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Volumn 6, Issue , 2012, Pages

Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

Author keywords

Cooperativity; Correlomics; Evolutionary constraint; Phenotypic plasticity; Protein protein interaction networks; Stochastic gene expression

Indexed keywords

SACCHAROMYCES CEREVISIAE;

EID: 84866714615     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-128     Document Type: Article
Times cited : (18)

References (59)
  • 1
    • 16644373292 scopus 로고    scopus 로고
    • Noise Minimization in Eukaryotic Gene Expression
    • 10.1371/journal.pbio.0020137, 400249, 15124029
    • Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. Noise Minimization in Eukaryotic Gene Expression. PLoS Biol 2004, 2:e137. 10.1371/journal.pbio.0020137, 400249, 15124029.
    • (2004) PLoS Biol , vol.2
    • Fraser, H.B.1    Hirsh, A.E.2    Giaever, G.3    Kumm, J.4    Eisen, M.B.5
  • 2
    • 42949131308 scopus 로고    scopus 로고
    • Selection to minimise noise in living systems and its implications for the evolution of gene expression
    • 4.
    • Lehner B. Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 2008, 4..
    • (2008) Mol Syst Biol
    • Lehner, B.1
  • 3
    • 77953797905 scopus 로고    scopus 로고
    • Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise
    • Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z. Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. P Natl Acad Sci USA 2010, 107:10472-10477.
    • (2010) P Natl Acad Sci USA , vol.107 , pp. 10472-10477
    • Li, J.1    Min, R.2    Vizeacoumar, F.J.3    Jin, K.4    Xin, X.5    Zhang, Z.6
  • 5
    • 83055182119 scopus 로고    scopus 로고
    • Categorizing biases in high-confidence high-throughput protein-protein interaction data sets
    • 10.1074/mcp.M111.012500, 3237088, 21876202
    • Yu X, Ivanic J, Memisević V, Wallqvist A, Reifman J. Categorizing biases in high-confidence high-throughput protein-protein interaction data sets. Mol Cell Proteomics 2011, 10:M111.012500. 10.1074/mcp.M111.012500, 3237088, 21876202.
    • (2011) Mol Cell Proteomics , vol.10
    • Yu, X.1    Ivanic, J.2    Memisević, V.3    Wallqvist, A.4    Reifman, J.5
  • 6
    • 33845262280 scopus 로고    scopus 로고
    • The effects of incomplete protein interaction data on structural and evolutionary inferences
    • 10.1186/1741-7007-4-39, 1665463, 17081312
    • de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, Wiuf C, Stumpf MPH. The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biol 2006, 4:39. 10.1186/1741-7007-4-39, 1665463, 17081312.
    • (2006) BMC Biol , vol.4 , pp. 39
    • de Silva, E.1    Thorne, T.2    Ingram, P.3    Agrafioti, I.4    Swire, J.5    Wiuf, C.6    Stumpf, M.P.H.7
  • 7
    • 84856252733 scopus 로고    scopus 로고
    • Assessing coverage of protein interaction data using capture-recapture models
    • 10.1007/s11538-011-9680-2, 21870201
    • Kelly WP, Stumpf MPH. Assessing coverage of protein interaction data using capture-recapture models. Bull Math Biol 2012, 74:356-374. 10.1007/s11538-011-9680-2, 21870201.
    • (2012) Bull Math Biol , vol.74 , pp. 356-374
    • Kelly, W.P.1    Stumpf, M.P.H.2
  • 9
    • 49449110197 scopus 로고    scopus 로고
    • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    • 2538908, 18682700
    • Zhang J, Maslov S, Shakhnovich EI. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 2008, 4:210. 2538908, 18682700.
    • (2008) Mol Syst Biol , vol.4 , pp. 210
    • Zhang, J.1    Maslov, S.2    Shakhnovich, E.I.3
  • 10
    • 31044448435 scopus 로고    scopus 로고
    • A simple physical model for scaling in protein-protein interaction networks
    • Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks. P Natl Acad Sci USA 2006, 103:311-316.
    • (2006) P Natl Acad Sci USA , vol.103 , pp. 311-316
    • Deeds, E.J.1    Ashenberg, O.2    Shakhnovich, E.I.3
  • 11
    • 78649708844 scopus 로고    scopus 로고
    • Conflict between Noise and Plasticity in Yeast
    • 10.1371/journal.pgen.1001185, 2973811, 21079670
    • Lehner B. Conflict between Noise and Plasticity in Yeast. PLoS Genet 2010, 6:e1001185. 10.1371/journal.pgen.1001185, 2973811, 21079670.
