Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model
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Costas D Maranas | Satyakam Dash | C. Maranas | E. Papoutsakis | Satyakam Dash | K. Venkataramanan | Eleftherios T Papoutsakis | T. Mueller | Keerthi P Venkataramanan | Thomas J Mueller
[1] H. Bahl,et al. A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--solvent stress caused by a transient n-butanol pulse. , 2012, Journal of biotechnology.
[2] E. Papoutsakis,et al. Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by Clostridium acetobutylicum. , 1999, Metabolic engineering.
[3] E. Papoutsakis,et al. Solventogenesis in Clostridium acetobutylicum fermentations related to carboxylic acid and proton concentrations , 1988, Biotechnology and bioengineering.
[4] G. Eggink,et al. Disruption of the acetate kinase (ack) gene of Clostridium acetobutylicum results in delayed acetate production , 2012, Applied Microbiology and Biotechnology.
[5] A. Barabasi,et al. Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.
[6] C. Schilling,et al. Flux coupling analysis of genome-scale metabolic network reconstructions. , 2004, Genome research.
[7] E. Papoutsakis,et al. Genome‐scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis , 2008, Biotechnology and bioengineering.
[8] E. Papoutsakis,et al. The transcriptional program underlying the physiology of clostridial sporulation , 2008, Genome Biology.
[9] Jeffrey D Orth,et al. What is flux balance analysis? , 2010, Nature Biotechnology.
[10] E. Papoutsakis,et al. The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum , 2013, BMC Genomics.
[11] B. Palsson,et al. Elimination of thermodynamically infeasible loops in steady-state metabolic models. , 2011, Biophysical journal.
[12] Bernhard O. Palsson,et al. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data , 2013, Bioinform..
[13] Y. Jang,et al. Enhanced Butanol Production Obtained by Reinforcing the Direct Butanol-Forming Route in Clostridium acetobutylicum , 2012, mBio.
[14] Dipak Barua,et al. An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models , 2010, PLoS Comput. Biol..
[15] Weihong Jiang,et al. Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio. , 2009, Metabolic engineering.
[16] Desmond S. Lun,et al. Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production , 2009, PLoS Comput. Biol..
[17] B. Palsson,et al. Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .
[18] A. Burgard,et al. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.
[19] New insights into the butyric acid metabolism of Clostridium acetobutylicum , 2012, Applied Microbiology and Biotechnology.
[20] Adam M. Feist,et al. Modeling methanogenesis with a genome‐scale metabolic reconstruction of Methanosarcina barkeri , 2006 .
[21] E. Papoutsakis. Engineering solventogenic clostridia. , 2008, Current opinion in biotechnology.
[22] K. Schwarz,et al. A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--cellular behavior in adaptation to n-butanol. , 2012, Journal of biotechnology.
[23] A. Barabasi,et al. Predicting synthetic rescues in metabolic networks , 2008, Molecular systems biology.
[24] T. Jeffries,et al. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. , 2004, Metabolic engineering.
[25] E. Papoutsakis,et al. Metabolite stress and tolerance in the production of biofuels and chemicals: Gene‐expression‐based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum , 2010, Biotechnology and bioengineering.
[26] Maciek R Antoniewicz,et al. Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis. , 2011, Biotechnology journal.
[27] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .
[28] E. T. Papoutsakis,et al. Continuous and biomass recycle fermentations of Clostridium acetobutylicum , 1989 .
[29] Eytan Ruppin,et al. Model-based identification of drug targets that revert disrupted metabolism and its application to ageing , 2013, Nature Communications.
[30] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[31] G. Stephanopoulos,et al. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. , 2005, Metabolic engineering.
[32] R. Sharan,et al. A genome-scale computational study of the interplay between transcriptional regulation and metabolism , 2007, Molecular systems biology.
[33] E. Papoutsakis,et al. Increased levels of ATP and NADH are associated with increased solvent production in continuous cultures of Clostridium acetobutylicum , 1989, Applied Microbiology and Biotechnology.
[34] Effect of acetoacetate, butyrate, and uncoupling ionophores on growth and product formation ofClostridium acetobutylicum , 2005, Biotechnology Letters.
[35] Sang Yup Lee,et al. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network , 2008, Applied Microbiology and Biotechnology.
[36] Costas D. Maranas,et al. OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions , 2010, PLoS Comput. Biol..
[37] N. Price,et al. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis , 2010, Proceedings of the National Academy of Sciences.
[38] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.
[39] E. Papoutsakis,et al. Carbon monoxide gasing leads to alcohol production and butyrate uptake without acetone formation in continuous cultures ofClostridium acetobutylicum , 1986, Applied Microbiology and Biotechnology.
[40] J. Rabinowitz,et al. Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum , 2011, Applied and Environmental Microbiology.
[41] Maciek R Antoniewicz,et al. Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for (13)C metabolic flux analysis. , 2014, Metabolic engineering.
[42] Ying Zhang,et al. Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway. , 2012, Metabolic engineering.
[43] Costas D. Maranas,et al. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases , 2012, BMC Bioinformatics.
[44] E. Papoutsakis,et al. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. , 2012, Current opinion in biotechnology.
[45] R. Tibshirani,et al. Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[46] B. Palsson,et al. Towards multidimensional genome annotation , 2006, Nature Reviews Genetics.
[47] Wei Zhu,et al. The TIGR Plant Transcript Assemblies database , 2006, Nucleic Acids Res..
[48] D. Lehmann,et al. Switching Clostridium acetobutylicum to an ethanol producer by disruption of the butyrate/butanol fermentative pathway. , 2011, Metabolic Engineering.
[49] Ryan S. Senger,et al. Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico , 2012, BMC Systems Biology.
[50] Chao Huang,et al. Engineering Clostridium acetobutylicum for alcohol production. , 2013, Journal of biotechnology.
[51] C. Maranas,et al. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. , 2006, Metabolic engineering.
[52] P. Soucaille,et al. Regulation of carbon and electron flow in Clostridium acetobutylicum grown in chemostat culture at neutral pH on mixtures of glucose and glycerol , 1994, Journal of bacteriology.
[53] Thomas J. Mueller,et al. Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow , 2013, BMC Systems Biology.
[54] B. Palsson,et al. Regulation of gene expression in flux balance models of metabolism. , 2001, Journal of theoretical biology.
[55] Kelvin H. Lee,et al. Workflow for quantitative proteomic analysis of Clostridium acetobutylicum ATCC 824 using iTRAQ tags. , 2013, Methods.
[56] Jochen Förster,et al. Modeling Lactococcus lactis using a genome-scale flux model , 2005, BMC Microbiology.
[57] Cathy H. Wu,et al. Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress , 2013, BMC Systems Biology.
[58] E. Papoutsakis. Equations and calculations for fermentations of butyric acid bacteria , 1984, Biotechnology and bioengineering.