Biochemical and genetic analysis of the yeast proteome with a movable ORF collection

Genes and Development

Volumn 19, Issue 23, 2005, Pages 2816-2826

  Gelperin, Daniel M ^b   White, Michael A ^a   Wilkinson, Martha L ^a   Kon, Yoshiko ^a   Kung, Li A ^b   Wise, Kevin J ^b   Lopez Hoyo, Nelson ^b   Jiang, Lixia ^b   Piccirillo, Stacy ^b   Yu, Haiyuan ^b   Gerstein, Mark ^b   Dumont, Mark E ^a   Phizicky, Eric M ^a   Snyder, Michael ^b   Grayhack, Elizabeth J ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Biochemical genomics; Galactose lethality; Glycosylation; High throughput expression; Protein microarray; Proteome

Indexed keywords

GLYCOPROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; FUNCTIONAL PROTEOMICS; FUNGAL GENE; GENE CONSTRUCT; GENE CONTROL; GENE EXPRESSION; GENE OVEREXPRESSION; GENETIC ANALYSIS; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; PROTEIN GLYCOSYLATION; PROTEIN MICROARRAY; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

CELL GROWTH PROCESSES; FUNGAL PROTEINS; GENE LIBRARY; GLYCOPROTEINS; OPEN READING FRAMES; PROTEOME; PROTEOMICS; YEASTS;

EID: 28444478789     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1362105     Document Type: Article

References (60)

