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Volumn 14, Issue 12, 2015, Pages 5306-5317

Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains

Author keywords

COX complex; deubiquitinases; high throughput proteomics; inorganic phosphate pathway; isobaric labeling; Orbitrap Fusion; quantitative proteomics; TMT; ubiquitin; UBP3

Indexed keywords

CYTOCHROME C OXIDASE; DEUBIQUITINASE; DEUBIQUITYLATING ENZYME UBP3; FUNGAL ENZYME; MUTANT PROTEIN; PHOSPHATE; PHOSPHATE TRANSPORTER; PROTEOME; UBIQUITIN; UNCLASSIFIED DRUG; NUCLEAR PROTEIN; OTU1 PROTEIN, S CEREVISIAE; PROTEINASE; SACCHAROMYCES CEREVISIAE PROTEIN; UBIQUITIN THIOLESTERASE; UBP10 PROTEIN, S CEREVISIAE; UBP15 PROTEIN, S CEREVISIAE; UBP3 PROTEIN, S CEREVISIAE;

EID: 84949036104     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00802     Document Type: Article
Times cited : (42)

References (48)
  • 4
    • 0037311417 scopus 로고    scopus 로고
    • Genome-wide screening of Saccharomyces cerevisiae to identify genes required for antibiotic insusceptibility of eukaryotes
    • Blackburn, A. S.; Avery, S. V. Genome-wide screening of Saccharomyces cerevisiae to identify genes required for antibiotic insusceptibility of eukaryotes Antimicrob. Agents Chemother. 2003, 47 (2) 676-81 10.1128/AAC.47.2.676-681.2003
    • (2003) Antimicrob. Agents Chemother. , vol.47 , Issue.2 , pp. 676-681
    • Blackburn, A.S.1    Avery, S.V.2
  • 5
    • 84930009075 scopus 로고    scopus 로고
    • Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity
    • Kachroo, A. H.; Laurent, J. M.; Yellman, C. M.; Meyer, A. G.; Wilke, C. O.; Marcotte, E. M. Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity Science 2015, 348 (6237) 921-5 10.1126/science.aaa0769
    • (2015) Science , vol.348 , Issue.6237 , pp. 921-925
    • Kachroo, A.H.1    Laurent, J.M.2    Yellman, C.M.3    Meyer, A.G.4    Wilke, C.O.5    Marcotte, E.M.6
  • 6
    • 84921362937 scopus 로고    scopus 로고
    • A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin
    • Paulo, J. A.; Gygi, S. P. A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin Proteomics 2015, 15 (2-3) 474-86 10.1002/pmic.201400155
    • (2015) Proteomics , vol.15 , Issue.2-3 , pp. 474-486
    • Paulo, J.A.1    Gygi, S.P.2
  • 7
    • 84940529199 scopus 로고    scopus 로고
    • Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae
    • Murphy, J. P.; Stepanova, E.; Everley, R. A.; Paulo, J. A.; Gygi, S. P. Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae Mol. Cell. Proteomics 2015, 14, 2454-65 10.1074/mcp.M114.045849
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 2454-2465
    • Murphy, J.P.1    Stepanova, E.2    Everley, R.A.3    Paulo, J.A.4    Gygi, S.P.5
  • 8
    • 80155205237 scopus 로고    scopus 로고
    • Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging
    • Wenger, C. D.; Lee, M. V.; Hebert, A. S.; McAlister, G. C.; Phanstiel, D. H.; Westphall, M. S.; Coon, J. J. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging Nat. Methods 2011, 8 (11) 933-5 10.1038/nmeth.1716
    • (2011) Nat. Methods , vol.8 , Issue.11 , pp. 933-935
    • Wenger, C.D.1    Lee, M.V.2    Hebert, A.S.3    McAlister, G.C.4    Phanstiel, D.H.5    Westphall, M.S.6    Coon, J.J.7
  • 10
    • 80155124832 scopus 로고    scopus 로고
    • MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
    • Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics Nat. Methods 2011, 8 (11) 937-40 10.1038/nmeth.1714
    • (2011) Nat. Methods , vol.8 , Issue.11 , pp. 937-940
    • Ting, L.1    Rad, R.2    Gygi, S.P.3    Haas, W.4
  • 11
    • 84904325891 scopus 로고    scopus 로고
    • MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes
    • McAlister, G. C.; Nusinow, D. P.; Jedrychowski, M. P.; Wuhr, M.; Huttlin, E. L.; Erickson, B. K.; Rad, R.; Haas, W.; Gygi, S. P. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes Anal. Chem. 2014, 86 (14) 7150-8 10.1021/ac502040v
