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Volumn 5, Issue , 2011, Pages

Codon usage variability determines the correlation between proteome and transcriptome fold changes

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEOME; TRANSFER RNA;

EID: 79951944240     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-33     Document Type: Article
Times cited : (34)

References (43)
  • 1
    • 38349164135 scopus 로고    scopus 로고
    • Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae
    • 10.1111/j.1567-1364.2007.00302.x, 17727659
    • Nielsen J, Jewett MC. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 2008, 8(1):122-131. 10.1111/j.1567-1364.2007.00302.x, 17727659.
    • (2008) FEMS Yeast Res , vol.8 , Issue.1 , pp. 122-131
    • Nielsen, J.1    Jewett, M.C.2
  • 3
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • 83965, 10022859
    • Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19(3):1720-1730. 83965, 10022859.
    • (1999) Mol Cell Biol , vol.19 , Issue.3 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 4
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • 10.1038/nbt1270, 17187058
    • Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2007, 25(1):117-124. 10.1038/nbt1270, 17187058.
    • (2007) Nat Biotechnol , vol.25 , Issue.1 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 5
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • 10.1126/science.1170160, 19359587
    • Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324(5924):255-258. 10.1126/science.1170160, 19359587.
    • (2009) Science , vol.324 , Issue.5924 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 6
    • 0347132484 scopus 로고    scopus 로고
    • Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations
    • 10.1002/bit.10860, 14708123
    • Mehra A, Lee KH, Hatzimanikatis V. Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol Bioeng 2003, 84(7):822-833. 10.1002/bit.10860, 14708123.
    • (2003) Biotechnol Bioeng , vol.84 , Issue.7 , pp. 822-833
    • Mehra, A.1    Lee, K.H.2    Hatzimanikatis, V.3
  • 7
    • 34250783088 scopus 로고    scopus 로고
    • Integrative Analysis of Transcriptome and Proteomic Data: Challenges, Solutions and Applications
    • 10.1080/07388550701334212, 17578703
    • Nie L, Wu G, Culley DE, Scholten JCM, Zhang W. Integrative Analysis of Transcriptome and Proteomic Data: Challenges, Solutions and Applications. Critical Reviews in Biotechnology 2007, 27:63-75. 10.1080/07388550701334212, 17578703.
    • (2007) Critical Reviews in Biotechnology , vol.27 , pp. 63-75
    • Nie, L.1    Wu, G.2    Culley, D.E.3    Scholten, J.C.M.4    Zhang, W.5
  • 8
    • 33645775569 scopus 로고    scopus 로고
    • An algorithmic framework for genome-wide modeling and analysis of translation networks
    • 10.1529/biophysj.105.062521, 1367265, 16299083
    • Mehra A, Hatzimanikatis V. An algorithmic framework for genome-wide modeling and analysis of translation networks. Biophys J 2006, 90(4):1136-1146. 10.1529/biophysj.105.062521, 1367265, 16299083.
    • (2006) Biophys J , vol.90 , Issue.4 , pp. 1136-1146
    • Mehra, A.1    Hatzimanikatis, V.2
  • 9
    • 33846820156 scopus 로고    scopus 로고
    • A model for protein translation: polysome self-organization leads to maximum protein synthesis rates
    • 10.1529/biophysj.106.087825, 1779991, 17098800
    • Zouridis H, Hatzimanikatis V. A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. Biophys J 2007, 92(3):717-730. 10.1529/biophysj.106.087825, 1779991, 17098800.
    • (2007) Biophys J , vol.92 , Issue.3 , pp. 717-730
    • Zouridis, H.1    Hatzimanikatis, V.2
  • 10
    • 51049096159 scopus 로고    scopus 로고
    • Effects of codon distributions and tRNA competition on protein translation
    • 10.1529/biophysj.107.126128, 2479585, 18359800
    • Zouridis H, Hatzimanikatis V. Effects of codon distributions and tRNA competition on protein translation. Biophys J 2008, 95(3):1018-1033. 10.1529/biophysj.107.126128, 2479585, 18359800.
    • (2008) Biophys J , vol.95 , Issue.3 , pp. 1018-1033
    • Zouridis, H.1    Hatzimanikatis, V.2
  • 11
    • 3042782585 scopus 로고    scopus 로고
    • Codon bias and heterologous protein expression
    • 10.1016/j.tibtech.2004.04.006, 15245907
    • Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol 2004, 22(7):346-353. 10.1016/j.tibtech.2004.04.006, 15245907.
