Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Javad Aminian-Dehkordi, Seyyed Mohammad Mousavi*, Arezou Jafari, Ivan Mijakovic, Sayed Amir Marashi

*Corresponding author for this work

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Abstract

Bacillus megaterium is a microorganism widely used in industrial biotechnology for production of enzymes and recombinant proteins, as well as in bioleaching processes. Precise understanding of its metabolism is essential for designing engineering strategies to further optimize B. megaterium for biotechnology applications. Here, we present a genome-scale metabolic model for B. megaterium DSM319, iJA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other Bacillus species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy, experimental data reported in the literature (growth behavior patterns, metabolite production capabilities, metabolic flux analysis using 13C glucose and formaldehyde inhibitory effect) were confronted with model predictions. This indicated a very good agreement between in silico results and experimental data. For example, our in silico study of fatty acid biosynthesis and lipid accumulation in B. megaterium highlighted the importance of adopting appropriate carbon sources for fermentation purposes. We conclude that the genome-scale metabolic model iJA1121 represents a useful tool for systems analysis and furthers our understanding of the metabolism of B. megaterium.

Original languageEnglish
Article number18762
JournalScientific Reports
Volume9
Issue number1
Number of pages14
ISSN2045-2322
DOIs
Publication statusPublished - 2019

Cite this

Aminian-Dehkordi, Javad ; Mousavi, Seyyed Mohammad ; Jafari, Arezou ; Mijakovic, Ivan ; Marashi, Sayed Amir. / Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. In: Scientific Reports. 2019 ; Vol. 9, No. 1.
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abstract = "Bacillus megaterium is a microorganism widely used in industrial biotechnology for production of enzymes and recombinant proteins, as well as in bioleaching processes. Precise understanding of its metabolism is essential for designing engineering strategies to further optimize B. megaterium for biotechnology applications. Here, we present a genome-scale metabolic model for B. megaterium DSM319, iJA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other Bacillus species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy, experimental data reported in the literature (growth behavior patterns, metabolite production capabilities, metabolic flux analysis using 13C glucose and formaldehyde inhibitory effect) were confronted with model predictions. This indicated a very good agreement between in silico results and experimental data. For example, our in silico study of fatty acid biosynthesis and lipid accumulation in B. megaterium highlighted the importance of adopting appropriate carbon sources for fermentation purposes. We conclude that the genome-scale metabolic model iJA1121 represents a useful tool for systems analysis and furthers our understanding of the metabolism of B. megaterium.",
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Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. / Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou; Mijakovic, Ivan; Marashi, Sayed Amir.

In: Scientific Reports, Vol. 9, No. 1, 18762, 2019.

Research output: Contribution to journalJournal articleResearchpeer-review

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