Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, et al. Thermophilic lignocellulose deconstruction. Rev: FEMS Microbiol; 2014.
Google Scholar
Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev. 2002;66:506–77.
Article
CAS
Google Scholar
Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, et al. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum. Metab Eng. 2015;31:44–52.
Article
CAS
Google Scholar
Dumitrache A, Klingeman DM, Natzke J, Rodriguez M Jr, Giannone RJ, Hettich RL, et al. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. Sci Rep. 2017;7:43583.
Article
Google Scholar
Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, et al. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. Sci. Adv. 2016;2:e1501254.
Article
Google Scholar
Bayer EA, Lamed R, White BA, Flints HJ. From cellulosomes to cellulosomics. Chem Rec. 2008;8:364–77.
Article
CAS
Google Scholar
Ellis LD, Holwerda EK, Hogsett D, Rogers S, Shao X, Tschaplinski T, et al. Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405). Bioresour Technol. 2012;103:293–9.
Article
CAS
Google Scholar
Holwerda EK, Thorne PG, Olson DG, Amador-Noguez D, Engle NL, Tschaplinski TJ, et al. The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading. Biotechnol Biofuels. 2014;7:155.
Article
Google Scholar
Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, Murphy DM, 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
Argyros DA, Tripathi SA, Barrett TF, Rogers SR, Feinberg LF, Olson DG, et al. High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. Appl Environ Microbiol. 2011;77:8288–94.
Article
CAS
Google Scholar
Rydzak T, Lynd LR, Guss AM. 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
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;9:1–7.
Google Scholar
Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, et al. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng. 2017;39:169–80.
Article
CAS
Google Scholar
Biswas R, Wilson CM, Zheng T, Giannone RJ, Dawn M, Olson DG, et al. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum. Biotechnol Biofuels. 2015;8:20.
Article
Google Scholar
Hon S, Olson DG, Holwerda EK, Lanahan AA, Murphy SJL, Maloney MI, et al. The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum. Metab Eng. 2017;42:175–84.
Article
CAS
Google Scholar
Lo J, Olson DG, Murphy SJL, Tian L, Hon S, Lanahan A, et al. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum. Metab Eng. 2017;39:71–9.
Article
CAS
Google Scholar
Tian L, Papanek B, Olson DG, Rydzak T, Holwerda EK, Zheng T, et al. Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum. Biotechnol Biofuels. 2016;9:116.
Article
Google Scholar
Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, et al. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci. 2011;108:13752–7.
Article
CAS
Google Scholar
Shao X, Raman B, Zhu M, Mielenz JR, Brown SD, Guss AM, et al. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum. Appl Microbiol Biotechnol. 2011;92:641–52.
Article
CAS
Google Scholar
Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, et al. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep. 2017;7:43355.
Article
CAS
Google Scholar
Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, et al. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. Biotechnol Biofuels. 2017;10:14.
Article
Google Scholar
Wu C-W, Spike T, Klingeman DM, Rodriguez M, Bremer VR, Brown SD. Generation and characterization of acid tolerant Fibrobacter succinogenes S85. Sci Rep. 2017;7:2277.
Article
Google Scholar
Nochur SV, Demain AL, Roberts MF. Carbohydrate utilization by Clostridium thermocellum: importance of internal pH in regulating growth. Enzyme Microb Technol. 1992;14:338–49.
Article
CAS
Google Scholar
Herrero AA, Gomez RF, Snedecor B, Tolman CJ, Roberts MF. Growth inhibition of Clostridium thermocellum by carboxylic acids: a mechanism based on uncoupling by weak acids. Appl Microbiol Biotechnol. 1985;22:53–62.
Article
CAS
Google Scholar
Mori Y. Characterization of symbiotic coculture of Clostridium thermohydrosulfuricum YM3 and Clostridium thermocellum YM4. Appl Environ Microbiol. 1990;56:37–42.
CAS
Google Scholar
Koeck DE, Zverlov VV, Liebl W, Schwarz WH. Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential. Microbiol: Syst Appl; 2014.
