The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: Version 2.0 update

Database

Volumn 2013, Issue , 2013, Pages

  Sadowski, Ivan ^a   Breitkreutz, Bobby Joe ^b   Stark, Chris ^b   Su, Ting Cheng ^a   Dahabieh, Matthew ^a   Raithatha, Sheetal ^a   Bernhard, Wendy ^a   Oughtred, Rose ^c   Dolinski, Kara ^c   Barreto, Kris ^a   Tyers, Mike ^b,d  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

^c PRINCETON UNIVERSITY   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOPROTEIN; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; HIGH THROUGHPUT SCREENING; METABOLISM; PHOSPHORYLATION; PROTEIN DATABASE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

DATABASES, PROTEIN; HIGH-THROUGHPUT SCREENING ASSAYS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 84885896190     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat026     Document Type: Article

References (50)

1. Seet,B.T., Dikic,I., Zhou,M.M. et al. (2006) Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol., 7, 473-483.
2. Stark,C., Su,T.C., Breitkreutz,A. et al. (2010) PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database, 2010, bap026.
3. Ingrell,C.R., Miller,M.L., Jensen,O.N. et al. (2007) NetPhosYeast: prediction of protein phosphorylation sites in yeast. Bioinformatics, 23, 895-897.
4. Cherry,J.M., Hong,E.L., Amundsen,C. et al. (2012) Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
5. Sayers,E.W., Barrett,T., Benson,D.A. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
6. Christie,K.R., Weng,S., Balakrishnan,R. et al. (2004) Saccharomyces genome database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32, D311-D314.
7. Teixeira,M.C., Monteiro,P., Jain,P. et al. (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res., 34, D446-D451.
8. Briache,A., Marrakchi,K., Kerzazi,A. et al. (2011) Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. BMC Bioinformatics, 13 (Suppl. 1), S7.
9. Stark,C., Breitkreutz,B.J., Chatr-Aryamontri,A. et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res., 39, D698-D704.
10. Huber,A., Bodenmiller,B., Uotila,A. et al. (2009) Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev., 23, 1929-1943.
11. Soulard,A., Cremonesi,A., Moes,S. et al. (2010) The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates. Mol. Biol. Cell, 21, 3475-3486.
12. Holt,L.J., Tuch,B.B., Villen,J. et al. (2009) Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science, 325, 1682-1686.
13. Breitkreutz,A., Choi,H., Sharom,J.R. et al. (2010) A global protein kinase and phosphatase interaction network in yeast. Science, 328, 1043-1046.
14. Soufi,B., Kelstrup,C.D., Stoehr,G. et al. (2009) Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol. Biosyst., 5, 1337-1346.
15. Chen,S.H., Albuquerque,C.P., Liang,J. et al. (2010) A proteome-wide analysis of kinase-substrate network in the DNA damage response. J. Biol. Chem., 285, 12803-12812.
16. Helbig,A.O., Rosati,S., Pijnappel,P.W. et al. (2011) Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics, 11, 685.
17. Bodenmiller,B., Wanka,S., Kraft,C. et al. (2010) Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci, Signal., 3, rs4.
18. Randell,J.C., Fan,A., Chan,C. et al. (2010) Mec1 is one of multiple kinases that prime the Mcm2-7 helicase for phosphorylation by Cdc7. Mol. Cell, 40, 353-363.
19. Kijanska,M., Dohnal,I., Reiter,W. et al. (2010) Activation of Atg1 kinase in autophagy by regulated phosphorylation. Autophagy, 6, 1168-11678.
20. Yeh,Y.Y., Shah,K.H., Chou,C.C. et al. (2011) The identification and analysis of phosphorylation sites on the Atg1 protein kinase. Autophagy, 7, 716-726.
21. Zegerman,P. and Diffley,J.F. (2010) Checkpoint-dependent inhibition of DNA replication initiation by Sld3 and Dbf4 phosphorylation. Nature, 467, 474-478.
22. Katis,V.L., Lipp,J.J., Imre,R. et al. (2010) Rec8 phosphorylation by casein kinase 1 and Cdc7-Dbf4 kinase regulates cohesin cleavage by separase during meiosis. Dev. Cell, 18, 397-409.
