Demain AL. Biosolutions to the energy problem. J Ind Microbiol Biotechnol. 2009;36:319–32.

Article
CAS
Google Scholar

Lynd L, Zyl W, McBride J, Laser M. Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol. 2005;16:577–83.

Article
CAS
Google Scholar

Lynd LR, Laser MS, Bransby D, Dale BE, Davison B, Hamilton R, Himmel M, Keller M, McMillan JD, Sheehan J, Wyman CE. How biotech can transform biofuels. Nat Biotechnol. 2008;26:169–72.

Article
CAS
Google Scholar

van Zyl WH, Lynd LR, den Haan R, McBride JE. Consolidated bioprocessing for bioethanol production using *Saccharomyces cerevisiae*. Adv Biochem Eng Biotechnol. 2007;108:205–35.

Google Scholar

Demain AL, Newcomb M, Wu JH. Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev. 2005;69:124–54.

Article
CAS
Google Scholar

Lynd L, Weimer P, van Zyl W, Pretorius I. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev. 2002;66:506–77.

Article
CAS
Google Scholar

Lamed R, Zeikus JG. Ethanol production by thermophilic bacteria: relationship between fermentation product yields of and catabolic enzyme activities in *Clostridium thermocellum* and *Thermoanaerobium brockii*. J Bacteriol. 1980;144:569–78.

CAS
Google Scholar

Levin DB, Islam R, Cicek N, Sparling R. Hydrogen production by *Clostridium thermocellum* 27405 from cellulosic biomass substrates. Int J Hydrogen Energy. 2006;31:1496–503.

Article
CAS
Google Scholar

Holwerda E, Thorne P, Olson D, Amador-Noguez D, Engle N, Tschaplinski T, van Dijken J, Lynd L. The exometabolome of *Clostridium thermocellum* reveals overflow metabolism at high cellulose loading. Biotechnol Biofuels. 2014;7:155.

Article
Google Scholar

Lamed R, Setter E, Bayer EA. Characterization of a cellulose-binding, cellulase-containing complex in *Clostridium thermocellum*. J Bacteriol. 1983;156:828–36.

CAS
Google Scholar

Bayer EA, Kenig R, Lamed R. Adherence of *Clostridium thermocellum* to cellulose. J Bacteriol. 1983;156:818–27.

CAS
Google Scholar

Shoham Y, Lamed R, Bayer EA. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides. Trends Microbiol. 1999;7:275–81.

Article
CAS
Google Scholar

Rydzak T, Levin D, Cicek N, Sparling R. Growth phase-dependant enzyme profile of pyruvate catabolism and end-product formation in *Clostridium thermocellum* ATCC 27405. J Biotechnol. 2009;140:169–75.

Article
CAS
Google Scholar

Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, Murphy DM, McCool JD, Warner AK, Rajgarhia VB, Lynd LR, et al. Development of *pyrF*-based genetic system for targeted gene deletion in *Clostridium thermocellum* and creation of a pta mutant. Appl Environ Microbiol. 2010;76:6591–9.

Article
CAS
Google Scholar

Biswas R, Prabhu S, Lynd LR, Guss AM. Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of *Clostridium thermocellum*. PLoS One. 2014;9:e86389.

Article
Google Scholar

van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, Engle NL, van den Berg RA, Argyros AD, Caiazza NC, et al. Characterization of *Clostridium thermocellum* strains with disrupted fermentation end-product pathways. J Ind Microbiol Biotechnol. 2013;40:725–34.

Article
CAS
Google Scholar

Biswas R, Zheng T, Olson D, Lynd L, Guss A. Elimination of hydrogenase active site assembly blocks H_{2} production and increases ethanol yield in *Clostridium thermocellum*. Biotechnol Biofuels. 2015;8:20.

Article
Google Scholar

Rydzak T, Lynd L, Guss A. Elimination of formate production in *Clostridium thermocellum*. J Ind Microbiol Biotechnol. 2015;42:1263–72.