    • (2004) Trends Biotechnol , vol.22 , Issue.7 , pp. 346-353
    • Gustafsson, C.1    Govindarajan, S.2    Minshull, J.3
  • 12
    • 0023650543 scopus 로고
    • The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications
    • 10.1093/nar/15.3.1281, 340524, 3547335
    • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15(3):1281-1295. 10.1093/nar/15.3.1281, 340524, 3547335.
    • (1987) Nucleic Acids Res , vol.15 , Issue.3 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 13
    • 4644280499 scopus 로고    scopus 로고
    • Solving the riddle of codon usage preferences: a test for translational selection
    • 10.1093/nar/gkh834, 521650, 15448185
    • dos Reis M, Savva R, Wernisch L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 2004, 32(17):5036-5044. 10.1093/nar/gkh834, 521650, 15448185.
    • (2004) Nucleic Acids Res , vol.32 , Issue.17 , pp. 5036-5044
    • dos Reis, M.1    Savva, R.2    Wernisch, L.3
  • 14
    • 75349102148 scopus 로고    scopus 로고
    • Universal function-specificity of codon usage
    • 10.1093/nar/gkp792, 2790905, 19773421
    • Najafabadi HS, Goodarzi H, Salavati R. Universal function-specificity of codon usage. Nucleic Acids Res 2009, 37(21):7014-7023. 10.1093/nar/gkp792, 2790905, 19773421.
    • (2009) Nucleic Acids Res , vol.37 , Issue.21 , pp. 7014-7023
    • Najafabadi, H.S.1    Goodarzi, H.2    Salavati, R.3
  • 15
    • 37849033856 scopus 로고    scopus 로고
    • Determinants of protein abundance and translation efficiency in S. cerevisiae
    • 10.1371/journal.pcbi.0030248, 2230678, 18159940
    • Tuller T, Kupiec M, Ruppin E. Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 2007, 3(12):e248. 10.1371/journal.pcbi.0030248, 2230678, 18159940.
    • (2007) PLoS Comput Biol , vol.3 , Issue.12
    • Tuller, T.1    Kupiec, M.2    Ruppin, E.3
  • 16
    • 77649245858 scopus 로고    scopus 로고
    • Translation efficiency is determined by both codon bias and folding energy
    • 10.1073/pnas.0909910107, 2840511, 20133581
    • Tuller T, Waldman YY, Kupiec M, Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci USA 2010, 107(8):3645-3650. 10.1073/pnas.0909910107, 2840511, 20133581.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.8 , pp. 3645-3650
    • Tuller, T.1    Waldman, Y.Y.2    Kupiec, M.3    Ruppin, E.4
  • 17
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • 10.1186/gb-2003-4-9-117, 193646, 12952525
    • Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4(9):117. 10.1186/gb-2003-4-9-117, 193646, 12952525.
    • (2003) Genome Biol , vol.4 , Issue.9 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 18
    • 0037311233 scopus 로고    scopus 로고
    • Eukaryotic translation initiation factors and regulators
    • 10.1016/S0959-440X(03)00009-5, 12581660
    • Sonenberg N, Dever TE. Eukaryotic translation initiation factors and regulators. Curr Opin Struct Biol 2003, 13(1):56-63. 10.1016/S0959-440X(03)00009-5, 12581660.
    • (2003) Curr Opin Struct Biol , vol.13 , Issue.1 , pp. 56-63
    • Sonenberg, N.1    Dever, T.E.2
  • 19
    • 3943080710 scopus 로고    scopus 로고
    • The molecular mechanics of eukaryotic translation
    • 10.1146/annurev.biochem.73.030403.080419, 15189156
    • Kapp LD, Lorsch JR. The molecular mechanics of eukaryotic translation. Annu Rev Biochem 2004, 73:657-704. 10.1146/annurev.biochem.73.030403.080419, 15189156.
