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Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism
- Source :
- Mol, V, Bennett, M, Sánchez, B J, Lisowska, B K, Herrgård, M J, Nielsen, A T, Leak, D J & Sonnenschein, N 2021, ' Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism ', Metabolic Engineering, vol. 65, pp. 123-134 . https://doi.org/10.1016/j.ymben.2021.03.002
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
Abstract
- Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.
- Subjects :
- In silico strain design
Flux balance analysis
Genome scale
Bioengineering
Anaerobic metabolism
Computational biology
Biology
Ferric Compounds
Applied Microbiology and Biotechnology
Metabolic engineering
03 medical and health sciences
Thermophile
Metabolic modeling
Anaerobiosis
Bacillaceae
030304 developmental biology
Genome-scale metaboli model
0303 health sciences
030306 microbiology
Systems metabolic engineering
Metabolic Model
Metabolic Engineering
Anaerobic growth
Parageobacillus
Anaerobic exercise
Biotechnology
Subjects
Details
- ISSN :
- 10967176
- Volume :
- 65
- Database :
- OpenAIRE
- Journal :
- Metabolic Engineering
- Accession number :
- edsair.doi.dedup.....3c879f390cd531fe82c6e03019413917