Article
CAS
Google Scholar

Papanek B, Biswas R, Rydzak T, Guss AM. Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in *Clostridium thermocellum*. Metab Eng. 2015;32:49–54.

Article
CAS
Google Scholar

Deng Y, Olson DG, Zhou J, Herring CD, Shaw AJ, Lynd LR. Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in *Clostridium thermocellum*. Metab Eng. 2013;15:151–8.

Article
CAS
Google Scholar

Brener D, Johnson B. Relationship between substrate concentration and fermentation product ratios in *Clostridium thermocellum* cultures. Appl Environ Microbiol. 1984;47:1126–9.

CAS
Google Scholar

Feist A, Palsson B. The growing scope of applications of genome-scale metabolic reconstructions using *Escherichia coli*. Nat Biotech. 2008;26:659–67.

Article
CAS
Google Scholar

Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods. Nat Rev Micro. 2012;10:291–305.

CAS
Google Scholar

Senger RS, Yen JY, Fong SS. A review of genome-scale metabolic flux modeling of anaerobiosis in biotechnology. Curr Opin Chem Eng. 2014;6:33–42.

Article
Google Scholar

Simeonidis E, Price N. Genome-scale modeling for metabolic engineering. J Ind Microbiol Biotechnol. 2015;42:327–38.

Article
CAS
Google Scholar

Roberts S, Gowen C, Brooks JP, Fong S. Genome-scale metabolic analysis of *Clostridium thermocellum* for bioethanol production. BMC Syst Biol. 2010;4:31.

Article
Google Scholar

Gowen CM, Fong SS. Genome-scale metabolic model integrated with RNAseq data to identify metabolic states of *Clostridium thermocellum*. Biotechnol J. 2010;5:759–67.

Article
CAS
Google Scholar

Dash S, Ng CY, Maranas CD. Metabolic modeling of clostridia: current developments and applications. FEMS Microbiol Lett. 2016;363(4). doi:10.1093/femsle/fnw004

Zhou J, Olson DG, Argyros DA, Deng Y, van Gulik WM, van Dijken JP, Lynd LR. Atypical glycolysis in *Clostridium thermocellum*. Appl Environ Microbiol. 2013;79:3000–8.

Article
CAS
Google Scholar

Rydzak T, McQueen PD, Krokhin OV, Spicer V, Ezzati P, Dwivedi RC, Shamshurin D, Levin DB, Wilkins JA, Sparling R. Proteomic analysis of *Clostridium thermocellum* core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. BMC Microbiol. 2012;12:214.

Article
CAS
Google Scholar

Carere C, Rydzak T, Cicek N, Levin D, Sparling R. Role of transcription and enzyme activities in redistribution of carbon and electron flux in response to N_{2} and H_{2} sparging of open-batch cultures of *Clostridium thermocellum* ATCC 27405. Appl Microbiol Biotechnol. 2014;98:2829–40.

Article
CAS
Google Scholar

Rydzak T, Grigoryan M, Cunningham Z, Krokhin O, Ezzati P, Cicek N, Levin D, Wilkins J, Sparling R. Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in *Clostridium thermocellum*. Appl Microbiol Biotechnol 2014;98(14):6497-510. doi:10.1007/s00253-014-5798-0.

Article
CAS
Google Scholar

Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, et al. Complete genome sequence of the cellulolytic thermophile *Clostridium thermocellum* DSM 1313. J Bacteriol. 2011;193:2906–7.

Article
CAS
Google Scholar

Olson DG, Lynd LR. Transformation of *Clostridium thermocellum* by electroporation. Methods Enzymol. 2012;510:317–30.

Article
CAS
Google Scholar

Zhang Y-HP, Lynd LR. Regulation of cellulase synthesis in batch and continuous cultures of *Clostridium thermocellum*. J Bacteriol. 2005;187:99–106.

Article
CAS
Google Scholar

Thompson RA, Layton DS, Guss AM, Olson DG, Lynd LR, Trinh CT. Elucidating central metabolic redox obstacles hindering ethanol production in *Clostridium thermocellum*. Metab Eng. 2015;32:207–19.

