Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

Thompson, R. Adam; Dahal, Sanjeev; Garcia, Sergio; Nookaew, Intawat; Trinh, Cong T.

doi:10.1186/s13068-016-0607-x

Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

Journal Article · Tue Sep 06 00:00:00 EDT 2016 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-016-0607-x· OSTI ID:1618657

Thompson, R. Adam; Dahal, Sanjeev; Garcia, Sergio; Nookaew, Intawat; Trinh, Cong T.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1618657

Alternate ID(s):: OSTI ID: 1626975

Journal Information:: Biotechnology for Biofuels, Journal Name: Biotechnology for Biofuels Journal Issue: 1 Vol. 9; ISSN 1754-6834

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (94)

Genome-scale metabolic model integrated with RNAseq data to identify metabolic states of Clostridium thermocellum Gowen, Christopher M.; Fong, Stephen S. Biotechnology Journal, Vol. 5, Issue 7 https://doi.org/10.1002/biot.201000084	journal	July 2010
Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing Salimi, Fahimeh; Zhuang, Kai; Mahadevan, Radhakrishnan Biotechnology Journal, Vol. 5, Issue 7 https://doi.org/10.1002/biot.201000159	journal	July 2010
Economic impact of total solids loading on enzymatic hydrolysis of dilute acid pretreated corn stover Humbird, David; Mohagheghi, Ali; Dowe, Nancy Biotechnology Progress, Vol. 26, Issue 5 https://doi.org/10.1002/btpr.441	journal	April 2010
Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds: Cofactor Specificity Prediction Geertz-Hansen, Henrik Marcus; Blom, Nikolaj; Feist, Adam M. Proteins: Structure, Function, and Bioinformatics, Vol. 82, Issue 9 https://doi.org/10.1002/prot.24536	journal	March 2014
Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Reprograming Microbial Metabolic Pathways Trinh, Cong T.; Thompson, R. Adam Subcellular Biochemistry https://doi.org/10.1007/978-94-007-5055-5_2	book	January 2012
Growth of the thermophilic bacterium Clostridium thermocellum in continuous culture Strobel, Herbert J. Current Microbiology, Vol. 31, Issue 4 https://doi.org/10.1007/BF00298375	journal	October 1995
A theoretical study on the amount of ATP required for synthesis of microbial cell material Stouthamer, A. H. Antonie van Leeuwenhoek, Vol. 39, Issue 1 https://doi.org/10.1007/BF02578899	journal	December 1973
Effect of substrate loading on hydrogen production during anaerobic fermentation by Clostridium thermocellum 27405 Islam, Rumana; Cicek, Nazim; Sparling, Richard Applied Microbiology and Biotechnology, Vol. 72, Issue 3 https://doi.org/10.1007/s00253-006-0316-7	journal	May 2006
End-product induced metabolic shifts in Clostridium thermocellum ATCC 27405 Rydzak, Thomas; Levin, David B.; Cicek, Nazim Applied Microbiology and Biotechnology, Vol. 92, Issue 1 https://doi.org/10.1007/s00253-011-3511-0	journal	August 2011
Role of transcription and enzyme activities in redistribution of carbon and electron flux in response to N2 and H2 sparging of open-batch cultures of Clostridium thermocellum ATCC 27405 Carere, Carlo R.; Rydzak, Thomas; Cicek, Nazim Applied Microbiology and Biotechnology, Vol. 98, Issue 6 https://doi.org/10.1007/s00253-013-5500-y	journal	January 2014
Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum Rydzak, Thomas; Grigoryan, Marina; Cunningham, Zack J. Applied Microbiology and Biotechnology, Vol. 98, Issue 14 https://doi.org/10.1007/s00253-014-5798-0	journal	May 2014
Biosolutions to the energy problem Demain, Arnold L. Journal of Industrial Microbiology & Biotechnology, Vol. 36, Issue 3 https://doi.org/10.1007/s10295-008-0521-8	journal	January 2009
A defined growth medium with very low background carbon for culturing Clostridium thermocellum Holwerda, Evert K.; Hirst, Kyle D.; Lynd, Lee R. Journal of Industrial Microbiology & Biotechnology, Vol. 39, Issue 6 https://doi.org/10.1007/s10295-012-1091-3	journal	February 2012
Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways van der Veen, Douwe; Lo, Jonathan; Brown, Steven D. Journal of Industrial Microbiology & Biotechnology, Vol. 40, Issue 7 https://doi.org/10.1007/s10295-013-1275-5	journal	May 2013
Genome-scale modeling for metabolic engineering Simeonidis, Evangelos; Price, Nathan D. Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 3 https://doi.org/10.1007/s10295-014-1576-3	journal	January 2015
