Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Sardiu, Mihaela E ^a   Gilmore, Joshua M ^a   Carrozza, Michael J ^b   Li, Bing ^c   Workmann, Jerry L ^a   Florens, Laurence ^a   Washburn, Michael P ^a  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE; TRANSCRIPTION FACTOR SIN3A; PROTEIN; REPRESSOR PROTEIN; RPD3 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SIN3 PROTEIN, S CEREVISIAE; UME1 PROTEIN, S CEREVISIAE;

ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; DNA PROTEIN COMPLEX; GENE DELETION; GENE MAPPING; GENE REGULATORY NETWORK; MATHEMATICAL COMPUTING; NONHUMAN; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEOMICS; SACCHAROMYCES CEREVISIAE; WILD TYPE; BIOLOGICAL MODEL; CHEMISTRY; CLUSTER ANALYSIS; GENOME; METABOLISM; METHODOLOGY; PROBABILITY; PROTEIN ANALYSIS; STATISTICAL MODEL;

SACCHAROMYCES CEREVISIAE;

CLUSTER ANALYSIS; GENE DELETION; GENOME; HISTONE DEACETYLASES; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROBABILITY; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 70350212549     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007310     Document Type: Article

References (33)

1. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
2. Pang CN, Krycer JR, Lek A, Wilkins MR (2008) Are protein complexes made of cores, modules and attachments? Proteomics 8: 425-434.
3. Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, et al. (2008) Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A 105: 1454-1459.
4. Shahbazian MD, Grunstein M (2007) Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem 76: 75-100.
5. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-592.
6. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593-605.
7. Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731: 77-87; discussion 75-76.
8. Bolden JE, Peart MJ, Johnstone RW (2006) Anticancer activities of histone deacetylase inhibitors. Nat Rev Drug Discov 5: 769-784.
9. Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, et al. (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40: 303-311.
10. Florens L, Washburn MP (2006) Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol 328: 159-175.
11. Liu WL, Coleman RA, Grob P, King DS, Florens L, et al. (2008) Structural changes in TAF4b-TFIID correlate with promoter selectivity. Mol Cell 29: 81-91.
12. Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, et al. (2006) Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 103: 18928-18933.
13. Mitchell L, Lambert JP, Gerdes M, Al-Madhoun AS, Skerjanc IS, et al. (2008) Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity. Mol Cell Biol 28: 2244-2256.
14. van de Peppel J, Kettelarij N, van Bakel H, Kockelkorn TT, van Leenen D, et al. (2005) Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol Cell 19: 511-522.
15. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450.
16. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, et al. (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135: 749-762.
17. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
18. Reva B, Antipin Y, Sander C (2007) Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol 8: R232.
19. Guenther MG, Yu J, Kao GD, Yen TJ, Lazar MA (2002) Assembly of the SMRT-histone deacetylase 3 repression complex requires the TCP-1 ring complex. Genes Dev 16: 3130-3135.
20. Lottersberger F, Panza A, Lucchini G, Longhese MP (2007) Functional and physical interactions between yeast 14-3-3 proteins, acetyltransferases, and deacetylases in response to DNA replication perturbations. Mol Cell Biol 27: 3266-3281.
21. Le Guezennec X, Vermeulen M, Stunnenberg HG (2006) Molecular characterization of Sin3 PAH-domain interactor specificity and identification of PAH partners. Nucleic Acids Res 34: 3929-3937.
22. Sahu SC, Swanson KA, Kang RS, Huang K, Brubaker K, et al. (2008) Conserved themes in target recognition by the PAH1 and PAH2 domains of the Sin3 transcriptional corepressor. J Mol Biol 375: 1444-1456.
23. van Ingen H, Baltussen MA, Aelen J, Vuister GW (2006) Role of structural and dynamical plasticity in Sin3: the free PAH2 domain is a folded module in mSin3B. J Mol Biol 358: 485-497.
24. Wang H, Clark I, Nicholson PR, Herskowitz I, Stillman DJ (1990) The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol 10: 5927-5936.
25. Laherty CD, Billin AN, Lavinsky RM, Yochum GS, Bush AC, et al. (1998) SAP30, a component of the mSin3 corepressor complex involved in N-CoR-mediated repression by specific transcription factors. Mol Cell 2: 33-42.
26. Viiri KM, Korkeamaki H, Kukkonen MK, Nieminen LK, Lindfors K, et al. (2006) SAP30L interacts with members of the Sin3A corepressor complex and targets Sin3A to the nucleolus. Nucleic Acids Res 34: 3288-3298.
27. Alland L, David G, Shen-Li H, Potes J, Muhle R, et al. (2002) Identification of mammalian Sds3 as an integral component of the Sin3/ histone deacetylase corepressor complex. Mol Cell Biol 22: 2743-2750.
28. David G, Turner GM, Yao Y, Protopopov A, DePinho RA (2003) mSin3-associated protein, mSds3, is essential for pericentric heterochromatin formation and chromosome segregation in mammalian cells. Genes Dev 17: 2396-2405.
29. Nikolaev AY, Papanikolaou NA, Li M, Qin J, Gu W (2004) Identification of a novel BRMS1-homologue protein p40 as a component of the mSin3A/ p33(ING1b)/HDAC1 deacetylase complex. Biochem Biophys Res Commun 323: 1216-1222.
30. Steeg PS (2003) Metastasis suppressors alter the signal transduction of cancer cells. Nat Rev Cancer 3: 55-63.
31. Meunier B, Dumas E, Piec I, Bechet D, Hebraud M, et al. (2007) Assessment of hierarchical clustering methodologies for proteomic data mining. J Proteome Res 6: 358-366.
32. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25: 1119-1126.
33. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.