Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824

ABSTRACT Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fe...

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Autores principales:	Matthew D. Servinsky, Rebecca L. Renberg, Matthew A. Perisin, Elliot S. Gerlach, Sanchao Liu, Christian J. Sund
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Clostridium acetobutylicum RNA-Seq biofuel carbohydrate metabolism Crh pentose Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f3173e71c58147848fd06a8797523d06
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spelling	oai:doaj.org-article:f3173e71c58147848fd06a8797523d062021-12-02T18:15:43ZArabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 82410.1128/mSystems.00064-182379-5077https://doaj.org/article/f3173e71c58147848fd06a8797523d062018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00064-18https://doaj.org/toc/2379-5077ABSTRACT Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452–1462, 2015, https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum and suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production. IMPORTANCE Clostridium acetobutylicum can ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire of C. acetobutylicum using synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.Matthew D. ServinskyRebecca L. RenbergMatthew A. PerisinElliot S. GerlachSanchao LiuChristian J. SundAmerican Society for MicrobiologyarticleClostridium acetobutylicumRNA-Seqbiofuelcarbohydrate metabolismCrhpentoseMicrobiologyQR1-502ENmSystems, Vol 3, Iss 5 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Clostridium acetobutylicum RNA-Seq biofuel carbohydrate metabolism Crh pentose Microbiology QR1-502
spellingShingle	Clostridium acetobutylicum RNA-Seq biofuel carbohydrate metabolism Crh pentose Microbiology QR1-502 Matthew D. Servinsky Rebecca L. Renberg Matthew A. Perisin Elliot S. Gerlach Sanchao Liu Christian J. Sund Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
description	ABSTRACT Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452–1462, 2015, https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum and suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production. IMPORTANCE Clostridium acetobutylicum can ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire of C. acetobutylicum using synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.
format	article
author	Matthew D. Servinsky Rebecca L. Renberg Matthew A. Perisin Elliot S. Gerlach Sanchao Liu Christian J. Sund
author_facet	Matthew D. Servinsky Rebecca L. Renberg Matthew A. Perisin Elliot S. Gerlach Sanchao Liu Christian J. Sund
author_sort	Matthew D. Servinsky
title	Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
title_short	Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
title_full	Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
title_fullStr	Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
title_full_unstemmed	Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824
title_sort	arabinose-induced catabolite repression as a mechanism for pentose hierarchy control in <italic toggle="yes">clostridium acetobutylicum</italic> atcc 824
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/f3173e71c58147848fd06a8797523d06
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Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <italic toggle="yes">Clostridium acetobutylicum</italic> ATCC 824

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