1. Akada, R., Yamamoto, J., and Yamashita, I. 1997. Screening and identification of yeast sequences that cause growth inhibition when overexpressed. Mol. Gen. Genet. 254: 267-274.
2. Alexandrov, A., Martzen, M.R., and Phizicky, E.M. 2002. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8: 1253-1266.
3. Apweiler, R., Hermjakob, H., and Sharon, N. 1999. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys. Acta 1473: 4-8.
4. Arava, Y., Wang, Y., Storey, J.D., Liu, C.L., Brown, P.O., and Herschlag, D. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 100: 3889-3894.
5. Bader, G.D., Heilbut, A., Andrews, B., Tyers, M., Hughes, T., and Boone, C. 2003. Functional genomics and proteomics: Charting a multidimensional map of the yeast cell. Trends Cell. Biol. 13: 344-356.
6. Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hong, E.L., Nash, R., et al. Saccharomyces Genome Database. ftp://ftp.yeastgenome.org/yeast. (See citations for dates of access.)
7. Ballou, C.E. 1990. Isolation, characterization, and properties of Saccharomyces cerevisiae mnn mutants with nonconditional protein glycosylation defects. Methods Enzymol. 185: 440-470.
8. Basrai, M.A., Hieter, P., and Boeke, J.D. 1997. Small open reading frames: Beautiful needles in the haystack. Genome Res. 7: 768-771.
9. Bendtsen, J.D., Nielsen, H., von Heijne, G., and Brunak, S. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340: 783-795.
10. Bieganowski, P. and Brenner, C. 2004. Discoveries of nicotinamide riboside as a nutrient and conserved NRK genes establish a Preiss-Handler independent route to NAD+ in fungi and humans. Cell 117: 495-502.
11. Blandin, G., Durrens, P., Tekaia, F., Aigle, M., Bolotin-Fukuhara, M., Bon, E., Casaregola, S., de Montigny, J., Gaillardin, C., Lepingle, A., et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett. 487: 31-36.
12. Boyer, J., Badis, G., Fairhead, C., Talla, E., Hantraye, F., Fabre, E., Fischer, G., Hennequin, C., Koszul, R., Lafontaine, I., et al. 2004. Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol. 5: R72.
13. Brachmann, C.B., Davies, A., Cost, G.J., Caputo, E., Li, J., Hieter, P., and Boeke, J.D. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132.
14. Clancy, S., Mann, C., Davis, R.W., and Calos, M.P. 1984. Deletion of plasmid sequences during Saccharomyces cerevisiae transformation. J. Bacteriol. 159: 1065-1067.
15. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 29: 29.
16. Csank, C., Costanzo, M.C., Hirschman, J., Hodges, P., Kranz, J.E., Mangan, M., O'Neill, K., Robertson, L.S., Skrzypek, M.S., Brooks, J., et al. 2002. Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD). Methods Enzymol. 350: 347-373.
17. Espinet, C., de la Torre, M.A., Aldea, M., and Herrero, E. 1995. An efficient method to isolate yeast genes causing overexpression-mediated growth arrest. Yeast 11: 25-32.
18. Friedlander, R., Jarosch, E., Urban, J., Volkwein, C., and Sommer, T. 2000. A regulatory link between ER-associated protein degradation and the unfolded-protein response. Nat. Cell. Biol. 2: 379-384.
19. 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. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
20. Ghaemmaghami, S., Huh, W.K., Bower, K., Howson, R.W., Belle, A., Dephoure, N., O'Shea, E.K., and Weissman, J.S. 2003. Global analysis of protein expression in yeast. Nature 425: 737-741.
21. Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
22. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., et al. 1996. Life with 6000 genes. Science 274: 546, 563-567.
23. Gu, W., Jackman, J.E., Lohan, A.J., Gray, M.W., and Phizicky, E.M. 2003. tRNAHis maturation: An essential yeast protein catalyzes addition of a guanine nucleotide to the 5′ end of tRNAHis. Genes & Dev. 17: 2889-2901.
24. Guinez, C., Morelle, W., Michalski, J.C., and Lefebvre, T. 2005. O-GlcNAc glycosylation: A signal for the nuclear transport of cytosolic proteins? Int. J. Biochem. Cell. Biol. 37: 765-774.
25. Hazbun, T.R. and Fields, S. 2002. A genome-wide screen for site-specific DNA-binding proteins. Mol. Cell. Proteomics 1: 538-543.
26. Hazbun, T.R., Malmstrom, L., Anderson, S., Graczyk, B.J., Fox, B., Riffle, M., Sundin, B.A., Aranda, J.D., McDonald, W.H., Chiu, C.H., et al. 2003. Assigning function to yeast proteins by integration of technologies. Mol. Cell 12: 1353-1365.
27. Helenius, A. and Aebi, M. 2004. Roles of N-linked glycans in the endoplasmic reticulum. Annu. Rev. Biochem. 73: 1019-1049.
28. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
29. Huang, J., Zhu, H., Haggarty, S.J., Spring, D.R., Hwang, H., Jin, F., Snyder, M., and Schreiber, S.L. 2004. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc. Natl. Acad. Sci. 101: 16594-16599.
30. Hudson Jr., J.R., Dawson, E.P., Rushing, K.L., Jackson, C.H., Lockshon, D., Conover, D., Lanciault, C., Harris, J.R., Simmons, S.J., Rothstein, R., et al. 1997. The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7: 1169-1173.
31. Hughes, T.R., Robinson, M.D., Mitsakakis, N., and Johnston, M. 2004. The promise of functional genomics: Completing the encyclopedia of a cell. Curr. Opin. Microbiol. 7: 546-554.
32. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S., and O'Shea, E.K. 2003. Global analysis of protein localization in budding yeast. Nature 425: 686-691.
33. Jackman, J.E., Montange, R.K., Malik, H.S., and Phizicky, E.M. 2003. Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 9: 574-585.
34. Kafadar, K.A., Zhu, H., Snyder, M., and Cyert, M.S. 2003. Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes & Dev. 17: 2698-2708.
35. Kall, L. and Sonnhammer, E.L. 2002. Reliability of transmembrane predictions in whole-genome data. FEBS Lett. 532: 415-418.
36. Kang, C.M. and Jiang, Y.W. 2005. Genome-wide survey of nonessential genes required for slowed DNA synthesis-induced filamentous growth in yeast. Yeast 22: 79-90.
37. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
38. Kessler, M.M., Zeng, Q., Hogan, S., Cook, R., Morales, A.J., and Cottarel, G. 2003. Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res. 13: 264-271.
39. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305: 567-580.
40. Kumar, A., Harrison, P.M., Cheung, K.H., Lan, N., Echols, N., Bertone, P., Miller, P., Gerstein, M.B., and Snyder, M. 2002. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20: 58-63.
41. Kus, B.M., Gajadhar, A., Stanger, K., Cho, R., Sun, W., Rouleau, N., Lee, T., Chan, D., Wolting, C., Edwards, A.M., et al. 2005. A high throughput screen to identify substrates for the ubiquitin ligase Rsp5. J. Biol. Chem. 280: 29470-29478.
42. Lamesch, P., Milstein, S., Hao, T., Rosenberg, J., Li, N., Sequerra, R., Bosak, S., Doucette-Stamm, L., Vandenhaute, J., Hill, D.E., et al. 2004. C. elegans ORFeome version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 14: 2064-2069.
43. Liu, H., Krizek, J., and Bretscher, A. 1992. Construction of a GAL1-regulated yeast cDNA expression library and its application to the identification of genes whose overexpression causes lethality in yeast. Genetics 132: 665-673.
44. Luan, C.H., Qiu, S., Finley, J.B., Carson, M., Gray, R.J., Huang, W., Johnson, D., Tsao, J., Reboul, J., Vaglio, P., et al. 2004. High-throughput expression of C. elegans proteins. Genome Res. 14: 2102-2110.
45. Ma, X., Zhao, X., and Yu, Y.T. 2003. Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J. 22: 1889-1897.
46. Martzen, M.R., McCraith, S.M., Spinelli, S.L., Torres, F.M., Fields, S., Grayhack, E.J., and Phizicky, E.M. 1999. A biochemical genomics approach for identifying genes by the activity of their products. Science 286: 1153-1155.
47. Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10: 1-6.
48. Oshiro, G., Wodicka, L.M., Washburn, J.R., Yates III, M.P., Lockhart, D.J., and Winzeler, E.A. 2002. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res. 12: 1210-1220.
49. Phizicky, E.M., Martzen, M.R., McCraith, S.M., Spinelli, S.L., Xing, F., Shull, N.P., Van Slyke, C., Montagne, R.K., Torres, F.M., Fields, S., et al. 2002. Biochemical genomics approach to map activities to genes. Methods Enzymol. 350: 546-559.
50. Phizicky, E., Bastiaens, P.I., Zhu, H., Snyder, M., and Fields, S. 2003. Protein analysis on a proteomic scale. Nature 422: 208-215.
51. Ramer, S.W., Elledge, S.J., and Davis, R.W. 1992. Dominant genetics using a yeast genomic library under the control of a strong inducible promoter. Proc. Natl. Acad. Sci. 89: 11589-11593.
52. Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., et al.2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteomescale protein expression. Nat. Genet. 34: 35-41.
53. Stevenson, L.F., Kennedy, B.K., and Harlow, E. 2001. A largescale overexpression screen in Saccharomyces cerevisiae identifies previously uncharacterized cell cycle genes. Proc. Natl. Acad. Sci. 98: 3946-3951.
54. Toikkanen, J., Gatti, E., Takei, K., Saloheimo, M., Olkkonen, V.M., Soderlund, H., De Camilli, P., and Keranen, S. 1996. Yeast protein translocation complex: Isolation of two genes SEB1 and SEB2 encoding proteins homologous to the Sec61 β subunit. Yeast 12: 425-438.
55. Tong, A.H., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G.F., Brost, R.L., Chang, M., et al. 2004. Global mapping of the yeast genetic interaction network. Science 303: 808-813.
56. Ubersax, J.A., Woodbury, E.L., Quang, P.N., Paraz, M., Blethrow, J.D., Shah, K., Shokat, K.M., and Morgan, D.O. 2003. Targets of the cyclin-dependent kinase Cdk1. Nature 425: 859-864.
57. 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. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
58. Wiedemann, N., Kozjak, V., Chacinska, A., Schonfisch, B., Rospert, S., Ryan, M.T., Pfanner, N., and Meisinger, C. 2003. Machinery for protein sorting and assembly in the mitochondrial outer membrane. Nature 424: 565-571.
59. Zhu, H., Klemic, J.F., Chang, S., Bertone, P., Casamayor, A., Klemic, K.G., Smith, D., Gerstein, M., Reed, M.A., and Snyder, M. 2000. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26: 283-289.
60. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., et al. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101-2105.