387369 Integrated Transcriptome and Proteome Analysis in Clostridial Stress Response Model Unveils the Complexity behind the Genetic Program and Post-Transcriptional Gene Regulation

Monday, November 17, 2014: 2:00 PM
214 (Hilton Atlanta)
Keerthi P. Venkataramanan1, Qinghua Wang2, Li-e Min3, Matthew Ralston4, Kelvin H. Lee5, Cathy H. Wu6, Hongzhan Huang6 and Eleftherios T. Papoutsakis1, (1)Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, (2)University of Delaware, Newark, DE, (3)Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, (4)Bioinformatics & Computational Biology, University of Delaware, Newark, DE, (5)Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, (6)Delaware Biotechnology Institute, University of Delaware, Newark, DE

Clostridium acetobutylicum is the model organism for the acetone-butanol-ethanol (ABE) fermentation. These clostridial cells face a variety of stress due to the toxic metabolic products such acids (butyrate) and solvents (butanol) that are produced during fermentation. Several genome level transcriptional studies have shown the complexity behind the regulation of the stress response and tolerance in Clostridia that is driven by major changes in the genetic program. Yet, the post-transcriptional regulation can be comprehensively understood only using a quantitative proteomic approach. In this work, we performed an integrated analysis of the quantitative proteomic data obtained using isobaric tag for relative and absolute quantification (iTRAQ) and genome-wide transcriptional data obtained using microarrays and deep sequencing using Illumina HiSeq 2.0 at multiple time points and levels of stress to two major metabolites stressors – butanol and butyrate. Our results demonstrate the additional layer of post-transcriptional gene regulation combined with the role of small regulatory non-coding RNA (sRNA) in mediating these post transcriptional gene regulation. Particularly, the heat shock proteins that were found to be upregulated in the proteome data under stress in the WT strain, were found to be down regulated in SolRH+pTAAD strain (overexpressing the sol operon (aad-ctfA-ctfB) and the KO of the solB sRNA upstream of the sol operon) under same stress conditions. Longer 5’ untranslated region (UTR) of these heat shock proteins revealed post-transcriptional gene regulation mediated by sRNAs and/or transcriptional factors.

This is the first comprehensive study that provides novel insights into the post-transcriptional gene regulation behind the complexity of stress response network, which can be targeted for practical purposes towards strain development for chemicals and fuels production.

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