    • (2010) PLoS Genet , vol.6
    • Lehner, B.1
  • 12
    • 79551475667 scopus 로고    scopus 로고
    • Gene expression variations are predictive for stochastic noise
    • 3025572, 20860999
    • Dong D, Shao X, Deng N, Zhang Z. Gene expression variations are predictive for stochastic noise. Nucleic Acids Res 2010, 39:403-413. 3025572, 20860999.
    • (2010) Nucleic Acids Res , vol.39 , pp. 403-413
    • Dong, D.1    Shao, X.2    Deng, N.3    Zhang, Z.4
  • 13
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    • 10.1038/nature04785, 16699522
    • Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846. 10.1038/nature04785, 16699522.
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.S.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4    Noble, M.5    DeRisi, J.L.6    Weissman, J.S.7
  • 14
    • 34547519199 scopus 로고    scopus 로고
    • Evolution of chromosome organization driven by selection for reduced gene expression noise
    • 10.1038/ng2071, 17660811
    • Batada NN, Hurst LD. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 2007, 39:945-949. 10.1038/ng2071, 17660811.
    • (2007) Nat Genet , vol.39 , pp. 945-949
    • Batada, N.N.1    Hurst, L.D.2
  • 15
    • 74549187509 scopus 로고    scopus 로고
    • Promoter architecture and the evolvability of gene expression
    • 10.1186/jbiol204, 2804285, 20017897
    • Tirosh I, Barkai N, Verstrepen KJ. Promoter architecture and the evolvability of gene expression. J Biol 2009, 8:95. 10.1186/jbiol204, 2804285, 20017897.
    • (2009) J Biol , vol.8 , pp. 95
    • Tirosh, I.1    Barkai, N.2    Verstrepen, K.J.3
  • 16
    • 63449105244 scopus 로고    scopus 로고
    • Intrinsic variability of gene expression encoded in nucleosome positioning sequences
    • 10.1038/ng.319, 19252489
    • Choi JK, Kim Y-J. Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 2009, 41:498-503. 10.1038/ng.319, 19252489.
    • (2009) Nat Genet , vol.41 , pp. 498-503
    • Choi, J.K.1    Kim, Y.-J.2
  • 17
    • 34250785284 scopus 로고    scopus 로고
    • Genetic Properties Influencing the Evolvability of Gene Expression
    • 10.1126/science.1140247, 17525304
    • Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. Genetic Properties Influencing the Evolvability of Gene Expression. Science 2007, 317:118-121. 10.1126/science.1140247, 17525304.
    • (2007) Science , vol.317 , pp. 118-121
    • Landry, C.R.1    Lemos, B.2    Rifkin, S.A.3    Dickinson, W.J.4    Hartl, D.L.5
  • 18
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • 10.1038/ng1819, 16783381
    • Tirosh I, Weinberger A, Carmi M, Barkai N. A genetic signature of interspecies variations in gene expression. Nat Genet 2006, 38:830-834. 10.1038/ng1819, 16783381.
    • (2006) Nat Genet , vol.38 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 19
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • 10.1101/gr.076059.108, 2493397, 18448704
    • Tirosh I, Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res 2008, 18:1084-1091. 10.1101/gr.076059.108, 2493397, 18448704.
    • (2008) Genome Res , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 20
    • 48249103910 scopus 로고    scopus 로고
    • The effects of protein interactions, gene essentiality and regulatory regions on expression variation
    • 10.1186/1752-0509-2-54, 2474594, 18582382
    • Zhou L, Ma X, Sun F. The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst Biol 2008, 2:54. 10.1186/1752-0509-2-54, 2474594, 18582382.
    • (2008) BMC Syst Biol , vol.2 , pp. 54
    • Zhou, L.1    Ma, X.2    Sun, F.3
  • 21
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • 10.1038/nrg2484, 2949280, 19015660
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 22
    • 67149141471 scopus 로고    scopus 로고
    • Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection
    • 10.1371/journal.pone.0005815, 2686099, 19503833
    • Ivanic J, Yu X, Wallqvist A, Reifman J. Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection. PLoS One 2009, 4:e5815. 10.1371/journal.pone.0005815, 2686099, 19503833.
    • (2009) PLoS One , vol.4