Elimination of formate production in Clostridium thermocellum Rydzak, Thomas; Lynd, Lee R.; Guss, Adam M. Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 9 https://doi.org/10.1007/s10295-015-1644-3	journal	July 2015
TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates Zhao, Min; Chen, YanMing; Qu, DaCheng Science China Life Sciences, Vol. 54, Issue 1 https://doi.org/10.1007/s11427-010-4125-y	journal	January 2011
Transformation of Clostridium Thermocellum by Electroporation Olson, Daniel G.; Lynd, Lee R. Cellulases https://doi.org/10.1016/B978-0-12-415931-0.00017-3	book	January 2012
Extreme Pathways and Kirchhoff's Second Law Price, Nathan D.; Famili, Iman; Beard, Daniel A. Biophysical Journal, Vol. 83, Issue 5 https://doi.org/10.1016/S0006-3495(02)75297-1	journal	November 2002
The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides Shoham, Yuval; Lamed, Raphael; Bayer, Edward A. Trends in Microbiology, Vol. 7, Issue 7 https://doi.org/10.1016/S0966-842X(99)01533-4	journal	July 1999
Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media Kridelbaugh, Donna M.; Nelson, Joshua; Engle, Nancy L. Bioresource Technology, Vol. 130 https://doi.org/10.1016/j.biortech.2012.12.006	journal	February 2013
A review of genome-scale metabolic flux modeling of anaerobiosis in biotechnology Senger, Ryan S.; Yen, Jiun Y.; Fong, Stephen S. Current Opinion in Chemical Engineering, Vol. 6 https://doi.org/10.1016/j.coche.2014.08.003	journal	November 2014
Consolidated bioprocessing of cellulosic biomass: an update Lynd, Lee R.; van Zyl, Willem H.; McBride, John E. Current Opinion in Biotechnology, Vol. 16, Issue 5, p. 577-583 https://doi.org/10.1016/j.copbio.2005.08.009	journal	October 2005
Hydrogen production by Clostridium thermocellum 27405 from cellulosic biomass substrates Levin, D.; Islam, R.; Cicek, N. International Journal of Hydrogen Energy, Vol. 31, Issue 11 https://doi.org/10.1016/j.ijhydene.2006.06.015	journal	September 2006
Growth phase-dependant enzyme profile of pyruvate catabolism and end-product formation in Clostridium thermocellum ATCC 27405 Rydzak, Thomas; Levin, David B.; Cicek, Nazim Journal of Biotechnology, Vol. 140, Issue 3-4 https://doi.org/10.1016/j.jbiotec.2009.01.022	journal	March 2009
Computing complex metabolic intervention strategies using constrained minimal cut sets Hädicke, Oliver; Klamt, Steffen Metabolic Engineering, Vol. 13, Issue 2 https://doi.org/10.1016/j.ymben.2010.12.004	journal	March 2011
Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum Deng, Yu; Olson, Daniel G.; Zhou, Jilai Metabolic Engineering, Vol. 15, p. 151-158 https://doi.org/10.1016/j.ymben.2012.11.006	journal	January 2013
Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum Lin, Paul P.; Mi, Luo; Morioka, Amy H. Metabolic Engineering, Vol. 31 https://doi.org/10.1016/j.ymben.2015.07.001	journal	September 2015
Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum Papanek, Beth; Biswas, Ranjita; Rydzak, Thomas Metabolic Engineering, Vol. 32 https://doi.org/10.1016/j.ymben.2015.09.002	journal	November 2015
Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M. Metabolic Engineering, Vol. 32 https://doi.org/10.1016/j.ymben.2015.10.004	journal	November 2015
Rational design of efficient modular cells Trinh, Cong T.; Liu, Yan; Conner, David J. Metabolic Engineering, Vol. 32 https://doi.org/10.1016/j.ymben.2015.10.005	journal	November 2015
The fermentation of cellulose by thermophilic bacteria Viljoen, J. A.; Fred, E. B.; Peterson, W. H. The Journal of Agricultural Science, Vol. 16, Issue 1 https://doi.org/10.1017/S0021859600088249	journal	January 1926
Global organization of metabolic fluxes in the bacterium Escherichia coli Almaas, E.; Kovács, B.; Vicsek, T. Nature, Vol. 427, Issue 6977 https://doi.org/10.1038/nature02289	journal	February 2004
How biotech can transform biofuels Lynd, Lee R.; Laser, Mark S.; Bransby, David Nature Biotechnology, Vol. 26, Issue 2, p. 169-172 https://doi.org/10.1038/nbt0208-169	journal	February 2008
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli Feist, Adam M.; Palsson, Bernhard Ø Nature Biotechnology, Vol. 26, Issue 6 https://doi.org/10.1038/nbt1401	journal	June 2008
