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

Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM - J. Proteome Res. (2014)

Bottom Line: For 703 genes observed by both shotgun proteomics and microarray experiments, we found that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains to an extent comparable to protein and mRNA abundances.In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level.Our data demonstrate that the magnitude and direction of the effect of protein abundance regulation occurring after the setting of mRNA levels is conserved between bacterial strains and is important for explaining the discordance between mRNA and protein abundances.

View Article: PubMed Central - PubMed

Affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin , 2500 Speedway, Austin, Texas 78712, United States.

ABSTRACT
Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here, we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we found that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that the magnitude and direction of the effect of protein abundance regulation occurring after the setting of mRNA levels is conserved between bacterial strains and is important for explaining the discordance between mRNA and protein abundances.

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. Differential expressionof the mexEF–oprN operonexplains differential chloramphanicol resistancein P. aeruginosa PAO1 and PA14 strains.(A) Protein expression levels of MexEF–OprN in PAO1 and PA14.Two biological replicates are plotted for each strain, as shown bythe same color bars. In PA14, we could not detect MexF or OprN, andthe protein abundance score for MexE was low (∼0.2). (B) mRNAlevels of mexEF–oprN in PAO1and PA14. Two biological replicates are plotted for each strain, asshown by the same color bars. (C) Chloramphenicol disk diffusion assay.Exponentially growing PAO1 and PA14 were swabbed on an agar plateand exposed to increasing levels of chloramphenicol. Three biologicalreplicates were performed, and a representative is shown.
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fig3: . Differential expressionof the mexEF–oprN operonexplains differential chloramphanicol resistancein P. aeruginosa PAO1 and PA14 strains.(A) Protein expression levels of MexEF–OprN in PAO1 and PA14.Two biological replicates are plotted for each strain, as shown bythe same color bars. In PA14, we could not detect MexF or OprN, andthe protein abundance score for MexE was low (∼0.2). (B) mRNAlevels of mexEF–oprN in PAO1and PA14. Two biological replicates are plotted for each strain, asshown by the same color bars. (C) Chloramphenicol disk diffusion assay.Exponentially growing PAO1 and PA14 were swabbed on an agar plateand exposed to increasing levels of chloramphenicol. Three biologicalreplicates were performed, and a representative is shown.

Mentions: Differentially expressed genesat both the protein and mRNA levelsincluded well-known virulence and antibiotic resistance genes, suchas algR and the pqs operon, andthe mexEF–oprN operon. Ithas been shown that overexpression of mexEF–oprN increases resistance to chloramphenicol.39 We therefore hypothesized that PAO1, which showshigher expression of mexEF–oprN, may exhibit higher resistance to chloramphenicol compared to PA14.To test this hypothesis, we used a disk diffusion assay to measuregrowth inhibition by chloramphenicol. As expected, the zones of inhibitionwere larger for PA14 with increasing chloramphenicol concentrations,whereas PAO1 growth was minimally inhibited by chloramphenicol (Figure 3). Additionally, genes involved in the metabolismof several amino acids were differentially expressed between PAO1and PA14 (Table 2), likely highlighting differentmetabolic characteristics of the two strains.


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

Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM - J. Proteome Res. (2014)

. Differential expressionof the mexEF–oprN operonexplains differential chloramphanicol resistancein P. aeruginosa PAO1 and PA14 strains.(A) Protein expression levels of MexEF–OprN in PAO1 and PA14.Two biological replicates are plotted for each strain, as shown bythe same color bars. In PA14, we could not detect MexF or OprN, andthe protein abundance score for MexE was low (∼0.2). (B) mRNAlevels of mexEF–oprN in PAO1and PA14. Two biological replicates are plotted for each strain, asshown by the same color bars. (C) Chloramphenicol disk diffusion assay.Exponentially growing PAO1 and PA14 were swabbed on an agar plateand exposed to increasing levels of chloramphenicol. Three biologicalreplicates were performed, and a representative is shown.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4012837&req=5

fig3: . Differential expressionof the mexEF–oprN operonexplains differential chloramphanicol resistancein P. aeruginosa PAO1 and PA14 strains.(A) Protein expression levels of MexEF–OprN in PAO1 and PA14.Two biological replicates are plotted for each strain, as shown bythe same color bars. In PA14, we could not detect MexF or OprN, andthe protein abundance score for MexE was low (∼0.2). (B) mRNAlevels of mexEF–oprN in PAO1and PA14. Two biological replicates are plotted for each strain, asshown by the same color bars. (C) Chloramphenicol disk diffusion assay.Exponentially growing PAO1 and PA14 were swabbed on an agar plateand exposed to increasing levels of chloramphenicol. Three biologicalreplicates were performed, and a representative is shown.
Mentions: Differentially expressed genesat both the protein and mRNA levelsincluded well-known virulence and antibiotic resistance genes, suchas algR and the pqs operon, andthe mexEF–oprN operon. Ithas been shown that overexpression of mexEF–oprN increases resistance to chloramphenicol.39 We therefore hypothesized that PAO1, which showshigher expression of mexEF–oprN, may exhibit higher resistance to chloramphenicol compared to PA14.To test this hypothesis, we used a disk diffusion assay to measuregrowth inhibition by chloramphenicol. As expected, the zones of inhibitionwere larger for PA14 with increasing chloramphenicol concentrations,whereas PAO1 growth was minimally inhibited by chloramphenicol (Figure 3). Additionally, genes involved in the metabolismof several amino acids were differentially expressed between PAO1and PA14 (Table 2), likely highlighting differentmetabolic characteristics of the two strains.

Bottom Line: For 703 genes observed by both shotgun proteomics and microarray experiments, we found that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains to an extent comparable to protein and mRNA abundances.In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level.Our data demonstrate that the magnitude and direction of the effect of protein abundance regulation occurring after the setting of mRNA levels is conserved between bacterial strains and is important for explaining the discordance between mRNA and protein abundances.

View Article: PubMed Central - PubMed

Affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin , 2500 Speedway, Austin, Texas 78712, United States.

ABSTRACT
Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here, we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we found that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that the magnitude and direction of the effect of protein abundance regulation occurring after the setting of mRNA levels is conserved between bacterial strains and is important for explaining the discordance between mRNA and protein abundances.

Show MeSH
Related in: MedlinePlus