Proteome survey reveals modularity of the yeast cell machinery

Nature

Volumn 440, Issue 7084, 2006, Pages 631-636

  Gavin, Anne Claude ^a,b   Aloy, Patrick ^b   Grandi, Paola ^a   Krause, Roland ^a,c   Boesche, Markus ^a   Marzioch, Martina ^a   Rau, Christina ^a   Jensen, Lars Juhl ^b   Bastuck, Sonja ^a   Dümpelfeld, Birgit ^a   Edelmann, Angela ^a   Heurtier, Marie Anne ^a   Hoffman, Verena ^a   Hoefert, Christian ^a   Klein, Karin ^a   Hudak, Manuela ^a   Michon, Anne Marie ^a   Schelder, Malgorzata ^a   Schirle, Markus ^a   Remor, Marita ^a   Rudi, Tatjana ^a   Hooper, Sean ^b   Bauer, Andreas ^a   Bouwmeester, Tewis ^a   Casari, Georg ^a   Drewes, Gerard ^a   Neubauer, Gitte ^a   Rick, Jens M ^a   Kuster, Bernhard ^a   Bork, Peer ^b   Russell, Robert B ^b   Superti Furga, Giulio ^a,d   more..

^a GLAXOSMITHKLINE   (United Kingdom)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^d ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; COMPLEXATION; DATA ACQUISITION; MATHEMATICAL MODELS; PROTEINS; SATURATION (MATERIALS COMPOSITION);

EUKARYOTIC CELLULAR MACHINES; EVOLUTIONARY CONSERVATION; OPEN READING FRAMES (ORF);

YEAST;

AMPHIPHYSIN; CHAPERONIN; GENE PRODUCT; MESSENGER RNA; OXOGLUTARATE DEHYDROGENASE; PROTEOME; PYRUVATE DEHYDROGENASE; SNARE PROTEIN;

CELLS AND CELL COMPONENTS; GENOME; MASS SPECTROMETRY; PROTEIN; YEAST;

ARTICLE; BIOLOGICAL ACTIVITY; CELL CYCLE; GENETIC CONSERVATION; MASS SPECTROMETRY; NONHUMAN; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN TARGETING; PROTEOMICS; RNA DEGRADATION; SACCHAROMYCES CEREVISIAE; SPOROGENESIS; YEAST CELL;

GENOME, FUNGAL; MULTIPROTEIN COMPLEXES; OPEN READING FRAMES; PHENOTYPE; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 33644555054     PISSN: 00280836     EISSN: 14764679     Source Type: Journal    
DOI: 10.1038/nature04532     Document Type: Article

References (43)

1. Hood, L., Heath, J. R., Phelps, M. E. & Lin, B. Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640-643 (2004).
2. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
3. Goh, C. S., Milburn, D. & Gerstein, M. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14, 104-109 (2004).
4. Kemmeren, P. et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133-1143 (2002).
5. Edwards, A. M. et al. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet. 18, 529-536 (2002).
6. Puig, O. et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229 (2001).
7. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030-1032 (1999).
8. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
9. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
10. Bouwmeester, T. et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nature Cell Biol. 6, 97-105 (2004).
11. Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537 (2005).
12. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
13. Rual, J. F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178 (2005).
14. Aloy, P. et al. Structure-based assembly of protein complexes in yeast. Science 303, 2026-2029 (2004).
15. de Lichtenberg, U., Jensen, L. J., Brunak, S. & Bork, P. Dynamic complex formation during the yeast cell cycle. Science 307, 724-727 (2005).
16. Kelley, R. & Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnol. 23, 561-566 (2005).
17. Mewes, H. W. et al. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30, 31-34 (2002).
18. Kumar, A. et al. An integrated approach for finding overlooked genes in yeast. Nature Biotechnol. 20, 58-63 (2002).
19. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
20. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
21. Washburn, M. P., Wolters, D. & Yates, J. R. III Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242-247 (2001).
22. Mewes, H. W. et al. MIPS: Analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-D44 (2004).
23. Liou, A. K. & Willison, K. R. Elucidation of the subunit orientation in CCT (chaperonin containing TCP1) from the subunit composition of CCT microcomplexes. EMBO J. 16, 4311-4316 (1997).
24. Kraynack, B. A. et al. Dsl1p, Tip20p, and the novel Dsl3(Sec39) protein are required for the stability of the Q/t-SNARE complex at the endoplasmic reticulum in yeast. Mol. Biol. Cell 16, 3963-3977 (2005).
25. Kao, L. R., Peterson, J., Ji, R., Bender, L. & Bender, A. Interactions between the ankyrin repeat-containing protein Akr1p and the pheromone response pathway in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 168-178 (1996).
26. Bader, G. D. & Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003).
27. Dezso, Z., Oltvai, Z. N. & Barabasi, A. L. Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res. 13, 2450-2454 (2003).
28. Orban, T. I. & Izaurralde, E. Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA 11, 459-469 (2005).
29. Sheth, U. & Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805-808 (2003).
30. Fortes, P. et al. The yeast nuclear cap binding complex can interact with translation factor elF4G and mediate translation initiation. Mol. Cell 6, 191-196 (2000).
31. 7 guanosine cap. Mol. Cell. Biol. 21, 3632-3641 (2001).
32. Jenkins, G. M. & Hannun, Y. A. Role for de novo sphingoid base biosynthesis in the heat-induced transient cell cycle arrest of Saccharomyces cerevisiae. J. Biol. Chem. 276, 8574-8581 (2001).
33. Sehnke, P. C. & Ferl, R. J. Plant 14-3-3s: Omnipotent metabolic phosphopartners? Sci. STKE 2000, PE1 (2000) (doi:10.1126/stke.2000.56.pe1).
34. Pozuelo Rubio, M. et al. 14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and trafficking. Biochem. J. 379, 395-408 (2004).
35. Winstall, E., Sadowski, M., Kuhn, U., Wahle, E. & Sachs, A. B. The Saccharomyces cerevisiae RNA-binding protein Rbp29 functions in cytoplasmic mRNA metabolism. J. Biol. Chem. 275, 21817-21826 (2000).
36. Shi, Y. & Shi, Y. Metabolic enzymes and coenzymes in transcription - a direct link between metabolism and transcription? Trends Genet. 20, 445-452 (2004).
37. Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. Lethality and centrality in protein networks. Nature 411, 41-42 (2001).
38. Dudley, A. M., Janse, D. M., Tanay, A., Shamir, R. & Church, G. M. A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Syst. Biol. published online 29 March 2005 (doi:10.1038/msb4100004).
39. Said, M. R., Begley, T. J., Oppenheim, A. V., Lauffenburger, D. A. & Samson, L. D. Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101, 18006-18011 (2004).
40. Bader, G. D. & Hogue, C. W. Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnol. 20, 991-997 (2002).
41. Subramanian, S., Woolford, C. A. & Jones, E. W. The Sec1/Munc18 protein, Vps33p, functions at the endosome and the vacuole of Saccharomyces cerevisiae. Mol. Biol. Cell 15, 2593-2605 (2004).
42. Friesen, H., Colwill, K., Robertson, K., Schub, O. & Andrews, B. Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to golgi vesicle trafficking. Genetics 170, 555-568 (2005).
43. Ross, J., Reid, G. A. & Dawes, I. W. The nucleotide sequence of the LPD1 gene encoding lipoamide dehydrogenase in Saccharomyces cerevisiae: comparison between eukaryotic and prokaryotic sequences for related enzymes and identification of potential upstream control sites. J. Gen. Microbiol. 134, 1131-1139 (1988).