Phosphorylation network rewiring by gene duplication

Molecular Systems Biology

Volumn 7, Issue , 2011, Pages

  Freschi, Luca ^a   Courcelles, Mathieu ^b,c   Thibault, Pierre ^b,c   Michnick, Stephen W ^c   Landry, Christian R ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOPROTEIN; PHOSPHOTRANSFERASE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOINFORMATICS; GENE DUPLICATION; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; YEAST; BIOLOGY; CHEMICAL STRUCTURE; COMPARATIVE STUDY; FUNGAL GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PHOSPHORYLATION; REPRODUCIBILITY;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENES, FUNGAL; MODELS, MOLECULAR; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 79960106694     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.43     Document Type: Article

References (44)

1. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H (2008) A multidimensional chromatography technology for indepth phosphoproteome analysis. Mol Cell Proteomics 7: 1389-1396 (Pubitemid 352038280)
2. Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y (2010) Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci USA 107: 2967-2971
3. Ba ANN, MosesAM(2010) Evolution of characterized phosphorylation sites in budding yeast. Mol Biol Evol 27: 2027-2037
4. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ (2009) Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol 7: e1000134
5. Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R (2007) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 4: 231-237 (Pubitemid 46358873)
6. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 104: 2193-2198 (Pubitemid 46391374)
7. Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938-950 (Pubitemid 352719432)
8. Courcelles M, Lemieux S, Voisin L, Meloche S, Thibault P (2011) ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses. Proteomics 11: 2654-2671
9. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797 (Pubitemid 38832724)
10. Force A, Lynch M, Pickett FB, Amores A, Yan Y-L, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545 (Pubitemid 29177561)
11. Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2: e398
12. Gnad F, de Godoy LMF, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M (2009) High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 9: 4642-4652
13. Gordon JL, Byrne KP, Wolfe KH (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet 5: e1000485
14. Gough NR, Wong W (2010) Focus issue: the evolution of complexity. Sci Signal 3: eg5
15. Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4: 310-327 (Pubitemid 40439774)
16. Holmberg CI, Tran SEF, Eriksson JE, Sistonen L (2002) Multisite phosphorylation provides sophisticated regulation of transcription factors. Trends Biochem Sci 27: 619-627 (Pubitemid 35435311)
17. Hurles M (2004) Gene duplication: the genomic trade in spare parts. PLoS Biol 2: 900-904
18. Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443: 594-597 (Pubitemid 44527297)
19. Kapoor M, Hamm R, Yan W, Taya Y, Lozano G (2000) Cooperative phosphorylation at multiple sites is required to activate p53 in response to UV radiation. Oncogene 19: 358-364 (Pubitemid 30077335)
20. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624 (Pubitemid 38524797)
21. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664
22. Landry CR, Levy ED, Michnick SW(2009)Weak functional constraints on phosphoproteomes. Trends Genet 25: 193-197
23. Li X, Gerber SA, Rudner AD, Beausoleil SA, HaasW, Villén J, Elias JE, Gygi SP (2007) Large-scale phosphorylation analysis of alpha-factorarrested Saccharomyces cerevisiae. J Proteome Res 6: 1190-1197 (Pubitemid 46480484)
24. Lienhard GE (2008) Non-functional phosphorylations? Trends Biochem Sci 33: 351-352
25. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473 (Pubitemid 30045935)
26. Marcantonio M, Trost M, Courcelles M, Desjardins M, Thibault P (2008) Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages. Mol Cell Proteomics 7: 645-660 (Pubitemid 351597477)
27. Mok J, Kim PM, Lam HYK, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma J-LN, Sheu Y-J, Sassi HE, Sopko R, Chan CSM, De Virgilio C et al (2010) Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal 3: ra12
28. Moses AM, Landry CR (2010)Moving from transcriptional to phosphoevolution: generalizing regulatory evolution? Trends Genet 26: 462-467
29. Musso G, Costanzo M, Huangfu M, Smith AM, Paw J, San Luis B-J, Boone C, Giaever G, Nislow C, Emili A, Zhang Z (2008) The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res 18: 1092-1099 (Pubitemid 351931160)
30. Papp B, Pal C, Hurst LD (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 19: 417-422 (Pubitemid 36930023)
31. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee S-J, Mah AS, Meng L, Stark MJR, Stern DF, De Virgilio C, Tyers M et al (2005) Global analysis of protein phosphorylation in yeast. Nature 438: 679-684 (Pubitemid 41740579)
32. Reinders Jr, Wagner K, Zahedi RP, Stojanovski D, Eyrich B, van der Laan M, Rehling P, Sickmann A, Pfanner N, Meisinger C (2007) Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol Cell Proteomics 6: 1896-1906 (Pubitemid 350201867)
33. Seoighe C, Wolfe KH (1999) Yeast genome evolution in the postgenome era. Curr Opin Microbiol 2: 548-554 (Pubitemid 29477185)
34. Serber Z, Ferrell Jr JE (2007) Tuning bulk electrostatics to regulate protein function. Cell 128: 441-444 (Pubitemid 46198900)
35. Souciet J-L, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe Vr, Ségurens Ba, Artiguenave Fo, Anthouard Vr, Vacherie B, Val M-E, Fulton RS, Minx P et al (2009) Comparative genomics of protoploid Saccharomycetaceae. Genome Res 19: 1696-1709
36. Thingholm TE, Jrgensen TJD, Jensen ON, Larsen MR (2006) Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 1: 1929-1935 (Pubitemid 46773313)
37. Tirosh I, Barkai N (2007) Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 8: R50
38. Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, Shah K, Shokat KM, Morgan DO (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425: 859-864 (Pubitemid 37351471)
39. van Hoof A (2005) Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication. Genetics 171: 1455-1461
40. Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18: 1283-1292 (Pubitemid 32660673)
41. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645 (Pubitemid 38326883)
42. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713 (Pubitemid 27270611)
43. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591 (Pubitemid 47236688)
44. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, SnyderM(2000) Analysis of yeast protein kinases using protein chips. Nat Genet 26: 283-289