    • (2014) Anal. Chem. , vol.86 , Issue.14 , pp. 7150-7158
    • McAlister, G.C.1    Nusinow, D.P.2    Jedrychowski, M.P.3    Wuhr, M.4    Huttlin, E.L.5    Erickson, B.K.6    Rad, R.7    Haas, W.8    Gygi, S.P.9
  • 12
    • 84867176120 scopus 로고    scopus 로고
    • The ubiquitin-proteasome system of Saccharomyces cerevisiae
    • Finley, D.; Ulrich, H. D.; Sommer, T.; Kaiser, P. The ubiquitin-proteasome system of Saccharomyces cerevisiae Genetics 2012, 192 (2) 319-60 10.1534/genetics.112.140467
    • (2012) Genetics , vol.192 , Issue.2 , pp. 319-360
    • Finley, D.1    Ulrich, H.D.2    Sommer, T.3    Kaiser, P.4
  • 13
    • 68049084674 scopus 로고    scopus 로고
    • Breaking the chains: Structure and function of the deubiquitinases
    • Komander, D.; Clague, M. J.; Urbe, S. Breaking the chains: structure and function of the deubiquitinases Nat. Rev. Mol. Cell Biol. 2009, 10 (8) 550-63 10.1038/nrm2731
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , Issue.8 , pp. 550-563
    • Komander, D.1    Clague, M.J.2    Urbe, S.3
  • 14
    • 84864222562 scopus 로고    scopus 로고
    • Atypical ubiquitylation - The unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages
    • Kulathu, Y.; Komander, D. Atypical ubiquitylation-the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages Nat. Rev. Mol. Cell Biol. 2012, 13 (8) 508-23 10.1038/nrm3394
    • (2012) Nat. Rev. Mol. Cell Biol. , vol.13 , Issue.8 , pp. 508-523
    • Kulathu, Y.1    Komander, D.2
  • 15
    • 0025978949 scopus 로고
    • Getting started with yeast
    • Sherman, F. Getting started with yeast Methods Enzymol. 1991, 194, 3-21 10.1016/0076-6879(91)94004-V
    • (1991) Methods Enzymol. , vol.194 , pp. 3-21
    • Sherman, F.1
  • 16
    • 0037317228 scopus 로고    scopus 로고
    • Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
    • Rappsilber, J.; Ishihama, Y.; Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics Anal. Chem. 2003, 75 (3) 663-70 10.1021/ac026117i
    • (2003) Anal. Chem. , vol.75 , Issue.3 , pp. 663-670
    • Rappsilber, J.1    Ishihama, Y.2    Mann, M.3
  • 18
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization Nat. Biotechnol. 2006, 24 (10) 1285-92 10.1038/nbt1240
    • (2006) Nat. Biotechnol. , vol.24 , Issue.10 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 19
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-14 10.1038/nmeth1019
    • (2007) Nat. Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 22
    • 0035940479 scopus 로고    scopus 로고
    • Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response
    • 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. 2001, 98, 12578-83 10.1073/pnas.211195798
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 12578-12583
    • Carroll, A.S.1    Bishop, A.C.2    DeRisi, J.L.3    Shokat, K.M.4    O'Shea, E.K.5
  • 23
    • 0033783007 scopus 로고    scopus 로고
    • Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae
    • Amerik, A. Y.; Li, S. J.; Hochstrasser, M. Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae Biol. Chem. 2000, 381 (9-10) 981-92 10.1515/BC.2000.121
    • (2000) Biol. Chem. , vol.381 , Issue.9-10 , pp. 981-992
    • Amerik, A.Y.1    Li, S.J.2    Hochstrasser, M.3
  • 25
    • 0036733722 scopus 로고    scopus 로고
    • Treasures and traps in genome-wide data sets: Case examples from yeast
    • Grunenfelder, B.; Winzeler, E. A. Treasures and traps in genome-wide data sets: case examples from yeast Nat. Rev. Genet. 2002, 3 (9) 653-61 10.1038/nrg886
    • (2002) Nat. Rev. Genet. , vol.3 , Issue.9 , pp. 653-661
    • Grunenfelder, B.1    Winzeler, E.A.2
  • 30
    • 79955470830 scopus 로고    scopus 로고
    • Trimming of ubiquitin chains by proteasome-associated deubiquitinating enzymes
    • Lee, M. J.; Lee, B. H.; Hanna, J.; King, R. W.; Finley, D. Trimming of ubiquitin chains by proteasome-associated deubiquitinating enzymes Mol. Cell. Proteomics 2011, 10 (5) R110.003871 10.1074/mcp.R110.003871