    • Ivanic, J.1    Yu, X.2    Wallqvist, A.3    Reifman, J.4
  • 23
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
    • 10.1016/j.cell.2008.05.042, 2696314, 18662548
    • Drummond DA, Wilke CO. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution. Cell 2008, 134:341-352. 10.1016/j.cell.2008.05.042, 2696314, 18662548.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 24
    • 79952744659 scopus 로고    scopus 로고
    • Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
    • Heo M, Maslov S, Shakhnovich E. Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. P Natl Acad Sci USA 2011, 108:4258-4263.
    • (2011) P Natl Acad Sci USA , vol.108 , pp. 4258-4263
    • Heo, M.1    Maslov, S.2    Shakhnovich, E.3
  • 25
    • 21244464335 scopus 로고    scopus 로고
    • Binding properties and evolution of homodimers in protein-protein interaction networks
    • 10.1093/nar/gki678, 1160523, 15983135
    • Ispolatov I, Yuryev A, Maslov S. Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res 2005, 33:3629-3635. 10.1093/nar/gki678, 1160523, 15983135.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3629-3635
    • Ispolatov, I.1    Yuryev, A.2    Maslov, S.3
  • 27
    • 84859473329 scopus 로고    scopus 로고
    • PNAS Plus: Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
    • Yang J-R, Liao B-Y, Zhuang S-M, Zhang J. PNAS Plus: Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. P Natl Acad Sci USA 2012, 109:E831-E840.
    • (2012) P Natl Acad Sci USA , vol.109
    • Yang, J.-R.1    Liao, B.-Y.2    Zhuang, S.-M.3    Zhang, J.4
  • 28
    • 67649635978 scopus 로고    scopus 로고
    • Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity
    • 10.1016/j.cell.2009.04.029, 19596244
    • Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity. Cell 2009, 138:198-208. 10.1016/j.cell.2009.04.029, 19596244.
    • (2009) Cell , vol.138 , pp. 198-208
    • Vavouri, T.1    Semple, J.I.2    Garcia-Verdugo, R.3    Lehner, B.4
  • 29
    • 56649114559 scopus 로고    scopus 로고
    • Genetic noise control via protein oligomerization
    • 10.1186/1752-0509-2-94, 2584638, 18980697
    • Ghim C-M, Almaas E. Genetic noise control via protein oligomerization. BMC Syst Biol 2008, 2:94. 10.1186/1752-0509-2-94, 2584638, 18980697.
    • (2008) BMC Syst Biol , vol.2 , pp. 94
    • Ghim, C.-M.1    Almaas, E.2
  • 30
    • 0037217334 scopus 로고    scopus 로고
    • The Role of Dimerization in Noise Reduction of Simple Genetic Networks
    • 10.1006/jtbi.2003.3164, 12468297
    • Bundschuh R, Hayot F, Jayaprakash C. The Role of Dimerization in Noise Reduction of Simple Genetic Networks. J Theor Biol 2003, 220:261-269. 10.1006/jtbi.2003.3164, 12468297.
    • (2003) J Theor Biol , vol.220 , pp. 261-269
    • Bundschuh, R.1    Hayot, F.2    Jayaprakash, C.3
  • 31
    • 35348813628 scopus 로고    scopus 로고
    • Propagation of large concentration changes in reversible protein-binding networks
    • Maslov S, Ispolatov I. Propagation of large concentration changes in reversible protein-binding networks. P Natl Acad Sci USA 2007, 104:13655-13660.
    • (2007) P Natl Acad Sci USA , vol.104 , pp. 13655-13660
    • Maslov, S.1    Ispolatov, I.2
  • 32
    • 0030445778 scopus 로고    scopus 로고
    • Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs
    • 10.1016/S0968-0004(96)20026-X, 9009826
    • Ferrell JE. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 1996, 21:460-466. 10.1016/S0968-0004(96)20026-X, 9009826.
    • (1996) Trends Biochem Sci , vol.21 , pp. 460-466
    • Ferrell, J.E.1
  • 33
    • 68949203710 scopus 로고    scopus 로고
    • Q&A: Cooperativity
    • 10.1186/jbiol157, 2737376, 19589184
    • Ferrell JE. Q&A: Cooperativity. J Biol 2009, 8:53. 10.1186/jbiol157, 2737376, 19589184.
    • (2009) J Biol , vol.8 , pp. 53
    • Ferrell, J.E.1
  • 34
    • 69449106377 scopus 로고    scopus 로고
    • Robustness: mechanisms and consequences
    • 10.1016/j.tig.2009.07.005, 2770586, 19717203
    • Masel J, Siegal ML. Robustness: mechanisms and consequences. Trends Genet 2009, 25:395-403. 10.1016/j.tig.2009.07.005, 2770586, 19717203.
