A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>

ABSTRACT Engineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing...

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Autores principales:	Minyeong Yoo, Gwenaelle Bestel-Corre, Christian Croux, Antoine Riviere, Isabelle Meynial-Salles, Philippe Soucaille
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/eca567eaa1ba47639f4f266dcf4a89f6
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spelling	oai:doaj.org-article:eca567eaa1ba47639f4f266dcf4a89f62021-11-15T15:41:24ZA Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>10.1128/mBio.01808-152150-7511https://doaj.org/article/eca567eaa1ba47639f4f266dcf4a89f62015-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01808-15https://doaj.org/toc/2150-7511ABSTRACT Engineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing bacterium Clostridium acetobutylicum, a microorganism used for the industrial production of solvent. An improved genome-scale model, iCac967, was first developed based on thorough biochemical characterizations of 15 key metabolic enzymes and on extensive literature analysis to acquire accurate fluxomic data. In parallel, quantitative transcriptomic and proteomic analyses were performed to assess the number of mRNA molecules per cell for all genes under acidogenic, solventogenic, and alcohologenic steady-state conditions as well as the number of cytosolic protein molecules per cell for approximately 700 genes under at least one of the three steady-state conditions. A complete fluxomic, transcriptomic, and proteomic analysis applied to different metabolic states allowed us to better understand the regulation of primary metabolism. Moreover, this analysis enabled the functional characterization of numerous enzymes involved in primary metabolism, including (i) the enzymes involved in the two different butanol pathways and their cofactor specificities, (ii) the primary hydrogenase and its redox partner, (iii) the major butyryl coenzyme A (butyryl-CoA) dehydrogenase, and (iv) the major glyceraldehyde-3-phosphate dehydrogenase. This study provides important information for further metabolic engineering of C. acetobutylicum to develop a commercial process for the production of n-butanol. IMPORTANCE Currently, there is a resurgence of interest in Clostridium acetobutylicum, the biocatalyst of the historical Weizmann process, to produce n-butanol for use both as a bulk chemical and as a renewable alternative transportation fuel. To develop a commercial process for the production of n-butanol via a metabolic engineering approach, it is necessary to better characterize both the primary metabolism of C. acetobutylicum and its regulation. Here, we apply a quantitative system-scale analysis to acidogenic, solventogenic, and alcohologenic steady-state C. acetobutylicum cells and report for the first time quantitative transcriptomic, proteomic, and fluxomic data. This approach allows for a better understanding of the regulation of primary metabolism and for the functional characterization of numerous enzymes involved in primary metabolism.Minyeong YooGwenaelle Bestel-CorreChristian CrouxAntoine RiviereIsabelle Meynial-SallesPhilippe SoucailleAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 6 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Minyeong Yoo Gwenaelle Bestel-Corre Christian Croux Antoine Riviere Isabelle Meynial-Salles Philippe Soucaille A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
description	ABSTRACT Engineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing bacterium Clostridium acetobutylicum, a microorganism used for the industrial production of solvent. An improved genome-scale model, iCac967, was first developed based on thorough biochemical characterizations of 15 key metabolic enzymes and on extensive literature analysis to acquire accurate fluxomic data. In parallel, quantitative transcriptomic and proteomic analyses were performed to assess the number of mRNA molecules per cell for all genes under acidogenic, solventogenic, and alcohologenic steady-state conditions as well as the number of cytosolic protein molecules per cell for approximately 700 genes under at least one of the three steady-state conditions. A complete fluxomic, transcriptomic, and proteomic analysis applied to different metabolic states allowed us to better understand the regulation of primary metabolism. Moreover, this analysis enabled the functional characterization of numerous enzymes involved in primary metabolism, including (i) the enzymes involved in the two different butanol pathways and their cofactor specificities, (ii) the primary hydrogenase and its redox partner, (iii) the major butyryl coenzyme A (butyryl-CoA) dehydrogenase, and (iv) the major glyceraldehyde-3-phosphate dehydrogenase. This study provides important information for further metabolic engineering of C. acetobutylicum to develop a commercial process for the production of n-butanol. IMPORTANCE Currently, there is a resurgence of interest in Clostridium acetobutylicum, the biocatalyst of the historical Weizmann process, to produce n-butanol for use both as a bulk chemical and as a renewable alternative transportation fuel. To develop a commercial process for the production of n-butanol via a metabolic engineering approach, it is necessary to better characterize both the primary metabolism of C. acetobutylicum and its regulation. Here, we apply a quantitative system-scale analysis to acidogenic, solventogenic, and alcohologenic steady-state C. acetobutylicum cells and report for the first time quantitative transcriptomic, proteomic, and fluxomic data. This approach allows for a better understanding of the regulation of primary metabolism and for the functional characterization of numerous enzymes involved in primary metabolism.
format	article
author	Minyeong Yoo Gwenaelle Bestel-Corre Christian Croux Antoine Riviere Isabelle Meynial-Salles Philippe Soucaille
author_facet	Minyeong Yoo Gwenaelle Bestel-Corre Christian Croux Antoine Riviere Isabelle Meynial-Salles Philippe Soucaille
author_sort	Minyeong Yoo
title	A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
title_short	A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
title_full	A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
title_fullStr	A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
title_full_unstemmed	A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>
title_sort	quantitative system-scale characterization of the metabolism of <named-content content-type="genus-species">clostridium acetobutylicum</named-content>
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/eca567eaa1ba47639f4f266dcf4a89f6
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A Quantitative System-Scale Characterization of the Metabolism of <named-content content-type="genus-species">Clostridium acetobutylicum</named-content>

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