Document Type
Article
Original Publication Date
2010
Journal/Book/Conference Title
BMC Systems Biology
Volume
4
Issue
31
DOI
10.1186/1752-0509-4-31
Date of Submission
July 2014
Abstract
Background
Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405) is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous.
Results
Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the metabolic network of C. thermocellum and facilitate efforts to engineer C. thermocellum for biofuel production. The model consists of 577 reactions involving 525 intracellular metabolites, 432 genes, and a proteomic-based representation of a cellulosome. The process of constructing this metabolic model led to suggested annotation refinements for 27 genes and identification of areas of metabolism requiring further study. The accuracy of the iSR432 model was tested using experimental growth and by-product secretion data for growth on cellobiose and fructose. Analysis using this model captures the relationship between the reduction-oxidation state of the cell and ethanol secretion and allowed for prediction of gene deletions and environmental conditions that would increase ethanol production.
Conclusions
By incorporating genomic sequence data, network topology, and experimental measurements of enzyme activities and metabolite fluxes, we have generated a model that is reasonably accurate at predicting the cellular phenotype of C. thermocellum and establish a strong foundation for rational strain design. In addition, we are able to draw some important conclusions regarding the underlying metabolic mechanisms for observed behaviors of C. thermocellum and highlight remaining gaps in the existing genome annotations.
Rights
© 2010 Roberts et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Is Part Of
VCU Chemical and Life Science Engineering Faculty Publications
Model details and results. This Excel workbook contains the final reaction list, metabolite definitions, biomass function, cellulosome reaction formulation, and gene-protein-reaction (GPR) relationships. In addition, it contains the complete list of results for the reciprocal best hits (RBH) of EC numbers missing from the current C. thermocellum annotations, and the complete results from the single gene- and reaction-deletion simulations and the model comparisons to growth on cellobiose and fructose.
1752-0509-4-31-s2.txt (86 kB)
This model file includes tab delimited GPR relationships, reaction list, and sources and escapes for growth on minimal media.
1752-0509-4-31-s3.xml (540 kB)
This file contains the model in SBML format.
1752-0509-4-31-s4.txt (69 kB)
Removed futile cycles. This results file shows reactions which were deleted from the original model build to remove futile cycles.
1752-0509-4-31-s5.doc (2564 kB)
Calculations and additional methods. This file contains detailed methods and sample calculations for determining the biomass objective reaction and the fatty acid content reactions as well as details about simulations of alternative media formulations.
Comments
Originally published open access online through Biomed Central at http://dx.doi.org/10.1186/1752-0509-4-31
Includes five supplemental files:
1. Model details and results. This Excel workbook contains the final reaction list, metabolite definitions, biomass function, cellulosome reaction formulation, and gene-protein-reaction (GPR) relationships. In addition, it contains the complete list of results for the reciprocal best hits (RBH) of EC numbers missing from the current C. thermocellum annotations, and the complete results from the single gene- and reaction-deletion simulations and the model comparisons to growth on cellobiose and fructose.
2. This model file includes tab delimited GPR relationships, reaction list, and sources and escapes for growth on minimal media.
3. This file contains the model in SBML format.
4. Removed futile cycles. This results file shows reactions which were deleted from the original model build to remove futile cycles.
5. Calculations and additional methods. This file contains detailed methods and sample calculations for determining the biomass objective reaction and the fatty acid content reactions as well as details about simulations of alternative media formulations.