    • (2004) Annu Rev Biochem , vol.73 , pp. 657-704
    • Kapp, L.D.1    Lorsch, J.R.2
  • 20
    • 34948856961 scopus 로고    scopus 로고
    • Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis
    • 10.1016/j.compbiolchem.2007.07.003, 2727733, 17897886
    • Fluitt A, Pienaar E, Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 2007, 31(5-6):335-346. 10.1016/j.compbiolchem.2007.07.003, 2727733, 17897886.
    • (2007) Comput Biol Chem , vol.31 , Issue.5-6 , pp. 335-346
    • Fluitt, A.1    Pienaar, E.2    Viljoen, H.3
  • 21
    • 0033891776 scopus 로고    scopus 로고
    • Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 1, Pages 66-73 (1984)
    • 10.1002/(SICI)1097-0290(20000320)67:6<805::AID-BIT16>3.0.CO;2-0, 10699859
    • Lee SB, Bailey JE. Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 1, Pages 66-73 (1984). Biotechnol Bioeng 2000, 67(6):805-812. 10.1002/(SICI)1097-0290(20000320)67:6<805::AID-BIT16>3.0.CO;2-0, 10699859.
    • (2000) Biotechnol Bioeng , vol.67 , Issue.6 , pp. 805-812
    • Lee, S.B.1    Bailey, J.E.2
  • 22
    • 0031804382 scopus 로고    scopus 로고
    • Simulation of prokaryotic genetic circuits
    • 10.1146/annurev.biophys.27.1.199, 9646867
    • McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct 1998, 27:199-224. 10.1146/annurev.biophys.27.1.199, 9646867.
    • (1998) Annu Rev Biophys Biomol Struct , vol.27 , pp. 199-224
    • McAdams, H.H.1    Arkin, A.2
  • 23
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • 10.1073/pnas.94.3.814, 19596, 9023339
    • McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 1997, 94(3):814-819. 10.1073/pnas.94.3.814, 19596, 9023339.
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.3 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 24
    • 0344100118 scopus 로고    scopus 로고
    • A mathematical model for elongation of a peptide chain
    • 10.1016/S0092-8240(03)00076-4, 14607290
    • Heyd A, Drew DA. A mathematical model for elongation of a peptide chain. Bull Math Biol 2003, 65(6):1095-1109. 10.1016/S0092-8240(03)00076-4, 14607290.
    • (2003) Bull Math Biol , vol.65 , Issue.6 , pp. 1095-1109
    • Heyd, A.1    Drew, D.A.2
  • 25
    • 0348013051 scopus 로고    scopus 로고
    • Hierarchy of sequence-dependent features associated with prokaryotic translation
    • 10.1101/gr.1485203, 403808, 14656971
    • Lithwick G, Margalit H. Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res 2003, 13(12):2665-2673. 10.1101/gr.1485203, 403808, 14656971.
    • (2003) Genome Res , vol.13 , Issue.12 , pp. 2665-2673
    • Lithwick, G.1    Margalit, H.2
  • 27
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation
    • 10.1073/pnas.96.6.2907, 15868, 10077610
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96(6):2907-2912. 10.1073/pnas.96.6.2907, 15868, 10077610.
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 28
  • 29
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • 10.1093/bioinformatics/bti551, 15972284
    • Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 30
    • 15044352042 scopus 로고    scopus 로고
    • Analysis of Microarray Gene Expression Data
    • Springer US
    • Mei-Ling TL. Analysis of Microarray Gene Expression Data. 2004, Springer US.
    • (2004)
    • Mei-Ling, T.L.1
  • 31
    • 0036545614 scopus 로고    scopus 로고
    • Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
    • 10.1074/mcp.M200001-MCP200, 12096114
    • Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002, 1(4):323-333. 10.1074/mcp.M200001-MCP200, 12096114.
    • (2002) Mol Cell Proteomics , vol.1 , Issue.4 , pp. 323-333
    • Griffin, T.J.1    Gygi, S.P.2    Ideker, T.3    Rist, B.4    Eng, J.5    Hood, L.6    Aebersold, R.7
  • 33
    • 0037453060 scopus 로고    scopus 로고
    • Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae
    • 10.1073/pnas.0634629100, 152254, 12626741
    • Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100(6):3107-3112. 10.1073/pnas.0634629100, 152254, 12626741.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.6 , pp. 3107-3112
    • Washburn, M.P.1    Koller, A.2    Oshiro, G.3    Ulaszek, R.R.4    Plouffe, D.5    Deciu, C.6    Winzeler, E.7    Yates, J.R.8
  • 34
    • 38649098761 scopus 로고    scopus 로고
    • Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods
    • 10.1021/pr700580m, 2538956, 18173223
    • Usaite R, Wohlschlegel J, Venable JD, Park SK, Nielsen J, Olsson L, Yates JR. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res 2008, 7(1):266-275. 10.1021/pr700580m, 2538956, 18173223.