Article
CAS
Google Scholar

Zhang Y-HP, Lynd LR. Kinetics and relative importance of phosphorolytic and hydrolytic cleavage of cellodextrins and cellobiose in cell extracts of *Clostridium thermocellum*. Appl Environ Microbiol. 2004;70:1563–9.

Article
CAS
Google Scholar

Zhang Y-HP, Lynd LR. Cellulose utilization by *Clostridium thermocellum*: bioenergetics and hydrolysis product assimilation. Proc Natl Acad Sci USA. 2005;102:7321–5.

Article
CAS
Google Scholar

Reed J, Vo T, Schilling C, Palsson B. An expanded genome-scale model of *Escherichia coli* K-12 (iJR904 GSM/GPR). Genome Biol. 2003;4:R54.

Article
Google Scholar

Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins. 2014;82:1819–28.

Article
CAS
Google Scholar

Dror TW, Morag E, Rolider A, Bayer EA, Lamed R, Shoham Y. Regulation of the cellulosomal celS (cel48A) gene of *Clostridium thermocellum* is growth rate dependent. J Bacteriol. 2003;185:3042–8.

Article
CAS
Google Scholar

Nataf Y, Yaron S, Stahl F, Lamed R, Bayer EA, Scheper T-H, Sonenshein AL, Shoham Y. Cellodextrin and laminaribiose ABC transporters in *Clostridium thermocellum*. J Bacteriol. 2009;191:203–9.

Article
CAS
Google Scholar

Raman B, Pan C, Hurst GB, Rodriguez M Jr, McKeown CK, Lankford PK, Samatova NF, Mielenz JR. Impact of pretreated switchgrass and biomass carbohydrates on *Clostridium thermocellum* ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One. 2009;4:e5271.

Article
Google Scholar

Holwerda EK, Hirst KD, Lynd LR. A defined growth medium with very low background carbon for culturing *Clostridium thermocellum*. J Ind Microbiol Biotechnol. 2012;39:943–7.

Article
CAS
Google Scholar

Neidhardt FC, Ingraham JL, Schaechter M. Physiology of the bacterial cell: a molecular approach. Sunderland: Sinauer Associates; 1990.

Google Scholar

Stouthamer AH. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie Van Leeuwenhoek. 1973;39:545–65.

Article
CAS
Google Scholar

Pirt S. The maintenance energy of bacteria in growing cultures. Proc R Soc Lond B Biol Sci. 1965;163:224–31.

Article
CAS
Google Scholar

Tempest DW, Neijssel OM. The status of YATP and maintenance energy as biologically interpretable phenomena. Annu Rev Microbiol. 1984;38:459–513.

Article
CAS
Google Scholar

Humbird D, Mohagheghi A, Dowe N, Schell DJ. Economic impact of total solids loading on enzymatic hydrolysis of dilute acid pretreated corn stover. Biotechnol Prog. 2010;26:1245–51.

Article
CAS
Google Scholar

Hädicke O, Klamt S. Computing complex metabolic intervention strategies using constrained minimal cut sets. Metab Eng. 2011;13:204–13.

Article
Google Scholar

Trinh CT, Unrean P, Srienc F. Minimal *Escherichia coli* cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol. 2008;74:3634–43.

Article
CAS
Google Scholar

Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, Papanek BA, Riley LA, Guss AM, Liao JC. Consolidated bioprocessing of cellulose to isobutanol using *Clostridium thermocellum*. Metab Eng. 2015;31:44–52.

Article
CAS
Google Scholar

Islam R, Cicek N, Sparling R, Levin D. Effect of substrate loading on hydrogen production during anaerobic fermentation by *Clostridium thermocellum* 27405. Appl Microbiol Biotechnol. 2006;72:576–83.

Article
CAS
Google Scholar

von Kamp A, Klamt S. Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput Biol. 2014;10:e1003378.

Article
Google Scholar

Strobel HJ. Growth of the thermophilic bacterium *Clostridium thermocellum* in continuous culture. Curr Microbiol. 1995;31:210–4.