    • (2009) Trends Genet , vol.25 , pp. 395-403
    • Masel, J.1    Siegal, M.L.2
  • 35
    • 43849088207 scopus 로고    scopus 로고
    • Choose your partners: dimerization in eukaryotic transcription factors
    • 10.1016/j.tibs.2008.02.002, 18406148
    • Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem Sci 2008, 33:220-229. 10.1016/j.tibs.2008.02.002, 18406148.
    • (2008) Trends Biochem Sci , vol.33 , pp. 220-229
    • Amoutzias, G.D.1    Robertson, D.L.2    Van de Peer, Y.3    Oliver, S.G.4
  • 37
    • 1542328960 scopus 로고    scopus 로고
    • Identification and Distinct Regulation of Yeast TATA Box-Containing Genes
    • 10.1016/S0092-8674(04)00205-3, 15006352
    • Basehoar AD, Zanton SJ, Pugh BF. Identification and Distinct Regulation of Yeast TATA Box-Containing Genes. Cell 2004, 116:699-709. 10.1016/S0092-8674(04)00205-3, 15006352.
    • (2004) Cell , vol.116 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 38
    • 33644875537 scopus 로고    scopus 로고
    • MIPS: analysis and annotation of proteins from whole genomes in 2005
    • 10.1093/nar/gkj148, 1347510, 16381839
    • Mewes HW. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 2006, 34:D169-D172. 10.1093/nar/gkj148, 1347510, 16381839.
    • (2006) Nucleic Acids Res , vol.34
    • Mewes, H.W.1
  • 39
    • 84871417770 scopus 로고    scopus 로고
    • SGD Expression Connection
    • SGD Expression Connection http://downloads.yeastgenome.org/expression/microarray/archive/Expression_connection_data/., SGD Expression Connection.
  • 42
    • 33746060530 scopus 로고    scopus 로고
    • Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling
    • 10.1007/s00438-006-0133-9, 16741729
    • Roberts GG, Hudson AP. Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling. Mol Genet Genomics 2006, 276:170-186. 10.1007/s00438-006-0133-9, 16741729.
    • (2006) Mol Genet Genomics , vol.276 , pp. 170-186
    • Roberts, G.G.1    Hudson, A.P.2
  • 45
    • 0033637520 scopus 로고    scopus 로고
    • New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis
    • 15074, 11102525
    • Ogawa N, DeRisi J, Brown PO. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 2000, 11:4309-4321. 15074, 11102525.
    • (2000) Mol Biol Cell , vol.11 , pp. 4309-4321
    • Ogawa, N.1    DeRisi, J.2    Brown, P.O.3
  • 47
    • 0037163129 scopus 로고    scopus 로고
    • Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae
    • 10.1074/jbc.M202718200, 12058033
    • Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem 2002, 277:31079-31088. 10.1074/jbc.M202718200, 12058033.
    • (2002) J Biol Chem , vol.277 , pp. 31079-31088
    • Yoshimoto, H.1    Saltsman, K.2    Gasch, A.P.3    Li, H.X.4    Ogawa, N.5    Botstein, D.6    Brown, P.O.7    Cyert, M.S.8
  • 49
    • 33748852396 scopus 로고    scopus 로고
    • Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae
    • 10.1128/EC.00107-06, 1563586, 16963631
    • Lai L-C, Kosorukoff AL, Burke PV, Kwast KE. Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 2006, 5:1468-1489. 10.1128/EC.00107-06, 1563586, 16963631.
    • (2006) Eukaryot Cell , vol.5 , pp. 1468-1489
    • Lai, L.-C.1    Kosorukoff, A.L.2    Burke, P.V.3    Kwast, K.E.4
  • 50
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • 10.1126/science.278.5338.680, 9381177
    • DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686. 10.1126/science.278.5338.680, 9381177.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 51
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • 25624, 9843569
    • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297. 25624, 9843569.
    • (1998) Mol Biol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1    Sherlock, G.2    Zhang, M.Q.3    Iyer, V.R.4    Anders, K.5    Eisen, M.B.6    Brown, P.O.7    Botstein, D.8    Futcher, B.9
  • 57
    • 9144248312 scopus 로고    scopus 로고
    • IntAct: an open source molecular interaction database
    • Hermjakob H. IntAct: an open source molecular interaction database. Nucleic Acids Res 2004, 32:452D-455.
    • (2004) Nucleic Acids Res , vol.32
    • Hermjakob, H.1


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