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.5 , pp. R110003871
    • Lee, M.J.1    Lee, B.H.2    Hanna, J.3    King, R.W.4    Finley, D.5
  • 31
    • 33845314756 scopus 로고    scopus 로고
    • A conserved late endosome-targeting signal required for Doa4 deubiquitylating enzyme function
    • Amerik, A.; Sindhi, N.; Hochstrasser, M. A conserved late endosome-targeting signal required for Doa4 deubiquitylating enzyme function J. Cell Biol. 2006, 175 (5) 825-35 10.1083/jcb.200605134
    • (2006) J. Cell Biol. , vol.175 , Issue.5 , pp. 825-835
    • Amerik, A.1    Sindhi, N.2    Hochstrasser, M.3
  • 32
    • 84895538371 scopus 로고    scopus 로고
    • Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells
    • Kulak, N. A.; Pichler, G.; Paron, I.; Nagaraj, N.; Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells Nat. Methods 2014, 11 (3) 319-24 10.1038/nmeth.2834
    • (2014) Nat. Methods , vol.11 , Issue.3 , pp. 319-324
    • Kulak, N.A.1    Pichler, G.2    Paron, I.3    Nagaraj, N.4    Mann, M.5
  • 33
    • 84924614087 scopus 로고    scopus 로고
    • Synthetic quantitative array technology identifies the Ubp3-Bre5 deubiquitinase complex as a negative regulator of mitophagy
    • Muller, M.; Kotter, P.; Behrendt, C.; Walter, E.; Scheckhuber, C. Q.; Entian, K. D.; Reichert, A. S. Synthetic quantitative array technology identifies the Ubp3-Bre5 deubiquitinase complex as a negative regulator of mitophagy Cell Rep. 2015, 10 (7) 1215-25 10.1016/j.celrep.2015.01.044
    • (2015) Cell Rep. , vol.10 , Issue.7 , pp. 1215-1225
    • Muller, M.1    Kotter, P.2    Behrendt, C.3    Walter, E.4    Scheckhuber, C.Q.5    Entian, K.D.6    Reichert, A.S.7
  • 34
    • 0033786796 scopus 로고    scopus 로고
    • The Doa4 deubiquitinating enzyme is functionally linked to the vacuolar protein-sorting and endocytic pathways
    • Amerik, A. Y.; Nowak, J.; Swaminathan, S.; Hochstrasser, M. The Doa4 deubiquitinating enzyme is functionally linked to the vacuolar protein-sorting and endocytic pathways Molecular biology of the cell 2000, 11 (10) 3365-80 10.1091/mbc.11.10.3365
    • (2000) Molecular Biology of the Cell , vol.11 , Issue.10 , pp. 3365-3380
    • Amerik, A.Y.1    Nowak, J.2    Swaminathan, S.3    Hochstrasser, M.4
  • 36
    • 84894067659 scopus 로고    scopus 로고
    • Fine-tuning of DNA damage-dependent ubiquitination by OTUB2 supports the DNA repair pathway choice
    • Kato, K.; Nakajima, K.; Ui, A.; Muto-Terao, Y.; Ogiwara, H.; Nakada, S. Fine-tuning of DNA damage-dependent ubiquitination by OTUB2 supports the DNA repair pathway choice Mol. Cell 2014, 53 (4) 617-30 10.1016/j.molcel.2014.01.030
    • (2014) Mol. Cell , vol.53 , Issue.4 , pp. 617-630
    • Kato, K.1    Nakajima, K.2    Ui, A.3    Muto-Terao, Y.4    Ogiwara, H.5    Nakada, S.6
  • 37
    • 79951975935 scopus 로고    scopus 로고
    • The mitochondrial respiratory chain
    • Rich, P. R.; Marechal, A. The mitochondrial respiratory chain Essays Biochem. 2010, 47, 1-23 10.1042/bse0470001
    • (2010) Essays Biochem. , vol.47 , pp. 1-23
    • Rich, P.R.1    Marechal, A.2
  • 38
    • 84860697026 scopus 로고    scopus 로고
    • Biogenesis and assembly of eukaryotic cytochrome c oxidase catalytic core
    • Soto, I. C.; Fontanesi, F.; Liu, J.; Barrientos, A. Biogenesis and assembly of eukaryotic cytochrome c oxidase catalytic core Biochim. Biophys. Acta, Bioenerg. 2012, 1817 (6) 883-97 10.1016/j.bbabio.2011.09.005
    • (2012) Biochim. Biophys. Acta, Bioenerg. , vol.1817 , Issue.6 , pp. 883-897
    • Soto, I.C.1    Fontanesi, F.2    Liu, J.3    Barrientos, A.4
  • 39
    • 84876379604 scopus 로고    scopus 로고
    • Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast
    • McIsaac, R. S.; Oakes, B. L.; Wang, X.; Dummit, K. A.; Botstein, D.; Noyes, M. B. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast Nucleic Acids Res. 2013, 41 (4) e57 10.1093/nar/gks1313
