Feierabend2021 - iCGB21FR - GEM of Corynebacterium glutamicum ATCC 13032 (Bielefeld)

Model Identifier
MODEL2102050001
Short description
The bacterium Corynebacterium glutamicum can produce ʟ-glutamic acid under certain growth conditions. ʟ-glutamic acid is used as a flavor enhancer, food supplement, or primary chemical raw material. It, therefore, plays an essential economic role with an annual production of over 2½ million tons. Due to metabolic development, the product range of C. glutamicum has been expanded to include all biogenic amino acids, vitamins, and more. Previously published metabolic models of C. glutamicum have been supplemented with new metabolic data and expanded with data from new systems biology programs to result in this consensus model.
Format
COMBINE archive (1.0)
Related Publication
  • High-quality genome-scale reconstruction of Corynebacterium glutamicum ATCC 13032 Click here to expand
  • Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, Andreas Dräger
  • Frontiers in Microbiology , 11/ 2021 , DOI: 10.3389/fmicb.2021.750206
  • 1. Department of Computer Science, Faculty of Sciences, University of Tübingen, Germany 2. Interfaculty Institute for Biomedical Informatics, University Hospital and Faculty of Medicine, University of Tübingen, Germany 3. Institut für Bio- und Geowissenschaften (IBG), Germany 4. Center for Computational Biomedicine, RWTH Aachen University, Germany
  • 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 1,042 metabolites, 1,539 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.
Contributors
Submitter of the first revision: Andreas Dräger
Submitter of this revision: Rahuman S Malik-Sheriff
Modellers: Rahuman S Malik-Sheriff, Andreas Dräger

Metadata information

is (1 statement)
BioModels Database MODEL2102050001

isDescribedBy (1 statement)

Curation status
Non-curated

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