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Volumn 13, Issue 5, 2014, Pages 2370-2380

Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains

Author keywords

proteomics; Pseudomonas aeruginosa; Transcriptomics

Indexed keywords

CHLORAMPHENICOL; MESSENGER RNA; PA 14 PROTEIN; PAO 1 PROTEIN; PROTEIN; PROTEOME; TRANSCRIPTOME; UNCLASSIFIED DRUG; BACTERIAL PROTEIN;

EID: 84899855470     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4011684     Document Type: Article
Times cited : (19)

References (53)
  • 5
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu, P.; Vogel, C.; Wang, R.; Yao, X.; Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat. Biotechnol. 2007, 25, 117-124
    • (2007) Nat. Biotechnol. , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 6
    • 28444475607 scopus 로고    scopus 로고
    • Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations
    • 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, 603-610
    • (2006) Biochem. Biophys. Res. Commun. , vol.339 , pp. 603-610
    • Nie, L.1    Wu, G.2    Zhang, W.3
  • 7
    • 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
    • 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, 2229-2243
    • (2006) Genetics , vol.174 , pp. 2229-2243
    • Nie, L.1    Wu, G.2    Zhang, W.3
  • 9
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel, C.; Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses Nat. Rev. Genet. 2012, 13, 227-232
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 11
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E coli proteome and transcriptome with single-molecule sensitivity in single cells
    • Taniguchi, Y.; Choi, P. J.; Li, G.-W. W.; Chen, H.; Babu, M.; Hearn, J.; Emili, A.; Xie, X. S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 2010, 329, 533-538
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.-W.W.3    Chen, H.4    Babu, M.5    Hearn, J.6    Emili, A.7    Xie, X.S.8
  • 16
    • 0033582314 scopus 로고    scopus 로고
    • Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis
    • Tan, M.-W.; Mahajan-Miklos, S.; Ausubel, F. M. Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 715-720
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 715-720
    • Tan, M.-W.1    Mahajan-Miklos, S.2    Ausubel, F.M.3
  • 17
    • 36549035760 scopus 로고    scopus 로고
    • Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum
    • Palmer, K. L.; Aye, L. M.; Whiteley, M. Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum J. Bacteriol. 2007, 189, 8079-8087
    • (2007) J. Bacteriol. , vol.189 , pp. 8079-8087
    • Palmer, K.L.1    Aye, L.M.2    Whiteley, M.3
  • 18
    • 78751522378 scopus 로고    scopus 로고
    • Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo
    • Huse, H. K.; Kwon, T.; Zlosnik, J. E. A.; Speert, D. P.; Marcotte, E. M.; Whiteley, M. Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo mBio 2010, 1, e00199-1-e00199-10
    • (2010) MBio , vol.1
    • Huse, H.K.1    Kwon, T.2    Zlosnik, J.E.A.3    Speert, D.P.4    Marcotte, E.M.5    Whiteley, M.6
  • 19
    • 1342288026 scopus 로고    scopus 로고
    • Affy-analysis of Affymetrix GeneChip data at the probe level
    • Gautier, L.; Cope, L.; Bolstad, B. M.; Irizarry, R. A. Affy-analysis of Affymetrix GeneChip data at the probe level Bioinformatics 2004, 20, 307-315
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 22
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater, G. S. C.; Birney, E. Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005, 6, 31-1-31-11
    • (2005) BMC Bioinformatics , vol.6 , pp. 311-3111
    • Slater, G.S.C.1    Birney, E.2
  • 24
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth, G. K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 2004, 3, Article3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3 , pp. 3
    • Smyth, G.K.1
  • 25
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 26
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392
    • (2002) Anal. Chem. , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 27
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • Keller, A.; Eng, J.; Zhang, N.; Li, X.-J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol. Syst. Biol. 2005, 1, 2005.0017-1-2005.0017-8
    • (2005) Mol. Syst. Biol. , vol.1 , pp. 200500171-200500178
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.-J.4    Aebersold, R.5
  • 28
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S.; Shu, H.; Frank, A.; Wang, L.-C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra Anal. Chem. 2005, 77, 4626-4639
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 30
    • 79959942025 scopus 로고    scopus 로고
    • MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines
    • Kwon, T.; Choi, H.; Vogel, C.; Nesvizhskii, A. I.; Marcotte, E. M. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines J. Proteome Res. 2011, 10, 2949-2958
    • (2011) J. Proteome Res. , vol.10 , pp. 2949-2958
    • Kwon, T.1    Choi, H.2    Vogel, C.3    Nesvizhskii, A.I.4    Marcotte, E.M.5
  • 31
    • 51649124498 scopus 로고    scopus 로고
    • Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
    • Vogel, C.; Marcotte, E. M. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data Nat. Protoc. 2008, 3, 1444-1451
    • (2008) Nat. Protoc. , vol.3 , pp. 1444-1451
    • Vogel, C.1    Marcotte, E.M.2
  • 32
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003, 75, 4646-4658
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 34
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics
    • Choi, H.; Fermin, D.; Nesvizhskii, A. I. Significance analysis of spectral count data in label-free shotgun proteomics Mol. Cell. Proteomics 2008, 7, 2373-2385
