:3870-3885.
25. Buljan M., Chalancon G., Eustermann S., Wagner G.P., Fuxreiter M., Bateman A., et al. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 2012, 46:871-883.
26. Stark C., Breitkreutz B.J., Chatr-Aryamontri A., Boucher L., Oughtred R., Livstone M.S., et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011, 39:D698-D704.
27. Byrne K.P., Wolfe K.H. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 2005, 15:1456-1461.
28. Ihmels J., Bergmann S., Barkai N. Defining transcription modules using large-scale gene expression data. Bioinformatics 2004, 20:1993-2003.
29. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636.
30. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643.
31. Tarassov K., Messier V., Landry C.R., Radinovic S., Serna Molina M.M., Shames I., et al. An in vivo map of the yeast protein interactome. Science 2008, 320:1465-1470.
32. R Development Core Team. R: A language and environment for statistical computing, reference index version 2.15.0. R Foundation for Statistical Computing, Vienna, Austria; 2005. ISBN 3-900051-07-0, URL.
33. Olson S.A. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 2002, 3:87-91.
34. Michnick S.W., Ear P.H., Landry C., Malleshaiah M.K., Messier V. A toolkit of protein-fragment complementation assays for studying and dissecting large-scale and dynamic protein-protein interactions in living cells. Methods Enzymol 2010, 470:335-368.
35. Michnick S.W., Ear P.H., Landry C., Malleshaiah M.K., Messier V. Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein-protein interactions in living cells. Methods Mol Biol 2011, 756:395-425.
36. Gelperin D.M., White M.A., Wilkinson M.L., Kon Y., Kung L.A., Wise K.J., et al. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev 2005, 19:2816-2826.
37. Ho C.H., Magtanong L., Barker S.L., Gresham D., Nishimura S., Natarajan P., et al. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol 2009, 27:369-377.
38. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901-906.
39. Kohrer K., Domdey H. Preparation of high molecular weight RNA. Guide to yeast genetics and molecular biology 1991, 398-405. C. Guthrie, G.R. Fink (Eds.).
40. Freschi L, Torres-Quiroz F, Dube A, Landry C. qPCA: a scalable tool to study the perturbation of protein-protein interactions in living cells. Mol Biosyst accepted for publication, doi:10.1039/C2MB25265A.
41. Gu Z., Nicolae D., Lu H.H., Li W.H. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 2002, 18:609-613.
42. Wang M., Weiss M., Simonovic M., Haertinger G., Schrimpf S.P., Hengartner M.O., et al. PaxDb, a database of protein abundance averages across all three domains of life. Mol Cell Proteomics 2012, 10.1074/mcp.O111.014704.
43. Wang Y., Liu C.L., Storey J.D., Tibshirani R.J., Herschlag D., Brown P.O. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A 2002, 99:5860-5865.
44. Musso G., Zhang Z., Emili A. Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends Genet 2007, 23:266-269.
45. Vavouri T., Semple J.I., Garcia-Verdugo R., Lehner B. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 2009, 138:198-208.