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Literature DB >> 16322557

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

Daniel M Gelperin¹, Michael A White, Martha L Wilkinson, Yoshiko Kon, Li A Kung, Kevin J Wise, Nelson Lopez-Hoyo, Lixia Jiang, Stacy Piccirillo, Haiyuan Yu, Mark Gerstein, Mark E Dumont, Eric M Phizicky, Michael Snyder, Elizabeth J Grayhack.

Abstract

Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was constructed, each expressing a sequence-verified ORF as a C-terminal ORF fusion protein, under regulated control. Analysis of 5573 MORFs demonstrates that nearly all verified ORFs are expressed, suggests the authenticity of 48 ORFs characterized as dubious, and implicates specific processes including cytoskeletal organization and transcriptional control in growth inhibition caused by overexpression. Global analysis of glycosylated proteins identifies 109 new confirmed N-linked and 345 candidate glycoproteins, nearly doubling the known yeast glycome.

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Year: 2005 PMID： 16322557 PMCID： PMC1315389 DOI： 10.1101/gad.1362105

Source DB: PubMed Journal: Genes Dev ISSN： 0890-9369 Impact factor: 11.361

59 in total

Review 1. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.

Authors: R Apweiler; H Hermjakob; N Sharon
Journal: Biochim Biophys Acta Date: 1999-12-06

2. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors: A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal: J Mol Biol Date: 2001-01-19 Impact factor: 5.469

3. A biochemical genomics approach for identifying genes by the activity of their products.

Authors: M R Martzen; S M McCraith; S L Spinelli; F M Torres; S Fields; E J Grayhack; E M Phizicky
Journal: Science Date: 1999-11-05 Impact factor: 47.728

4. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited.

Authors: G Blandin; P Durrens; F Tekaia; M Aigle; M Bolotin-Fukuhara; E Bon; S Casarégola; J de Montigny; C Gaillardin; A Lépingle; B Llorente; A Malpertuy; C Neuvéglise; O Ozier-Kalogeropoulos; A Perrin; S Potier; J Souciet; E Talla; C Toffano-Nioche; M Wésolowski-Louvel; C Marck; B Dujon
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

5. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Authors: P Uetz; L Giot; G Cagney; T A Mansfield; R S Judson; J R Knight; D Lockshon; V Narayan; M Srinivasan; P Pochart; A Qureshi-Emili; Y Li; B Godwin; D Conover; T Kalbfleisch; G Vijayadamodar; M Yang; M Johnston; S Fields; J M Rothberg
Journal: Nature Date: 2000-02-10 Impact factor: 49.962

6. A regulatory link between ER-associated protein degradation and the unfolded-protein response.

Authors: R Friedlander; E Jarosch; J Urban; C Volkwein; T Sommer
Journal: Nat Cell Biol Date: 2000-07 Impact factor: 28.824

7. Yeast protein translocation complex: isolation of two genes SEB1 and SEB2 encoding proteins homologous to the Sec61 beta subunit.

Authors: J Toikkanen; E Gatti; K Takei; M Saloheimo; V M Olkkonen; H Söderlund; P De Camilli; S Keränen
Journal: Yeast Date: 1996-04 Impact factor: 3.239

8. Analysis of yeast protein kinases using protein chips.

Authors: H Zhu; J F Klemic; S Chang; P Bertone; A Casamayor; K G Klemic; D Smith; M Gerstein; M A Reed; M Snyder
Journal: Nat Genet Date: 2000-11 Impact factor: 38.330

Review 9. Life with 6000 genes.

Authors: A Goffeau; B G Barrell; H Bussey; R W Davis; B Dujon; H Feldmann; F Galibert; J D Hoheisel; C Jacq; M Johnston; E J Louis; H W Mewes; Y Murakami; P Philippsen; H Tettelin; S G Oliver
Journal: Science Date: 1996-10-25 Impact factor: 47.728

10. An efficient method to isolate yeast genes causing overexpression-mediated growth arrest.

Authors: C Espinet; M A de la Torre; M Aldea; E Herrero
Journal: Yeast Date: 1995-01 Impact factor: 3.239

270 in total

1. tRNAHis guanylyltransferase adds G-1 to the 5' end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases.

Authors: Jane E Jackman; Eric M Phizicky
Journal: RNA Date: 2006-04-19 Impact factor: 4.942

2. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs.

Authors: Sara Sharifpoor; Dewald van Dyk; Michael Costanzo; Anastasia Baryshnikova; Helena Friesen; Alison C Douglas; Ji-Young Youn; Benjamin VanderSluis; Chad L Myers; Balázs Papp; Charles Boone; Brenda J Andrews
Journal: Genome Res Date: 2012-01-26 Impact factor: 9.043

3. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements.

Authors: Graham M West; Chandra L Tucker; Tao Xu; Sung Kyu Park; Xuemei Han; John R Yates; Michael C Fitzgerald
Journal: Proc Natl Acad Sci U S A Date: 2010-05-03 Impact factor: 11.205

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

Review 1. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.

2. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

3. A biochemical genomics approach for identifying genes by the activity of their products.

4. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited.

5. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

6. A regulatory link between ER-associated protein degradation and the unfolded-protein response.

7. Yeast protein translocation complex: isolation of two genes SEB1 and SEB2 encoding proteins homologous to the Sec61 beta subunit.

8. Analysis of yeast protein kinases using protein chips.

Review 9. Life with 6000 genes.

10. An efficient method to isolate yeast genes causing overexpression-mediated growth arrest.

1. tRNAHis guanylyltransferase adds G-1 to the 5' end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases.

2. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs.

3. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements.

4. SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor.

5. Shedding of the mucin-like flocculin Flo11p reveals a new aspect of fungal adhesion regulation.

6. Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions.

7. La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast.

8. Cardiolipin deficiency causes triacylglycerol accumulation in Saccharomyces cerevisiae.

9. Characteristics affecting expression and solubilization of yeast membrane proteins.

10. Global identification of protein kinase substrates by protein microarray analysis.