Article
CAS
Google Scholar

Strobel HJ, Caldwell FC, Dawson KA. Carbohydrate transport by the anaerobic thermophile *Clostridium thermocellum* LQRI. Appl Environ Microbiol. 1995;61:4012–5.

CAS
Google Scholar

Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium *Escherichia coli*. Nature. 2004;427:839–43.

Article
CAS
Google Scholar

Schellenberger J, Palsson BO. Use of randomized sampling for analysis of metabolic networks. J Biol Chem. 2009;284:5457–61.

Article
CAS
Google Scholar

Bordel S, Agren R, Nielsen J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput Biol. 2010;6:e1000859.

Article
Google Scholar

Chung BK, Lee DY. Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. BMC Syst Biol. 2009;3:117.

Article
Google Scholar

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular biology of the cell. 4th ed. New York: Garland Science; 2002.

Google Scholar

Riederer A, Takasuka TE, Makino S-I, Stevenson DM, Bukhman YV, Elsen NL, Fox BG. Global gene expression patterns in *Clostridium thermocellum* as determined by microarray analysis of chemostat cultures on cellulose or cellobiose. Appl Environ Microbiol. 2011;77:1243–53.

Article
CAS
Google Scholar

Stevenson DM, Weimer PJ. Expression of 17 Genes in *Clostridium thermocellum* ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture. Appl Environ Microbiol. 2005;71:4672–8.

Article
CAS
Google Scholar

Raman B, McKeown CK, Rodriguez M Jr, Brown SD, Mielenz JR. Transcriptomic analysis of *Clostridium thermocellum* ATCC 27405 cellulose fermentation. BMC Microbiol. 2011;11:134.

Article
CAS
Google Scholar

Taillefer M, Rydzak T, Levin DB, Oresnik IJ, Sparling R. Reassessment of the transhydrogenase/malate shunt pathway in *Clostridium thermocellum* ATCC 27405 through kinetic characterization of malic enzyme and malate dehydrogenase. Appl Environ Microbiol. 2015;81:2423–32.

Article
CAS
Google Scholar

Rydzak T, Levin DB, Cicek N, Sparling R. End-product induced metabolic shifts in *Clostridium thermocellum* ATCC 27405. Appl Microbiol Biotechnol. 2011;92:199–209.

Article
CAS
Google Scholar

Wei H, Fu Y, Magnusson L, Baker JO, Maness P-C, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, et al. Comparison of transcriptional profiles of *Clostridium thermocellum* grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front Microbiol. 2014;5:142.

Article
Google Scholar

Sander K, Wilson CM, Rodriguez M, Klingeman DM, Rydzak T, Davison BH, Brown SD. *Clostridium thermocellum* DSM 1313 transcriptional responses to redox perturbation. Biotechnol Biofuels. 2015;8:211.

Article
Google Scholar

Viljoen JA, Fred EB, Peterson WH. The fermentation of cellulose by thermophilic bacteria. Journal Agric Sci. 1926;16:1–17.

Article
CAS
Google Scholar

Akinosho H, Yee K, Close D, Ragauskas A. The emergence of *Clostridium thermocellum* as a high utility candidate for consolidated bioprocessing applications. Front Chem. 2014;2:66.

Article
Google Scholar

Weimer PJ, Zeikus JG. Fermentation of cellulose and cellobiose by *Clostridium thermocellum* in the absence of *Methanobacterium thermoautotrophicum*. Appl Environ Microbiol. 1977;33:289–97.

CAS
Google Scholar

Trinh CT, Liu Y, Conner DJ. Rational design of efficient modular cells. Metab Eng. 2015;32:220–31.

Article
CAS
Google Scholar

Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for *Penicillium chrysogenum*. PLoS Comput Biol. 2013;9:e1002980.

Article
CAS
Google Scholar

Zdobnov EM, Apweiler R. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847–8.

Article
CAS
Google Scholar

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 2010;38:W695–9.

