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Title: Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

Abstract

Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. In particular, Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress-related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.

Authors:
 [1];  [1];  [2];  [2];  [1]
  1. Pennsylvania State Univ., University Park, PA (United States)
  2. Delaware Biotechnology Institute, Newark, DE (United States); Univ. of Delaware, Newark, DE (United States)
Publication Date:
Research Org.:
Pennsylvania State Univ., University Park, PA (United States); Univ. of Delaware, Newark, DE (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1221631
Alternate Identifier(s):
OSTI ID: 1454689
Grant/Contract Number:  
SC0007092; sc0007092
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.; 59 BASIC BIOLOGICAL SCIENCES; Clostridium acetobutylicum; CoreReg; regulation; genome-scale metabolic model

Citation Formats

Dash, Satyakam, Mueller, Thomas J., Venkataramanan, Keerthi P., Papoutsakis, Eleftherios T., and Maranas, Costas D. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model. United States: N. p., 2014. Web. doi:10.1186/s13068-014-0144-4.
Dash, Satyakam, Mueller, Thomas J., Venkataramanan, Keerthi P., Papoutsakis, Eleftherios T., & Maranas, Costas D. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model. United States. https://doi.org/10.1186/s13068-014-0144-4
Dash, Satyakam, Mueller, Thomas J., Venkataramanan, Keerthi P., Papoutsakis, Eleftherios T., and Maranas, Costas D. 2014. "Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model". United States. https://doi.org/10.1186/s13068-014-0144-4. https://www.osti.gov/servlets/purl/1221631.
@article{osti_1221631,
title = {Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model},
author = {Dash, Satyakam and Mueller, Thomas J. and Venkataramanan, Keerthi P. and Papoutsakis, Eleftherios T. and Maranas, Costas D.},
abstractNote = {Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. In particular, Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress-related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.},
doi = {10.1186/s13068-014-0144-4},
url = {https://www.osti.gov/biblio/1221631}, journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 7,
place = {United States},
year = {Tue Oct 14 00:00:00 EDT 2014},
month = {Tue Oct 14 00:00:00 EDT 2014}
}

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Cited by: 43 works
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Works referenced in this record:

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Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
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Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003


Genome-scale model for Clostridium acetobutylicum : Part I. Metabolic network resolution and analysis
journal, December 2008


Equations and calculations for fermentations of butyric acid bacteria
journal, February 1984


Regulation of Gene Expression in Flux Balance Models of Metabolism
journal, November 2001


Disruption of the acetate kinase (ack) gene of Clostridium acetobutylicum results in delayed acetate production
journal, January 2012


New insights into the butyric acid metabolism of Clostridium acetobutylicum
journal, May 2012


Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models
journal, February 2011


Engineering solventogenic clostridia
journal, October 2008


A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum – Cellular behavior in adaptation to n-butanol
journal, October 2012


A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum—Solvent stress caused by a transient n-butanol pulse
journal, October 2012


A genome‐scale computational study of the interplay between transcriptional regulation and metabolism
journal, January 2007


Global organization of metabolic fluxes in the bacterium Escherichia coli
journal, February 2004


Model-based identification of drug targets that revert disrupted metabolism and its application to ageing
journal, October 2013


Towards multidimensional genome annotation
journal, February 2006


Significance analysis of microarrays applied to the ionizing radiation response
journal, April 2001


Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli
journal, May 2002


Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
journal, January 2012


Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
journal, January 2013


OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
journal, April 2010


Predicting synthetic rescues in metabolic networks
text, January 2008


Works referencing / citing this record:

Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973
journal, January 2017


Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol
journal, June 2017


Gsmodutils: A python based framework for test-driven genome scale metabolic model development
journal, September 2018


System-level modeling of acetone–butanol–ethanol fermentation
journal, March 2016


Impact of iron reduction on the metabolism of Clostridium acetobutylicum
journal, May 2019


Recent progress in biobutanol tolerance in microbial systems with an emphasis on Clostridium
journal, January 2016


Gsmodutils: a python based framework for test-driven genome scale metabolic model development
journal, February 2019


Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
journal, March 2019


Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations
journal, May 2017


Mathematical modelling of clostridial acetone-butanol-ethanol fermentation
journal, February 2017


Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973
journal, January 2017


Gsmodutils: A python based framework for test-driven genome scale metabolic model development
journal, September 2018


Impact of iron reduction on the metabolism of Clostridium acetobutylicum
journal, May 2019


Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol
journal, June 2017


Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
journal, March 2019


Kinetic Study of Acetone-Butanol-Ethanol Fermentation in Continuous Culture
journal, August 2016