    • (2008) J Proteome Res , vol.7 , Issue.1 , pp. 266-275
    • Usaite, R.1    Wohlschlegel, J.2    Venable, J.D.3    Park, S.K.4    Nielsen, J.5    Olsson, L.6    Yates, J.R.7
  • 35
    • 73149091660 scopus 로고    scopus 로고
    • Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
    • 10.1038/msb.2009.67, 2795470, 19888214
    • Usaite R, Jewett MC, Oliveira AP, Yates JR, Olsson L, Nielsen J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Syst Biol 2009, 5:319. 10.1038/msb.2009.67, 2795470, 19888214.
    • (2009) Mol Syst Biol , vol.5 , pp. 319
    • Usaite, R.1    Jewett, M.C.2    Oliveira, A.P.3    Yates, J.R.4    Olsson, L.5    Nielsen, J.6
  • 37
    • 34047223024 scopus 로고    scopus 로고
    • Posttranscriptional expression regulation: what determines translation rates?
    • 10.1371/journal.pcbi.0030057, 1829480, 17381238
    • Brockmann R, Beyer A, Heinisch JJ, Wilhelm T. Posttranscriptional expression regulation: what determines translation rates?. PLoS Comput Biol 2007, 3(3):e57. 10.1371/journal.pcbi.0030057, 1829480, 17381238.
    • (2007) PLoS Comput Biol , vol.3 , Issue.3
    • Brockmann, R.1    Beyer, A.2    Heinisch, J.J.3    Wilhelm, T.4
  • 38
    • 28444475607 scopus 로고    scopus 로고
    • Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations
    • 10.1016/j.bbrc.2005.11.055, 16310166
    • Nie L, Wu G, Zhang W. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations. Biochem Biophys Res Commun 2006, 339(2):603-610. 10.1016/j.bbrc.2005.11.055, 16310166.
    • (2006) Biochem Biophys Res Commun , vol.339 , Issue.2 , pp. 603-610
    • Nie, L.1    Wu, G.2    Zhang, W.3
  • 39
    • 33845790070 scopus 로고    scopus 로고
    • Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis
    • 10.1534/genetics.106.065862, 1698625, 17028312
    • Nie L, Wu G, Zhang W. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 2006, 174(4):2229-2243. 10.1534/genetics.106.065862, 1698625, 17028312.
    • (2006) Genetics , vol.174 , Issue.4 , pp. 2229-2243
    • Nie, L.1    Wu, G.2    Zhang, W.3
  • 40
    • 14244266085 scopus 로고    scopus 로고
    • Relative predicted protein levels of functionally associated proteins are conserved across organisms
    • 10.1093/nar/gki261, 549420, 15718304
    • Lithwick G, Margalit H. Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res 2005, 33(3):1051-1057. 10.1093/nar/gki261, 549420, 15718304.
    • (2005) Nucleic Acids Res , vol.33 , Issue.3 , pp. 1051-1057
    • Lithwick, G.1    Margalit, H.2
  • 41
    • 70349199628 scopus 로고    scopus 로고
    • Design parameters to control synthetic gene expression in Escherichia coli
    • 10.1371/journal.pone.0007002, 2736378, 19759823
    • Welch M, Govindarajan S, Ness JE, Villalobos A, Gurney A, Minshull J, Gustafsson C. Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 2009, 4(9):e7002. 10.1371/journal.pone.0007002, 2736378, 19759823.
    • (2009) PLoS One , vol.4 , Issue.9
    • Welch, M.1    Govindarajan, S.2    Ness, J.E.3    Villalobos, A.4    Gurney, A.5    Minshull, J.6    Gustafsson, C.7
  • 42
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 43
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • 1462678, 12930740
    • Akashi H. Translational selection and yeast proteome evolution. Genetics 2003, 164(4):1291-1303. 1462678, 12930740.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1291-1303
    • Akashi, H.1


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