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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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.750206/full |
| _version_ | 1818568849862164480 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T06:40:29Z |
| format | Article |
| id | doaj.art-eb879d8e7d04495f956f54a1887fdcd2 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-14T06:40:29Z |
| publishDate | 2021-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-eb879d8e7d04495f956f54a1887fdcd22022-12-21T23:13:14ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-11-011210.3389/fmicb.2021.750206750206High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032Martina Feierabend0Martina Feierabend1Alina Renz2Alina Renz3Elisabeth Zelle4Katharina Nöh5Wolfgang Wiechert6Wolfgang Wiechert7Andreas Dräger8Andreas Dräger9Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, GermanyDepartment of Computer Science, University of Tübingen, Tübingen, GermanyComputational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, GermanyDepartment of Computer Science, University of Tübingen, Tübingen, GermanyInstitute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, GermanyInstitute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, GermanyInstitute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, GermanyComputational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, GermanyComputational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, GermanyDepartment of Computer Science, University of Tübingen, Tübingen, GermanyCorynebacterium 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.750206/fullCorynebacterium glutamicumgenome-scale metabolic modelconstraint-based reconstructionoptimizationmetabolic engineeringFAIR |
| spellingShingle | 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 Frontiers in Microbiology Corynebacterium glutamicum genome-scale metabolic model constraint-based reconstruction optimization metabolic engineering FAIR |
| title | 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_short | High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032 |
| title_sort | high quality genome scale reconstruction of corynebacterium glutamicum atcc 13032 |
| topic | Corynebacterium glutamicum genome-scale metabolic model constraint-based reconstruction optimization metabolic engineering FAIR |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.750206/full |
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