A protocol for generating a high-quality genome-scale metabolic reconstruction Thiele, Ines; Palsson, Bernhard Ø Nature Protocols, Vol. 5, Issue 1 https://doi.org/10.1038/nprot.2009.203	journal	January 2010
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T. Nature Protocols, Vol. 6, Issue 9 https://doi.org/10.1038/nprot.2011.308	journal	August 2011
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O. Nature Reviews Microbiology, Vol. 10, Issue 4 https://doi.org/10.1038/nrmicro2737	journal	February 2012
Cellulose utilization by Clostridium thermocellum: Bioenergetics and hydrolysis product assimilation Zhang, Y. -H. P.; Lynd, L. R. Proceedings of the National Academy of Sciences, Vol. 102, Issue 20 https://doi.org/10.1073/pnas.0408734102	journal	May 2005
Use of Randomized Sampling for Analysis of Metabolic Networks Schellenberger, Jan; Palsson, Bernhard Ø. Journal of Biological Chemistry, Vol. 284, Issue 9 https://doi.org/10.1074/jbc.R800048200	journal	October 2008
Reconciliation of metabolites and biochemical reactions for metabolic networks Bernard, T.; Bridge, A.; Morgat, A. Briefings in Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1093/bib/bbs058	journal	November 2012
InterProScan - an integration platform for the signature-recognition methods in InterPro Zdobnov, E. M.; Apweiler, R. Bioinformatics, Vol. 17, Issue 9, p. 847-848 https://doi.org/10.1093/bioinformatics/17.9.847	journal	September 2001
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks Ganter, M.; Bernard, T.; Moretti, S. Bioinformatics, Vol. 29, Issue 6 https://doi.org/10.1093/bioinformatics/btt036	journal	January 2013
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition Hunt, Kristopher A.; Folsom, James P.; Taffs, Reed L. Bioinformatics, Vol. 30, Issue 11 https://doi.org/10.1093/bioinformatics/btu021	journal	February 2014
FluxModeCalculator: an efficient tool for large-scale flux mode computation: Table 1. van Klinken, Jan Bert; Willems van Dijk, Ko Bioinformatics, Vol. 32, Issue 8 https://doi.org/10.1093/bioinformatics/btv742	journal	December 2015
Metabolic modeling of clostridia: current developments and applications Dash, Satyakam; Ng, Chiam Yu; Maranas, Costas D. FEMS Microbiology Letters, Vol. 363, Issue 4 https://doi.org/10.1093/femsle/fnw004	journal	January 2016
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
BRENDA, the enzyme information system in 2011 Scheer, M.; Grote, A.; Chang, A. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1089	journal	November 2010
A new bioinformatics analysis tools framework at EMBL-EBI Goujon, M.; McWilliam, H.; Li, W. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq313	journal	May 2010
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, R.; Altman, T.; Dreher, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1014	journal	November 2011
HMMER web server: 2015 update Finn, Robert D.; Clements, Jody; Arndt, William Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv397	journal	May 2015
The maintenance energy of bacteria in growing cultures Pirt, S. J. Proceedings of the Royal Society of London. Series B. Biological Sciences, Vol. 163, Issue 991, p. 224-231 https://doi.org/10.1098/rspb.1965.0069	journal	October 1965
Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium thermocellum and Creation of a pta Mutant Tripathi, S. A.; Olson, D. G.; Argyros, D. A. Applied and Environmental Microbiology, Vol. 76, Issue 19, p. 6591-6599 https://doi.org/10.1128/AEM.01484-10	journal	August 2010
Global Gene Expression Patterns in Clostridium thermocellum as Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose Riederer, Allison; Takasuka, Taichi E.; Makino, Shin-ichi Applied and Environmental Microbiology, Vol. 77, Issue 4 https://doi.org/10.1128/AEM.02008-10	journal	December 2010
Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses Trinh, C. T.; Unrean, P.; Srienc, F. Applied and Environmental Microbiology, Vol. 74, Issue 12, p. 3634-3643 https://doi.org/10.1128/AEM.02708-07	journal	April 2008
Reassessment of the Transhydrogenase/Malate Shunt Pathway in Clostridium thermocellum ATCC 27405 through Kinetic Characterization of Malic Enzyme and Malate Dehydrogenase Taillefer, M.; Rydzak, T.; Levin, D. B. Applied and Environmental Microbiology, Vol. 81, Issue 7 https://doi.org/10.1128/AEM.03360-14	journal	January 2015
