Abstract
BackgroundClostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation.ResultsThe identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5′UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5′UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress.ConclusionsThe integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0260-9) contains supplementary material, which is available to authorized users.
Highlights
Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production
As in the corresponding microarray [16] and RNAseq [15] studies, cultures were stressed with three levels of butyrate (0 mM - control; 30 mM - low; 40 mM medium; and 50 mM - high) and three levels of butanol (0 mM - control; 30 mM - low; 60 mM - medium; and 90 mM - high) stress at a cell density (A600) of 1.0
It appears that uptake of the exogenous butyrate minimizes the impact of this carboxylic acid on cell growth [12, 15, 16]
Summary
Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. C. acetobutylicum has the ability to ferment a very large range of carbon sources for the production of a wide array of products, including carboxylic acids (butyrate and acetate) and solvents (ABE) [1, 2]. These products are toxic and affect cell growth and survival. We will show here that regulation of this core HSP response is considerably more complex that has been so far revealed by transcriptional studies.
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