ArticleBMC systems biology2012
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.
Article in BMC systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 80 citations in OpenAlex.
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- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives.Journal of industrial microbiology & biotechnology · 2020Review
- Development of a Genome-Scale Metabolic Model ofFrontiers in bioengineering and biotechnology · 2020Article
- Distributed flux balance analysis simulations of serial biomass fermentation by two organisms.PloS one · 2020Article
- Gsmodutils: a python based framework for test-driven genome scale metabolic model development.Bioinformatics (Oxford, England) · 2019Article
- CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design.BMC bioinformatics · 2018Article
- Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model.Microbial cell factories · 2018Article
- In silico engineering ofPeerJ · 2018Article
- Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.BMC systems biology · 2017Article
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Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico.
resultsA new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production.
conclusionsFBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.