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SRNA scr5239 involved in important feedback loop of S. coelicolor central metabolism

ABSTRACT: The project is focused on the highly conserved sRNA scr5329 in Streptomyces coelicolor. A proteomics approach revealed that the sRNA regulates several metabolic enzymes, among them the Phosphoenolpyruvate-Carboxykinase (PEPCK), a key enzyme of the central carbon metabolism. The sRNA scr5239 promotes its degradation on the post-transcriptional level. The expression itself is dependent on the global transcriptional regulator DasR, which is N-acetylglucosamine-responsive thereby creating a feedback regulation. By post-transcriptional regulation of PEPCK and likely more targets, scr5239 adds an additional layer to the DasR regulatory network, providing a tool to control the metabolism in dependency to the carbon source.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Streptomyces Coelicolor Bacteria

TISSUE(S): Cell Culture

SUBMITTER: Elena Ossipova

LAB HEAD: Beatix Suess

PROVIDER: PXD016811 | Pride | 2020-01-28

REPOSITORIES: Pride

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Project description: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 such studies, instances of divergent trends are frequently observed indicating the existence of post-transcriptional regulation. 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 streptomycetes as they encompass 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(TM) 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 general consensus, 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 were co-regulated independently as mRNA and/or proteins despite observations of apparent mRNA-protein discordance. This clearly suggests that post-transcriptional regulatory mechanisms are prominent even amongst prokaryotes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level. Keywords: Time course Time-course study involved analysis of 8 samples (7h, 11h, 14h, 16h, 22h, 26h, 34h, 38h). Of these, 14h, 22h, 26h and 38h were analyzed in duplicate arrays. All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.

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SRNA scr5239 involved in important feedback loop of S. coelicolor central metabolism

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