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Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor.

Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS - PLoS ONE (2008)

Bottom Line: Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels.Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends.Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in many studies, examples of divergent trends are frequently observed. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in microbiology as they pertain to the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides (iTRAQ) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes exhibit mRNA-protein discordance in a similar fashion. Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

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Related in: MedlinePlus

Correlation between mRNA and protein abundance.A plot of mRNA abundance calculated as [mRNA/gDNA] from microarray experiments against protein abundance calculated as emPAI based on number of MS/MS spectral evidences is shown in log2 scale. The top ten percentile (highest) CAI ranked genes (blue circles), bottom ten percentile CAI ranked genes (red circles) and all other genes (green circles) are shown. For the sake of clarity, five data points with exceptionally high protein abundance (log2[emPAI]>20) are not shown here. All data points were, however, included in the Pearson's correlation coefficient (r) calculation.
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pone-0002097-g003: Correlation between mRNA and protein abundance.A plot of mRNA abundance calculated as [mRNA/gDNA] from microarray experiments against protein abundance calculated as emPAI based on number of MS/MS spectral evidences is shown in log2 scale. The top ten percentile (highest) CAI ranked genes (blue circles), bottom ten percentile CAI ranked genes (red circles) and all other genes (green circles) are shown. For the sake of clarity, five data points with exceptionally high protein abundance (log2[emPAI]>20) are not shown here. All data points were, however, included in the Pearson's correlation coefficient (r) calculation.

Mentions: Since hybridizations were performed with genomic DNA as reference, the resulting mRNA/gDNA ratio (reported here in logarithmic scale and referred to as log2 mRNA abundance ratio) is an indicator of relative mRNA abundance in the cell. A scatter plot of average log2 mRNA abundance ratio versus emPAI estimated using total number of MS/MS spectra identified from all three proteomic runs revealed a moderate correlation between mRNA and protein abundance (Figure 3). The Pearson's correlation coefficient (r) for a straight line fit for this data was a modest 0.63. Interestingly, this correlation improved when only the top 50 high ranking genes in terms of CAI values (optimal codon containing genes) were considered (r  =  0.8). For low ranking genes (those with 50 lowest CAI values among proteins identified), this correlation dropped to r  =  0.35. One possible reason for this observation could be that low CAI ranking proteins are generally less abundant and emPAI correlates rather poorly with protein abundance in such cases (since emPAI values tend to be discrete when peptide counts are low).


Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor.

Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS - PLoS ONE (2008)

Correlation between mRNA and protein abundance.A plot of mRNA abundance calculated as [mRNA/gDNA] from microarray experiments against protein abundance calculated as emPAI based on number of MS/MS spectral evidences is shown in log2 scale. The top ten percentile (highest) CAI ranked genes (blue circles), bottom ten percentile CAI ranked genes (red circles) and all other genes (green circles) are shown. For the sake of clarity, five data points with exceptionally high protein abundance (log2[emPAI]>20) are not shown here. All data points were, however, included in the Pearson's correlation coefficient (r) calculation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2367054&req=5

pone-0002097-g003: Correlation between mRNA and protein abundance.A plot of mRNA abundance calculated as [mRNA/gDNA] from microarray experiments against protein abundance calculated as emPAI based on number of MS/MS spectral evidences is shown in log2 scale. The top ten percentile (highest) CAI ranked genes (blue circles), bottom ten percentile CAI ranked genes (red circles) and all other genes (green circles) are shown. For the sake of clarity, five data points with exceptionally high protein abundance (log2[emPAI]>20) are not shown here. All data points were, however, included in the Pearson's correlation coefficient (r) calculation.
Mentions: Since hybridizations were performed with genomic DNA as reference, the resulting mRNA/gDNA ratio (reported here in logarithmic scale and referred to as log2 mRNA abundance ratio) is an indicator of relative mRNA abundance in the cell. A scatter plot of average log2 mRNA abundance ratio versus emPAI estimated using total number of MS/MS spectra identified from all three proteomic runs revealed a moderate correlation between mRNA and protein abundance (Figure 3). The Pearson's correlation coefficient (r) for a straight line fit for this data was a modest 0.63. Interestingly, this correlation improved when only the top 50 high ranking genes in terms of CAI values (optimal codon containing genes) were considered (r  =  0.8). For low ranking genes (those with 50 lowest CAI values among proteins identified), this correlation dropped to r  =  0.35. One possible reason for this observation could be that low CAI ranking proteins are generally less abundant and emPAI correlates rather poorly with protein abundance in such cases (since emPAI values tend to be discrete when peptide counts are low).

Bottom Line: Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels.Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends.Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in many studies, examples of divergent trends are frequently observed. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in microbiology as they pertain to the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides (iTRAQ) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes exhibit mRNA-protein discordance in a similar fashion. Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

Show MeSH
Related in: MedlinePlus