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Title: Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass - namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-a-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK andmore » ACK enzymes are the most effective in increasing succinate production.« less
Authors:
 [1] ; ORCiD logo [2] ;  [2] ;  [2]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States). Computational Science Center
  2. National Renewable Energy Lab. (NREL), Golden, CO (United States). Biosciences Center
Publication Date:
Report Number(s):
NREL/JA-2700-70444
Journal ID: ISSN 1932-6203
Grant/Contract Number:
AC36-08GO28308
Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 13; Journal Issue: 1; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; bicarbonates; fermentation; metabolic networks; glucose; enzymes; ethanol; glycogens; metabolic pathways
OSTI Identifier:
1418730
Alternate Identifier(s):
OSTI ID: 1423185

Nag, Ambarish, St. John, Peter C., Crowley, Michael F., and Bomble, Yannick J.. Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes. United States: N. p., Web. doi:10.1371/journal.pone.0189144.
Nag, Ambarish, St. John, Peter C., Crowley, Michael F., & Bomble, Yannick J.. Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes. United States. doi:10.1371/journal.pone.0189144.
Nag, Ambarish, St. John, Peter C., Crowley, Michael F., and Bomble, Yannick J.. 2018. "Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes". United States. doi:10.1371/journal.pone.0189144.
@article{osti_1418730,
title = {Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes},
author = {Nag, Ambarish and St. John, Peter C. and Crowley, Michael F. and Bomble, Yannick J.},
abstractNote = {Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass - namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-a-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.},
doi = {10.1371/journal.pone.0189144},
journal = {PLoS ONE},
number = 1,
volume = 13,
place = {United States},
year = {2018},
month = {1}
}

Works referenced in this record:

13C-metabolic flux analysis of Actinobacillus succinogenes fermentative metabolism at different NaHCO3 and H2 concentrations
journal, January 2008