Impact of genome-wide functional analyses on cell biology research

Current Opinion in Cell Biology

Volumn 15, Issue 1, 2003, Pages 6-13

  Martin, Adam C ^a   Drubin, David G ^a  

^a University of California Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN;

CELL ORGANELLE; CENTROMERE; CYTOLOGY; DNA MICROARRAY; GENE DELETION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INTERACTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME ANALYSIS; MEDICAL RESEARCH; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 0037222329     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0955-0674(02)00009-1     Document Type: Review

References (55)

1. Green E.D. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2:2001;573-583.
2. Kumar A., Snyder M. Emerging technologies in yeast genomics. Nat. Rev. Genet. 2:2001;302-312.
3. Miklos G.L., Rubin G.M. The role of the genome project in determining gene function: insights from model organisms. Cell. 86:1996;521-529.
4. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868.
5. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D.et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.
6. DeRisi J.L., Iyer V.R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686.
7. Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11:2000;4241-4257.
8. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P.et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
9. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98:2001;4569-4574.
10. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M.et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
11. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K.et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:2002;180-183.
12. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18:2000;1257-1261.
13. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H.et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 285:1999;901-906.
14. Giaever G., Chu A.M., Ni L., Connelly C., Riles L., Veronneau S., Dow S., Lucau-Danila A., Anderson K., Andre B.et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418:2002;387-391 A collection of gene deletions covering 96.5% of the genome was used to identify genes required for growth under various conditions, and to identify deletions resulting in aberrant cell shape.
15. Ni L., Snyder M. A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol. Biol. Cell. 12:2001;2147-2170 The gene deletion collection was used to identify novel genes required for proper bud site selection.
16. Tong A.H., Evangelista M., Parsons A.B., Xu H., Bader G.D., Page N., Robinson M., Raghibizadeh S., Hogue C.W., Bussey H.et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 294:2001;2364-2368 The first use of a highly innovative technique that automates genetic analysis in yeast is described. This was used to identify synthetic lethal interactions with mutations in genes involved in actin assembly, spindle orientation, and DNA synthesis.
17. Grunenfelder B., Winzeler E.A. Treasures and traps in genome-wide data sets: case examples from yeast. Nat. Rev. Genet. 3:2002;653-661.
18. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417:2002;399-403.
19. Li R. Bee1, a yeast protein with homology to Wiscott-Aldrich syndrome protein, is critical for the assembly of cortical actin cytoskeleton. J. Cell. Biol. 136:1997;649-658.
20. Madania A., Dumoulin P., Grava S., Kitamoto H., Scharer-Brodbeck C., Soulard A., Moreau V., Winsor B. The Saccharomyces cerevisiae homologue of human Wiskott-Aldrich syndrome protein Las17p interacts with the Arp2/3 complex. Mol. Biol. Cell. 10:1999;3521-3538.
21. Pruyne D., Bretscher A. Polarization of cell growth in yeast. J. Cell. Sci. 113:2000;571-585.
22. Higgs H.N., Pollard T.D. Regulation of actin filament network formation through Arp2/3 complex: activation by a diverse array of proteins. Annu. Rev. Biochem. 70:2001;649-676.
23. Tong A.H., Drees B., Nardelli G., Bader G.D., Brannetti B., Castagnoli L., Evangelista M., Ferracuti S., Nelson B., Paoluzi S.et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 295:2002;321-324 This study combines computational and experimental approaches to identify comprehensively protein-protein interactions for Src homology 3 (SH3)-domain-containing proteins in yeast. A highly interconnected interaction network was identified that could possibly be involved in regulating actin assembly.
24. Drees B.L., Sundin B., Brazeau E., Caviston J.P., Chen G.C., Guo W., Kozminski K.G., Lau M.W., Moskow J.J., Tong A.et al. A protein interaction map for cell polarity development. J. Cell. Biol. 154:2001;549-571 Systematic two-hybrid screening was used to identify interacting partners of 54 proteins involved in cell polarity.
25. Carroll A.S., O'Shea E.K. Pho85 and signaling environmental conditions. Trends Biochem. Sci. 27:2002;87-93.
26. Carroll A.S., Bishop A.C., DeRisi J.L., Shokat K.M., O'Shea E.K. Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response. Proc. Natl. Acad. Sci. U.S.A. 98:2001;12578-12583 An inhibitor-sensitive allele of Pho85 was used in combination with gene expression profiling to suggest a possible role for Pho85 in responding to diverse cellular stresses.
27. Huang D., Moffat J., Andrews B. Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity. Mol. Cell. Biol. 22:2002;5076-5088 A combination of synthetic genetic array (SGA) analysis and gene expression profiling was used to suggest a role for Pho85 in cell integrity. This is the first study to use SGA analysis to identify second-site suppressors.
28. Wigge P.A., Jensen O.N., Holmes S., Soues S., Mann M., Kilmartin J.V. Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J. Cell. Biol. 141:1998;967-977.
29. Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell. Biol. 148:2000;635-651.
30. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., Yates J.R. iii Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17:1999;676-682.
31. Cheeseman I.M., Anderson S., Jwa M., Green E., Kang J., Yates J.R., Chan C.S.M., Drubin D., Barnes G. Phosphoregulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell. 111:2002;163-172 This study demonstrates the usefulness of mass spectrometry in identifying components of protein complexes and specific phosphorylation sites within these complexes.
32. Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil P.A. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22:2002;4723-4738 This study demonstrates how systematic purification of protein complexes based on affinity to different subunits, in combination with statistical analysis, can be utilized to identify associated proteins.
33. Tanaka T.U., Rachidi N., Janke C., Pereira G., Galova M., Schiebel E., Stark M.J., Nasmyth K. Evidence that the Ipl1-Sli15 (Aurora kinase-INCENP) complex promotes chromosome bi-orientation by altering kinetochore-spindle pole connections. Cell. 108:2002;317-329.
34. MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A.et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U.S.A. 99:2002;7900-7905.
35. Seeley E.S., Kato M., Margolis N., Wickner W., Eitzen G. Genomic analysis of homotypic vacuole fusion. Mol. Biol. Cell. 13:2002;782-794 The gene deletion collection was used to identify proteins required for normal vacuolar morphology, identifying genes required for proper vacuole fusion.
36. Bonangelino C.J., Chavez E.M., Bonifacino J.S. Genomic screen for vacuolar protein sorting genes in Saccharomyces cerevisiae. Mol. Biol. Cell. 13:2002;2486-2501 The gene deletion collection was used to identify proteins required for proper sorting of a vacuole protein.
37. Eitzen G., Wang L., Thorngren N., Wickner W. Remodeling of organelle-bound actin is required for yeast vacuole fusion. J. Cell. Biol. 158:2002;669-679.
38. Dimmer K.S., Fritz S., Fuchs F., Messerschmitt M., weinbach N., Neupert W., Westermann B. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:2002;847-853 The gene deletion collection was used to identify proteins required for respiration and proper mitochondrial morphology.
39. Giaever G., Shoemaker D.D., Jones T.W., Liang H., Winzeler E.A., Astromoff A., Davis R.W. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21:1999;278-283.
40. Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M., Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y.et al. Subcellular localization of the yeast proteome. Genes Dev. 16:2002;707-719.
41. Nislow C., Adams C., Schneiders E., Sigal N., Oestreicher D., Sabry J., Drubin D. Phenotyping yeast using automated image acquisition and analysis on a genome-wide scale. Mol. Biol. Cell. 11:2000;124a-125a.
42. Jorgensen P., Nishikawa J.L., Breitkreutz B.J., Tyers M. Systematic identification of pathways that couple cell growth and division in yeast. Science. 297:2002;395-400 This study uses a combination of genome-wide deletion screens, synthetic genetic array (SGA) analysis, and gene expression profiling to identify genes involved in cell cycle control and regulation of cell size.
43. Martzen M.R., McCraith S.M., Spinelli S.L., Torres F.M., Fields S., Grayhack E.J., Phizicky E.M. A biochemical genomics approach for identifying genes by the activity of their products. Science. 286:1999;1153-1155.
44. Zhu H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K.G., Smith D., Gerstein M., Reed M.A., Snyder M. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:2000;283-289.
45. Pawson T., Scott J.D. Signaling through scaffold, anchoring, and adaptor proteins. Science. 278:1997;2075-2080.
46. Chance M.R., Bresnick A.R., Burley S.K., Jiang J.S., Lima C.D., Sali A., Almo S.C., Bonanno J.B., Buglino J.A., Boulton S.et al. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 11:2002;723-738.
47. Boulton S.J., Vincent S., Vidal M. Use of protein-interaction maps to formulate biological questions. Curr. Opin. Chem. Biol. 5:2001;57-62.
48. Gonczy P., Echeverri C., Oegema K., Coulson A., Jones S.J., Copley R.R., Duperon J., Oegema J., Brehm M., Cassin E.et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature. 408:2000;331-336.
49. Zipperlen P., Fraser A.G., Kamath R.S., Martinez-Campos M., Ahringer J. Roles for 147 embryonic lethal genes on C. elegans chromosome I identified by RNA interference and video microscopy. EMBO J. 20:2001;3984-3992.
50. Kim S.K., Lund J., Kiraly M., Duke K., Jiang M., Stuart J.M., Eizinger A., Wylie B.N., Davidson G.S. A gene expression map for Caenorhabditis elegans. Science. 293:2001;2087-2092.
51. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:2001;494-498.
52. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W.et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
53. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A.et al. The sequence of the human genome. Science. 291:2001;1304-1351.
54. Mochida J., Yamamoto T., Fujimura-Kamada K., Tanaka K. The novel adaptor protein, Mti1p, and Vrp1p, a homolog of Wiskott-Aldrich syndrome protein-interacting protein (WIP), may antagonistically regulate type I myosins in Saccharomyces cerevisiae. Genetics. 160:2002;923-934.
55. Dewar H., Warren D.T., Gardiner F.C., Gourlay C.G., Satish N., Richardson M.R., Andrews P.D., Ayscough K.R. Novel proteins linking the actin cytoskeleton to the endocytic machinery in Saccharomyces cerevisiae. Mol. Biol. Cell. 13:2002;3646-3661.