    • (2013) Nucleic Acids Res. , vol.41 , Issue.4 , pp. e57
    • McIsaac, R.S.1    Oakes, B.L.2    Wang, X.3    Dummit, K.A.4    Botstein, D.5    Noyes, M.B.6
  • 40
    • 0022507007 scopus 로고
    • Redox balances in the metabolism of sugars by yeasts
    • van Dijken, J. P.; Scheffers, W. A. Redox balances in the metabolism of sugars by yeasts FEMS Microbiol. Lett. 1986, 32 (3-4) 199-224 10.1016/0378-1097(86)90291-0
    • (1986) FEMS Microbiol. Lett. , vol.32 , Issue.3-4 , pp. 199-224
    • Van Dijken, J.P.1    Scheffers, W.A.2
  • 41
    • 84859881869 scopus 로고    scopus 로고
    • Identification and characterization of genes related to the production of organic acids in yeast
    • Yoshida, S.; Yokoyama, A. Identification and characterization of genes related to the production of organic acids in yeast J. Biosci. Bioeng. 2012, 113 (5) 556-61 10.1016/j.jbiosc.2011.12.017
    • (2012) J. Biosci. Bioeng. , vol.113 , Issue.5 , pp. 556-561
    • Yoshida, S.1    Yokoyama, A.2
  • 42
    • 0035692234 scopus 로고    scopus 로고
    • Phosphate transport and sensing in Saccharomyces cerevisiae
    • Wykoff, D. D.; O'Shea, E. K. Phosphate transport and sensing in Saccharomyces cerevisiae Genetics 2001, 159 (4) 1491-9
    • (2001) Genetics , vol.159 , Issue.4 , pp. 1491-1499
    • Wykoff, D.D.1    O'Shea, E.K.2
  • 43
    • 0030272212 scopus 로고    scopus 로고
    • Signaling phosphate starvation
    • Lenburg, M. E.; O'Shea, E. K. Signaling phosphate starvation Trends Biochem. Sci. 1996, 21 (10) 383-7 10.1016/0968-0004(96)10048-7
    • (1996) Trends Biochem. Sci. , vol.21 , Issue.10 , pp. 383-387
    • Lenburg, M.E.1    O'Shea, E.K.2
  • 44
    • 18844442599 scopus 로고    scopus 로고
    • A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation
    • Huang, S.; O'Shea, E. K. A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation Genetics 2005, 169 (4) 1859-71 10.1534/genetics.104.038695
    • (2005) Genetics , vol.169 , Issue.4 , pp. 1859-1871
    • Huang, S.1    O'Shea, E.K.2
  • 45
    • 0028052088 scopus 로고
    • Phosphate-regulated inactivation of the kinase PHO80-PHO85 by the CDK inhibitor PHO81
    • Schneider, K. R.; Smith, R. L.; O'Shea, E. K. Phosphate-regulated inactivation of the kinase PHO80-PHO85 by the CDK inhibitor PHO81 Science 1994, 266 (5182) 122-6 10.1126/science.7939631
    • (1994) Science , vol.266 , Issue.5182 , pp. 122-126
    • Schneider, K.R.1    Smith, R.L.2    O'Shea, E.K.3
  • 46
    • 0030059223 scopus 로고    scopus 로고
    • Regulation of PHO4 nuclear localization by the PHO80-PHO85 cyclin-CDK complex
    • O'Neill, E. M.; Kaffman, A.; Jolly, E. R.; O'Shea, E. K. Regulation of PHO4 nuclear localization by the PHO80-PHO85 cyclin-CDK complex Science 1996, 271 (5246) 209-12 10.1126/science.271.5246.209
    • (1996) Science , vol.271 , Issue.5246 , pp. 209-212
    • O'Neill, E.M.1    Kaffman, A.2    Jolly, E.R.3    O'Shea, E.K.4
  • 47
    • 0035940479 scopus 로고    scopus 로고
    • Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response
    • 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. 2001, 98 (22) 12578-83 10.1073/pnas.211195798
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , Issue.22 , pp. 12578-12583
    • Carroll, A.S.1    Bishop, A.C.2    DeRisi, J.L.3    Shokat, K.M.4    O'Shea, E.K.5
  • 48
    • 34748916981 scopus 로고    scopus 로고
    • Quantitative mass spectrometry in proteomics: A critical review
    • Bantscheff, M.; Schirle, M.; Sweetman, G.; Rick, J.; Kuster, B. Quantitative mass spectrometry in proteomics: a critical review Anal. Bioanal. Chem. 2007, 389 (4) 1017-31 10.1007/s00216-007-1486-6
    • (2007) Anal. Bioanal. Chem. , vol.389 , Issue.4 , pp. 1017-1031
    • Bantscheff, M.1    Schirle, M.2    Sweetman, G.3    Rick, J.4    Kuster, B.5


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