Atypical Glycolysis in Clostridium thermocellum Zhou, Jilai; Olson, Daniel G.; Argyros, D. Aaron Applied and Environmental Microbiology, Vol. 79, Issue 9, p. 3000-3008 https://doi.org/10.1128/AEM.04037-12	journal	February 2013
Fermentation of cellulose and cellobiose by Clostridium thermocellum in the absence of Methanobacterium thermoautotrophicum. Weimer, P. J.; Zeikus, J. G. Applied and Environmental Microbiology, Vol. 33, Issue 2 https://doi.org/10.1128/AEM.33.2.289-297.1977	journal	January 1977
Relationship Between Substrate Concentration and Fermentation Product Ratios in Clostridium thermocellum Cultures † Brener, David; Johnson, Byron F. Applied and Environmental Microbiology, Vol. 47, Issue 5 https://doi.org/10.1128/AEM.47.5.1126-1129.1984	journal	January 1984
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Varma, A.; Palsson, B. O. Applied and Environmental Microbiology, Vol. 60, Issue 10 https://doi.org/10.1128/AEM.60.10.3724-3731.1994	journal	January 1994
Carbohydrate Transport by the Anaerobic Thermophile Clostridium thermocellum LQRI. Strobel, H. J.; Caldwell, F. C.; Dawson, K. A. Applied and environmental microbiology, Vol. 61, Issue 11 https://doi.org/10.1128/AEM.61.11.4012-4015.1995	journal	January 1995
Kinetics and Relative Importance of Phosphorolytic and Hydrolytic Cleavage of Cellodextrins and Cellobiose in Cell Extracts of Clostridium thermocellum Zhang, Y. -H. P.; Lynd, L. R. Applied and Environmental Microbiology, Vol. 70, Issue 3 https://doi.org/10.1128/AEM.70.3.1563-1569.2004	journal	March 2004
Expression of 17 Genes in Clostridium thermocellum ATCC 27405 during Fermentation of Cellulose or Cellobiose in Continuous Culture Stevenson, D. M.; Weimer, P. J. Applied and Environmental Microbiology, Vol. 71, Issue 8 https://doi.org/10.1128/AEM.71.8.4672-4678.2005	journal	August 2005
Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313 Feinberg, L.; Foden, J.; Barrett, T. Journal of Bacteriology, Vol. 193, Issue 11, p. 2906-2907 https://doi.org/10.1128/JB.00322-11	journal	April 2011
Global View of the Clostridium thermocellum Cellulosome Revealed by Quantitative Proteomic Analysis Gold, N. D.; Martin, V. J. J. Journal of Bacteriology, Vol. 189, Issue 19 https://doi.org/10.1128/JB.00882-07	journal	July 2007
Cellodextrin and Laminaribiose ABC Transporters in Clostridium thermocellum Nataf, Y.; Yaron, S.; Stahl, F. Journal of Bacteriology, Vol. 191, Issue 1 https://doi.org/10.1128/JB.01190-08	journal	October 2008
Ethanol Production by Thermophilic Bacteria: Relationship Between Fermentation Product Yields of and Catabolic Enzyme Activities in Clostridium thermocellum and Thermoanaerobium brockii Lamed, R.; Zeikus, J. G. Journal of Bacteriology, Vol. 144, Issue 2 https://doi.org/10.1128/JB.144.2.569-578.1980	journal	January 1980
Adherence of Clostridium thermocellum to cellulose. Bayer, E. A.; Kenig, R.; Lamed, R. Journal of Bacteriology, Vol. 156, Issue 2 https://doi.org/10.1128/JB.156.2.818-827.1983	journal	January 1983
Characterization of a cellulose-binding, cellulase-containing complex in Clostridium thermocellum. Lamed, R.; Setter, E.; Bayer, E. A. Journal of Bacteriology, Vol. 156, Issue 2 https://doi.org/10.1128/JB.156.2.828-836.1983	journal	January 1983
Regulation of the Cellulosomal celS (cel48A) Gene of Clostridium thermocellum Is Growth Rate Dependent Dror, T. W.; Morag, E.; Rolider, A. Journal of Bacteriology, Vol. 185, Issue 10 https://doi.org/10.1128/JB.185.10.3042-3048.2003	journal	May 2003
Regulation of Cellulase Synthesis in Batch and Continuous Cultures of Clostridium thermocellum Zhang, Y.-H. P.; Lynd, L. R. Journal of Bacteriology, Vol. 187, Issue 1, p. 99-106 https://doi.org/10.1128/JB.187.1.99-106.2005	journal	December 2004
Microbial Cellulose Utilization: Fundamentals and Biotechnology Lynd, L. R.; Weimer, P. J.; van Zyl, W. H. Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577 https://doi.org/10.1128/MMBR.66.3.506-577.2002	journal	September 2002
Cellulase, Clostridia, and Ethanol Demain, A. L.; Newcomb, M.; Wu, J. H. D. Microbiology and Molecular Biology Reviews, Vol. 69, Issue 1, p. 124-154 https://doi.org/10.1128/MMBR.69.1.124-154.2005	journal	March 2005
