Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.

Saccharomyces cerevisiae is the most well characterized eukaryote, the preferred microbial cell factory for the largest industrial biotechnology product (bioethanol), and a robust commerically compatible scaffold to be exploitted for diverse chemical production. Succinic acid is a highly sought afte...

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Autores principales:	José Manuel Otero, Donatella Cimini, Kiran R Patil, Simon G Poulsen, Lisbeth Olsson, Jens Nielsen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6f3c7ae30657450793f72e6ce2b597da
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spelling	oai:doaj.org-article:6f3c7ae30657450793f72e6ce2b597da2021-11-18T08:00:45ZIndustrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.1932-620310.1371/journal.pone.0054144https://doaj.org/article/6f3c7ae30657450793f72e6ce2b597da2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23349810/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Saccharomyces cerevisiae is the most well characterized eukaryote, the preferred microbial cell factory for the largest industrial biotechnology product (bioethanol), and a robust commerically compatible scaffold to be exploitted for diverse chemical production. Succinic acid is a highly sought after added-value chemical for which there is no native pre-disposition for production and accmulation in S. cerevisiae. The genome-scale metabolic network reconstruction of S. cerevisiae enabled in silico gene deletion predictions using an evolutionary programming method to couple biomass and succinate production. Glycine and serine, both essential amino acids required for biomass formation, are formed from both glycolytic and TCA cycle intermediates. Succinate formation results from the isocitrate lyase catalyzed conversion of isocitrate, and from the α-keto-glutarate dehydrogenase catalyzed conversion of α-keto-glutarate. Succinate is subsequently depleted by the succinate dehydrogenase complex. The metabolic engineering strategy identified included deletion of the primary succinate consuming reaction, Sdh3p, and interruption of glycolysis derived serine by deletion of 3-phosphoglycerate dehydrogenase, Ser3p/Ser33p. Pursuing these targets, a multi-gene deletion strain was constructed, and directed evolution with selection used to identify a succinate producing mutant. Physiological characterization coupled with integrated data analysis of transcriptome data in the metabolically engineered strain were used to identify 2(nd)-round metabolic engineering targets. The resulting strain represents a 30-fold improvement in succinate titer, and a 43-fold improvement in succinate yield on biomass, with only a 2.8-fold decrease in the specific growth rate compared to the reference strain. Intuitive genetic targets for either over-expression or interruption of succinate producing or consuming pathways, respectively, do not lead to increased succinate. Rather, we demonstrate how systems biology tools coupled with directed evolution and selection allows non-intuitive, rapid and substantial re-direction of carbon fluxes in S. cerevisiae, and hence show proof of concept that this is a potentially attractive cell factory for over-producing different platform chemicals.José Manuel OteroDonatella CiminiKiran R PatilSimon G PoulsenLisbeth OlssonJens NielsenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e54144 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q José Manuel Otero Donatella Cimini Kiran R Patil Simon G Poulsen Lisbeth Olsson Jens Nielsen Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
description	Saccharomyces cerevisiae is the most well characterized eukaryote, the preferred microbial cell factory for the largest industrial biotechnology product (bioethanol), and a robust commerically compatible scaffold to be exploitted for diverse chemical production. Succinic acid is a highly sought after added-value chemical for which there is no native pre-disposition for production and accmulation in S. cerevisiae. The genome-scale metabolic network reconstruction of S. cerevisiae enabled in silico gene deletion predictions using an evolutionary programming method to couple biomass and succinate production. Glycine and serine, both essential amino acids required for biomass formation, are formed from both glycolytic and TCA cycle intermediates. Succinate formation results from the isocitrate lyase catalyzed conversion of isocitrate, and from the α-keto-glutarate dehydrogenase catalyzed conversion of α-keto-glutarate. Succinate is subsequently depleted by the succinate dehydrogenase complex. The metabolic engineering strategy identified included deletion of the primary succinate consuming reaction, Sdh3p, and interruption of glycolysis derived serine by deletion of 3-phosphoglycerate dehydrogenase, Ser3p/Ser33p. Pursuing these targets, a multi-gene deletion strain was constructed, and directed evolution with selection used to identify a succinate producing mutant. Physiological characterization coupled with integrated data analysis of transcriptome data in the metabolically engineered strain were used to identify 2(nd)-round metabolic engineering targets. The resulting strain represents a 30-fold improvement in succinate titer, and a 43-fold improvement in succinate yield on biomass, with only a 2.8-fold decrease in the specific growth rate compared to the reference strain. Intuitive genetic targets for either over-expression or interruption of succinate producing or consuming pathways, respectively, do not lead to increased succinate. Rather, we demonstrate how systems biology tools coupled with directed evolution and selection allows non-intuitive, rapid and substantial re-direction of carbon fluxes in S. cerevisiae, and hence show proof of concept that this is a potentially attractive cell factory for over-producing different platform chemicals.
format	article
author	José Manuel Otero Donatella Cimini Kiran R Patil Simon G Poulsen Lisbeth Olsson Jens Nielsen
author_facet	José Manuel Otero Donatella Cimini Kiran R Patil Simon G Poulsen Lisbeth Olsson Jens Nielsen
author_sort	José Manuel Otero
title	Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
title_short	Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
title_full	Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
title_fullStr	Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
title_full_unstemmed	Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
title_sort	industrial systems biology of saccharomyces cerevisiae enables novel succinic acid cell factory.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/6f3c7ae30657450793f72e6ce2b597da
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_version_	1718422672021389312

Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.

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