Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum.
BACKGROUND
Clostridium 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.


RESULTS
The 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.


CONCLUSIONS
The 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.
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Keerthi P
KP
Venkataramanan
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Lie
L
Min
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Shuyu
S
Hou
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Shawn W
SW
Jones
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 15 Innovation Way, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA.
Matthew T
MT
Ralston
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
Kelvin H
KH
Lee
15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA ; 150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA.
E Terry
ET
Papoutsakis
Integrative analysis; Metabolite stress; Microarray; Post-transcriptional regulation; RNAseq; iTRAQ proteome