Article
CAS
Google Scholar

Milne C, Eddy J, Raju R, Ardekani S, Kim P-J, Senger R, Jin Y-S, Blaschek H, Price N. Metabolic network reconstruction and genome-scale model of butanol-producing strain *Clostridium beijerinckii* NCIMB 8052. BMC Syst Biol. 2011;5:130.

Article
CAS
Google Scholar

Salimi F, Zhuang K, Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J. 2010;5:726–38.

Article
CAS
Google Scholar

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. HMMER web server: 2015 update. Nucleic Acids Res. 2015;43:W30–8.

Article
Google Scholar

Zhao M, Chen Y, Qu D, Qu H. TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates. Sci China Life Sci. 2011;54:60–4.

Article
CAS
Google Scholar

Kridelbaugh DM, Nelson J, Engle NL, Tschaplinski TJ, Graham DE. Nitrogen and sulfur requirements for *Clostridium thermocellum* and *Caldicellulosiruptor bescii* on cellulosic substrates in minimal nutrient media. Bioresour Technol. 2013;130:125–35.

Article
CAS
Google Scholar

Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010;5:93–121.

Article
CAS
Google Scholar

Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.

Article
CAS
Google Scholar

Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2012;40:D742–53.

Article
CAS
Google Scholar

Ganter M, Bernard T, Moretti S, Stelling J, Pagni M. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics. 2013;29:815–6.

Article
CAS
Google Scholar

Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform. 2014;15:123–35.

Article
Google Scholar

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691–702.

Article
CAS
Google Scholar

Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 2011;39:D670–6.

Article
CAS
Google Scholar

Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type *Escherichia coli* W3110. Appl Environ Microbiol. 1994;60:3724.

CAS
Google Scholar

Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2.0. Nat Protoc. 2011;6:1290–307.

Article
CAS
Google Scholar

Price ND, Famili I, Beard DA, Palsson BO. Extreme pathways and Kirchhoff’s second law. Biophys J. 2002;83:2879–82.

Article
CAS
Google Scholar

Hogsett D. Cellulose hydrolysis and fermentation by *Clostridium thermocellum* for the production of ethanol. Dartmouth University, Thayer School of Engineering; 1995.

Trinh C, Thompson RA. Elementary mode analysis: a useful metabolic pathway analysis tool for reprogramming microbial metabolic pathways. In: Wang X, Chen J, Quinn P, editors. Reprogramming microbial metabolic pathways, vol. 64. Berlin: Springer; 2012. p. 21–42 **(Subcellular Biochemistry)**.

Chapter
Google Scholar

Hunt KA, Folsom JP, Taffs RL, Carlson RP. Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. Bioinformatics. 2014;30:1569–78.

Article
CAS
Google Scholar

van Klinken JB, van Dijk KW. FluxModeCalculator: an efficient tool for large-scale flux mode computation. Bioinformatics. 2016;32(8):1265-6. doi:10.1093/bioinformatics/btv742.

Article
Google Scholar

Wilson C, Rodriguez M, Johnson C, Martin S, Chu T, Wolfinger R, Hauser L, Land M, Klingeman D, Syed M, et al. Global transcriptome analysis of *Clostridium thermocellum* ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. Biotechnol Biofuels. 2013;6:179.

Article
Google Scholar

Gold N, Martin V. Global view of the *Clostridium thermocellum* cellulosome revealed by quantitative proteomic analysis. J Bacteriol. 2007;189:6787–95.

Article
CAS
Google Scholar

McAnulty MJ, Yen JY, Freedman BG, Senger RS. Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. BMC Syst Biol. 2012;6:42.

Article
CAS
Google Scholar

Megchelenbrink W, Huynen M, Marchiori E. *optGpSampler*: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks. PLoS One. 2014;9:e86587.

Article
Google Scholar

Verduyn C, Postma E, Scheffers WA, van Dijken JP. Energetics of *Saccharomyces cerevisiae* in anaerobic glucose-limited chemostat cultures. Microbiology. 1990;136:405–12.

CAS
Google Scholar