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Improving ethanol production by studying the effect of pH using a modified metabolic model and a systemic approach
  • Sajjad Ghaffarinasab,
  • Ehsan Motamedian
Sajjad Ghaffarinasab
Tarbiat Modares University Faculty of Chemical Engineering
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Ehsan Motamedian
Tarbiat Modares University
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Abstract

pH is an important factor affecting the growth and production of microorganisms; especially, it is effective on the efficiency of ethanologenic microorganisms. It can change the ionization state of metabolites via the change in the charge of their functional groups that may lead to metabolic alteration. Here, we estimated the ionization state of metabolites and balanced the charge of reactions in genome-scale metabolic models of Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis at pH levels 5, 6, and 7. The robustness analysis was first implemented to anticipate the effect of proton exchange flux on growth rates for the constructed metabolic models at various pH. In accordance with previous experimental reports, the models predict that Z. mobilis is more sensitive to pH rather than S. cerevisiae and the yeast is more regulated by pH rather than E. coli. Then, a systemic approach was proposed to predict the pH effect on metabolic change and to find effective reactions on ethanol production in S. cerevisiae. The correlated reactions with ethanol production at predicted optimal pH in a range of proton exchange rates determined by robustness analysis were identified using the Pearson correlation coefficient. Then, fluxes of these reactions were applied to cluster the various pHs by principal component analysis and to identify the role of these reactions on metabolic differentiation because of pH change. Finally, 12 reactions were selected for up and down-regulation to improve ethanol production. Enzyme Regulators of the selected reactions were identified using the Brenda database and 11 selected regulators were screened and optimized via Plackett-Burman and 2-level full factorial designs, respectively. The proposed approach has enhanced yields of ethanol from 0.18 to 0.36 mol/mol carbon. Hence, not only a comprehensive approach for understanding the effect of pH on metabolism was proposed in this work, but also it successfully introduced key manipulations for ethanol overproduction.

Peer review status:ACCEPTED

01 Oct 2020Submitted to Biotechnology and Bioengineering
03 Oct 2020Submission Checks Completed
03 Oct 2020Assigned to Editor
12 Oct 2020Reviewer(s) Assigned
14 Nov 2020Editorial Decision: Revise Major
14 Nov 2020Review(s) Completed, Editorial Evaluation Pending
11 Dec 20201st Revision Received
12 Dec 2020Assigned to Editor
12 Dec 2020Submission Checks Completed
29 Dec 2020Reviewer(s) Assigned
03 Feb 2021Review(s) Completed, Editorial Evaluation Pending
03 Feb 2021Editorial Decision: Revise Major
19 Mar 20212nd Revision Received
20 Mar 2021Assigned to Editor
20 Mar 2021Submission Checks Completed
21 Apr 2021Review(s) Completed, Editorial Evaluation Pending
21 Apr 2021Editorial Decision: Accept