23. Nishizawa,M., Tanigawa,M., Hayashi,M. et al. (2010) Pho85 kinase, a cyclin-dependent kinase, regulates nuclear accumulation of the Rim101 transcription factor in the stress response of Saccharomyces cerevisiae. Eukaryot. Cell, 9, 943-951.
24. Ohouo,P.Y., Bastos de Oliveira,F.M., Almeida,B.S. et al. (2010) DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Mol. Cell, 39, 300-306.
25. Zhu,Z., Mori,S., Oshiumi,H. et al. (2010) Cyclin-dependent kinase promotes formation of the synaptonemal complex in yeast meiosis. Genes Cells, 15, 1036-1050.
26. Lai,Y.J., Lin,F.M., Chuang,M.J. et al. (2010) Genetic requirements and meiotic function of phosphorylation of the yeast axial element protein Red1. Mol. Cell Biol., 31, 912-923.
27. Graczyk,D., Debski,J., Muszynska,G. et al . (2011) Casein kinase II-mediated phosphorylation of general repressor Maf1 triggers RNA polymerase III activation. Proc. Natl. Acad. Sci. USA, 108, 4926-4931.
28. Lopez-Mosqueda,J., Maas,N.L., Jonsson,Z.O. et al. (2010) Damage-induced phosphorylation of Sld3 is important to block late origin firing. Nature, 467, 479-483.
29. Mayer,A., Lidschreiber,M., Siebert,M. et al. (2010) Uniform transitions of the general RNA polymerase II transcription complex. Nat. Struct. Mol. Biol., 17, 1272-1278.
30. Kim,H., Erickson,B., Luo,W. et al. (2010) Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat. Struct. Mol. Biol., 17, 1279-1286.
31. Kim,M., Suh,H., Cho,E.J. et al. (2009) Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J. Biol. Chem., 284, 26421-26426.
32. Akhtar,M.S., Heidemann,M., Tietjen,J.R. et al. (2009) TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol. Cell, 34, 387-393.
33. Liu,Y., Warfield,L., Zhang,C. et al. (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol. Cell Biol., 29, 4852-4863.
34. Dinkel,H., Chica,C., Via,A. et al. (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res., 39, D261-D267.
35. Amoutzias,G.D., He,Y., Lilley,K.S. et al. (2012) Evaluation and properties of the budding yeast phosphoproteome. Mol. Cell Proteomics, 11, M111 009555.
36. Beltrao,P., Trinidad,J.C., Fiedler,D. et al. (2009) Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol., 7, e1000134.
37. Ghaemmaghami,S., Huh,W.K., Bower,K. et al. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
38. Batada,N.N., Hurst,L.D. and Tyers,M. (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput. Biol., 2, e88.
39. Raithatha,S., Su,T.C., Lourenco,P. et al. (2012) Cdk8 regulates stability of the transcription factor Phd1 to control pseudohyphal differentiation of Saccharomyces cerevisiae. Mol. Cell Biol., 32, 664-674.
40. Gibson,T.J. (2009) Cell regulation: determined to signal discrete cooperation. Trends Biochem. Sci., 34, 471-482.
41. Gruhler,A., Olsen,J.V., Mohammed,S. et al. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell Proteomics, 4, 310-327.
42. Mok,J., Kim,P.M., Lam,H.Y. et al. (2012) Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal., 3, ra12.
43. Brautigan,D.L. (2013) Protein Ser/Thr phosphatases - the ugly ducklings of cell signalling. FEBS J., 280, 324-345.
44. Landry,C.R., Levy,E.D. and Michnick,S.W. (2009) Weak functional constraints on phosphoproteomes. Trends Genet., 25, 193-197.
45. Ferrell,J.E. Jr (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem. Sci., 21, 460-466.
46. Cohen,P. (2000) The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem. Sci., 25, 596-601.
47. Ferrell,J.E. Jr (2001) Six steps to destruction. Nature, 414, 498-499.
48. Ferrell,J.E. Jr (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol., 14, 140-148.
49. Kim,S.Y. and Ferrell,J.E. Jr (2007) Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell, 128, 1133-1145.
50. Tang,X., Orlicky,S., Mittag,T. et al. (2012) Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase. Proc. Natl. Acad. Sci. USA, 109, 3287-3292.