The Status of YATP and Maintenance Energy as Biologically Interpretable Phenomena Tempest, D. W.; Neijssel, O. M. Annual Review of Microbiology, Vol. 38, Issue 1 https://doi.org/10.1146/annurev.mi.38.100184.002331	journal	October 1984
Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation Raman, Babu; McKeown, Catherine K; Rodriguez, Miguel BMC Microbiology, Vol. 11, Issue 1, Article No. 134 https://doi.org/10.1186/1471-2180-11-134	journal	January 2011
Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression Rydzak, Thomas; McQueen, Peter D.; Krokhin, Oleg V. BMC Microbiology, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2180-12-214	journal	January 2012
Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network Chung, Bevan Kai Sheng; Lee, Dong-Yup BMC Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1186/1752-0509-3-117	journal	December 2009
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production Roberts, Seth B.; Gowen, Christopher M.; Brooks, J. Paul BMC Systems Biology, Vol. 4, Issue 1, Article No. 31 https://doi.org/10.1186/1752-0509-4-31	journal	January 2010
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 Milne, Caroline B.; Eddy, James A.; Raju, Ravali BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-130	journal	January 2011
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico McAnulty, Michael J.; Yen, Jiun Y.; Freedman, Benjamin G. BMC Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1186/1752-0509-6-42	journal	January 2012
Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass Wilson, Charlotte M.; Rodriguez, Miguel; Johnson, Courtney M. Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-179	journal	January 2013
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H. Genome Biology, Vol. 4, Issue 9, p. R54 https://doi.org/10.1186/gb-2003-4-9-r54	journal	August 2003
The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading Holwerda, Evert K.; Thorne, Philip G.; Olson, Daniel G. Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/s13068-014-0155-1	journal	October 2014
Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G. Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0204-4	journal	January 2015
Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation Sander, Kyle; Wilson, Charlotte M.; Rodriguez, Miguel Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0394-9	journal	December 2015
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes Bordel, Sergio; Agren, Rasmus; Nielsen, Jens PLoS Computational Biology, Vol. 6, Issue 7 https://doi.org/10.1371/journal.pcbi.1000859	journal	July 2010
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum Agren, Rasmus; Liu, Liming; Shoaie, Saeed PLoS Computational Biology, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pcbi.1002980	journal	March 2013
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks von Kamp, Axel; Klamt, Steffen PLoS Computational Biology, Vol. 10, Issue 1 https://doi.org/10.1371/journal.pcbi.1003378	journal	January 2014
Impact of Pretreated Switchgrass and Biomass Carbohydrates on Clostridium thermocellum ATCC 27405 Cellulosome Composition: A Quantitative Proteomic Analysis Raman, Babu; Pan, Chongle; Hurst, Gregory B. PLoS ONE, Vol. 4, Issue 4, Article No. e5271 https://doi.org/10.1371/journal.pone.0005271	journal	April 2009
Increase in Ethanol Yield via Elimination of Lactate Production in an Ethanol-Tolerant Mutant of Clostridium thermocellum Biswas, Ranjita; Prabhu, Sandeep; Lynd, Lee R. PLoS ONE, Vol. 9, Issue 2 https://doi.org/10.1371/journal.pone.0086389	journal	February 2014
optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks Megchelenbrink, Wout; Huynen, Martijn; Marchiori, Elena PLoS ONE, Vol. 9, Issue 2 https://doi.org/10.1371/journal.pone.0086587	journal	February 2014
The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications Akinosho, Hannah; Yee, Kelsey; Close, Dan Frontiers in Chemistry, Vol. 2 https://doi.org/10.3389/fchem.2014.00066	journal	August 2014
Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq Wei, Hui; Fu, Yan; Magnusson, Lauren Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00142	journal	April 2014

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Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

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