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 2373-2385
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 35
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26, 1367-1372
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 36
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm, M.; Storm, C. E.; Sonnhammer, E. L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol. 2001, 314, 1041-1052
    • (2001) J. Mol. Biol. , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 37
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybriziation
    • Markham, N. R.; Zuker, M. UNAFold: Software for nucleic acid folding and hybriziation Methods Mol. Biol. 2008, 453, 3-31
    • (2008) Methods Mol. Biol. , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 39
    • 78751684152 scopus 로고    scopus 로고
    • MexEF-oprN multidrug efflux operon of Pseudomonas aeruginosa: Regulation by the MexT activator in response to nitrosative stress and chloramphenicol
    • Fetar, H.; Gilmour, C.; Klinoski, R.; Daigle, D. M.; Dean, C. R.; Poole, K. mexEF-oprN multidrug efflux operon of Pseudomonas aeruginosa: Regulation by the MexT activator in response to nitrosative stress and chloramphenicol Antimicrob. Agents Chemother. 2011, 55, 508-514
    • (2011) Antimicrob. Agents Chemother. , vol.55 , pp. 508-514
    • Fetar, H.1    Gilmour, C.2    Klinoski, R.3    Daigle, D.M.4    Dean, C.R.5    Poole, K.6
  • 40
    • 0036786891 scopus 로고    scopus 로고
    • Correlation between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
    • Ma, J.; Campbell, A.; Karlin, S. Correlation between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures J. Bacteriol. 2002, 184, 5733-5745
    • (2002) J. Bacteriol. , vol.184 , pp. 5733-5745
    • Ma, J.1    Campbell, A.2    Karlin, S.3
  • 41
    • 79959273668 scopus 로고    scopus 로고
    • Small RNAs as regulators of primary and secondary metabolism in Pseudomonas species
    • Sonnleitner, E.; Haas, D. Small RNAs as regulators of primary and secondary metabolism in Pseudomonas species Appl. Microbiol. Biotechnol. 2011, 91, 63-79
    • (2011) Appl. Microbiol. Biotechnol. , vol.91 , pp. 63-79
    • Sonnleitner, E.1    Haas, D.2
  • 42
    • 84868028972 scopus 로고    scopus 로고
    • Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
    • Marguerat, S.; Schmidt, A.; Codlin, S.; Chen, W.; Aebersold, R.; Bähler, J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells Cell 2012, 151, 671-683
    • (2012) Cell , vol.151 , pp. 671-683
    • Marguerat, S.1    Schmidt, A.2    Codlin, S.3    Chen, W.4    Aebersold, R.5    Bähler, J.6
  • 43
    • 0344131941 scopus 로고    scopus 로고
    • Characterization of MexT, the regulator of the MexE-MexF-OprN multidrug efflux system of Pseudomonas aeruginosa
    • Köhler, T.; Epp, S. F.; Curty, L. K.; Pechère, J. C. Characterization of MexT, the regulator of the MexE-MexF-OprN multidrug efflux system of Pseudomonas aeruginosa J. Bacteriol. 1999, 181, 6300-6305
    • (1999) J. Bacteriol. , vol.181 , pp. 6300-6305
    • Köhler, T.1    Epp, S.F.2    Curty, L.K.3    Pechère, J.C.4
  • 44
    • 80055040233 scopus 로고    scopus 로고
    • Evidence of MexT-independent overexpression of MexEF-OprN multidrug efflux pump of Pseudomonas aeruginosa in presence of metabolic stress
    • Kumar, A.; Schweizer, H. P. Evidence of MexT-independent overexpression of MexEF-OprN multidrug efflux pump of Pseudomonas aeruginosa in presence of metabolic stress PLoS One 2011, 6, e26520-1-e26520-8
    • (2011) PLoS One , vol.6
    • Kumar, A.1    Schweizer, H.P.2
  • 47
    • 27144555357 scopus 로고    scopus 로고
    • Regulation of translation via mRNA structure in prokaryotes and eukaryotes
    • Kozak, M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes Gene 2005, 361, 13-37
    • (2005) Gene , vol.361 , pp. 13-37
    • Kozak, M.1
  • 48
    • 34247099372 scopus 로고    scopus 로고
    • Regulatory mechanisms employed by cis-encoded antisense RNAs
    • Brantl, S. Regulatory mechanisms employed by cis-encoded antisense RNAs Curr. Opin. Microbiol. 2007, 10, 102-109
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 102-109
    • Brantl, S.1
  • 49
    • 76049120271 scopus 로고    scopus 로고
    • Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa
    • Sonnleitner, E.; Abdou, L.; Haas, D. Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 21866-21871
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 21866-21871
    • Sonnleitner, E.1    Abdou, L.2    Haas, D.3
  • 51
    • 43249087505 scopus 로고    scopus 로고
    • Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species
    • González, N.; Heeb, S.; Valverde, C.; Kay, E.; Reimmann, C.; Junier, T.; Haas, D. Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species BMC Genomics 2008, 9, 167-1-167-14
    • (2008) BMC Genomics , vol.9 , pp. 1671-16714
    • González, N.1    Heeb, S.2    Valverde, C.3    Kay, E.4    Reimmann, C.5    Junier, T.6    Haas, D.7
  • 52
    • 79960433506 scopus 로고    scopus 로고
    • Hfq and its constellation of RNA
    • Vogel, J.; Luisi, B. F. Hfq and its constellation of RNA Nat. Rev. Microbiol. 2011, 9, 578-589
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 578-589
    • Vogel, J.1    Luisi, B.F.2
  • 53
    • 33645065354 scopus 로고    scopus 로고
    • Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa
    • Sonnleitner, E.; Schuster, M.; Sorger-Domenigg, T.; Greenberg, E. P.; Bläsi, U.; Blasi, U. Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa Mol. Microbiol. 2006, 59, 1542-1558
    • (2006) Mol. Microbiol. , vol.59 , pp. 1542-1558
    • Sonnleitner, E.1    Schuster, M.2    Sorger-Domenigg, T.3    Greenberg, E.P.4    Bläsi, U.5    Blasi, U.6


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