High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

Corynebacterium glutamicum belongs to the microbes of enormous biotechnological relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at an industrial scale. Its apparent robustness also turns it into a favorable platform host for a wide range of further compound...

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Autores principales:	Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, Andreas Dräger
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Corynebacterium glutamicum genome-scale metabolic model constraint-based reconstruction optimization metabolic engineering FAIR Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/eb879d8e7d04495f956f54a1887fdcd2
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spelling	oai:doaj.org-article:eb879d8e7d04495f956f54a1887fdcd22021-11-15T06:44:25ZHigh-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 130321664-302X10.3389/fmicb.2021.750206https://doaj.org/article/eb879d8e7d04495f956f54a1887fdcd22021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.750206/fullhttps://doaj.org/toc/1664-302XCorynebacterium glutamicum belongs to the microbes of enormous biotechnological relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at an industrial scale. Its apparent robustness also turns it into a favorable platform host for a wide range of further compounds, mainly because of emerging bio-based economies. A deep understanding of the biochemical processes in C. glutamicum is essential for a sustainable enhancement of the microbe's productivity. Computational systems biology has the potential to provide a valuable basis for driving metabolic engineering and biotechnological advances, such as increased yields of healthy producer strains based on genome-scale metabolic models (GEMs). Advanced reconstruction pipelines are now available that facilitate the reconstruction of GEMs and support their manual curation. This article presents iCGB21FR, an updated and unified GEM of C. glutamicum ATCC 13032 with high quality regarding comprehensiveness and data standards, built with the latest modeling techniques and advanced reconstruction pipelines. It comprises 1042 metabolites, 1539 reactions, and 805 genes with detailed annotations and database cross-references. The model validation took place using different media and resulted in realistic growth rate predictions under aerobic and anaerobic conditions. The new GEM produces all canonical amino acids, and its phenotypic predictions are consistent with laboratory data. The in silico model proved fruitful in adding knowledge to the metabolism of C. glutamicum: iCGB21FR still produces L-glutamate with the knock-out of the enzyme pyruvate carboxylase, despite the common belief to be relevant for the amino acid's production. We conclude that integrating high standards into the reconstruction of GEMs facilitates replicating validated knowledge, closing knowledge gaps, and making it a useful basis for metabolic engineering. The model is freely available from BioModels Database under identifier MODEL2102050001.Martina FeierabendMartina FeierabendAlina RenzAlina RenzElisabeth ZelleKatharina NöhWolfgang WiechertWolfgang WiechertAndreas DrägerAndreas DrägerFrontiers Media S.A.articleCorynebacterium glutamicumgenome-scale metabolic modelconstraint-based reconstructionoptimizationmetabolic engineeringFAIRMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Corynebacterium glutamicum genome-scale metabolic model constraint-based reconstruction optimization metabolic engineering FAIR Microbiology QR1-502
spellingShingle	Corynebacterium glutamicum genome-scale metabolic model constraint-based reconstruction optimization metabolic engineering FAIR Microbiology QR1-502 Martina Feierabend Martina Feierabend Alina Renz Alina Renz Elisabeth Zelle Katharina Nöh Wolfgang Wiechert Wolfgang Wiechert Andreas Dräger Andreas Dräger High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
description	Corynebacterium glutamicum belongs to the microbes of enormous biotechnological relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at an industrial scale. Its apparent robustness also turns it into a favorable platform host for a wide range of further compounds, mainly because of emerging bio-based economies. A deep understanding of the biochemical processes in C. glutamicum is essential for a sustainable enhancement of the microbe's productivity. Computational systems biology has the potential to provide a valuable basis for driving metabolic engineering and biotechnological advances, such as increased yields of healthy producer strains based on genome-scale metabolic models (GEMs). Advanced reconstruction pipelines are now available that facilitate the reconstruction of GEMs and support their manual curation. This article presents iCGB21FR, an updated and unified GEM of C. glutamicum ATCC 13032 with high quality regarding comprehensiveness and data standards, built with the latest modeling techniques and advanced reconstruction pipelines. It comprises 1042 metabolites, 1539 reactions, and 805 genes with detailed annotations and database cross-references. The model validation took place using different media and resulted in realistic growth rate predictions under aerobic and anaerobic conditions. The new GEM produces all canonical amino acids, and its phenotypic predictions are consistent with laboratory data. The in silico model proved fruitful in adding knowledge to the metabolism of C. glutamicum: iCGB21FR still produces L-glutamate with the knock-out of the enzyme pyruvate carboxylase, despite the common belief to be relevant for the amino acid's production. We conclude that integrating high standards into the reconstruction of GEMs facilitates replicating validated knowledge, closing knowledge gaps, and making it a useful basis for metabolic engineering. The model is freely available from BioModels Database under identifier MODEL2102050001.
format	article
author	Martina Feierabend Martina Feierabend Alina Renz Alina Renz Elisabeth Zelle Katharina Nöh Wolfgang Wiechert Wolfgang Wiechert Andreas Dräger Andreas Dräger
author_facet	Martina Feierabend Martina Feierabend Alina Renz Alina Renz Elisabeth Zelle Katharina Nöh Wolfgang Wiechert Wolfgang Wiechert Andreas Dräger Andreas Dräger
author_sort	Martina Feierabend
title	High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
title_short	High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
title_full	High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
title_fullStr	High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
title_full_unstemmed	High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
title_sort	high-quality genome-scale reconstruction of corynebacterium glutamicum atcc 13032
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/eb879d8e7d04495f956f54a1887fdcd2
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High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

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