Google Scholar
Freier D, Mothershed CP, Wiegel J. Characterization of Clostridium thermocellum JW20. Appl Environ Microbiol. 1988;54:204–11.
CAS
Google Scholar
Cotter PD, Hill C. Surviving the acid test: responses of Gram-positive bacteria to low pH. Microbiol Mol Biol Rev. 2003;67:429–53.
Article
CAS
Google Scholar
Lund P, Tramonti A, De Biase D. Coping with low pH: molecular strategies in neutralophilic bacteria. FEMS Microbiol Rev. 2014;38:1091–125.
Article
CAS
Google Scholar
Kobayashis H, Murakami N, Unemoto T. Regulation of the Cytoplasmic pH in. 1982;257:13246–52.
Google Scholar
Terahara N, Noguchi Y, Nakamura S, Kami-ike N, Ito M, Namba K, et al. Load- and polysaccharide-dependent activation of the Na+-type MotPS stator in the Bacillus subtilis flagellar motor. Sci Rep. 2017;7:46081.
Article
CAS
Google Scholar
Rhee HJ, Kim EJ, Lee JK. Physiological polyamines: simple primordial stress molecules. J Cell Mol Med. 2007;11:685–703.
Article
CAS
Google Scholar
Mearls EB, Lynd LR. The identification of four histidine kinases that influence sporulation in Clostridium thermocellum. Anaerobe. 2014;28:109–19.
Article
CAS
Google Scholar
Mearls EB, Izquierdo JA, Lynd LR. Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms. BMC Microbiol. 2012;12:180.
Article
CAS
Google Scholar
Wilson CM, Yang S, Rodriguez M Jr, Ma Q, Johnson CM, Dice L, et al. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnol Biofuels. 2013;6:131.
Article
CAS
Google Scholar
Sohlenkamp C. Membrane homeostasis in bacteria upon pH challenge. Biogenesis of fatty acids, lipids and membranes. Berlin: Springer; 2017. p. 1–13.
Book
Google Scholar
Kobayashi H, Suzuki T, Unemoto T. Streptococcal cytoplasmic pH is regulated by changes in amount and activity of a proton-translocating ATPase. J Biol Chem. 1986;261:627–30.
CAS
Google Scholar
Zhou J, Olson DG, Argyros DA, Deng Y, van Gulik WM, van Dijken JP, et al. 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, et al. 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
Baltsche M, Schultz A, Baltsche H. H+-PPases : a tightly membrane-bound family. FEBS Lett. 1999;457:527–33.
Article
Google Scholar
Lynd LR, Guss AM, Himmel ME, Beri D, Herring C, Holwerda EK, et al. Advances in consolidated bioprocessing using Clostridium thermocellum and Thermoanaerobacter saccharolyticum. In: Industrial biotechnology. Weinheim: Wiley-VCH; 2016. p. 365–94.
Ouameur AA, Bourassa P, Tajmir-Riahi H-A. Probing tRNA interaction with biogenic polyamines. RNA. 2010;16:1968–79.
Article
CAS
Google Scholar
Tsuchiya K, Nishimura K, Iwahara M. Purification and characterization of glutamate decarboxylase from Aspergillus oryzae. Food Sci Technol Res. 2003;9:283–7.
Article
CAS
Google Scholar
Seo M-J, Nam Y-D, Lee S-Y, Park S-L, Yi S-H, Lim S-I. Expression and characterization of a glutamate decarboxylase from Lactobacillus brevis 877G producing γ-aminobutyric acid. Biosci Biotechnol Biochem. 2013;77:853–6.
Article
CAS
Google Scholar
Park K-B, Ji G-E, Park M-S, Oh S-H. Expression of rice glutamate decarboxylase in Bifidobacterium longum enhances gamma-aminobutyric acid production. Biotechnol Lett. 2005;27:1681–4.
Article
CAS
Google Scholar
Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, et al. Deletion of type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum. Metab Eng. 2017;41:182–91.
Article
CAS
Google Scholar
van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, 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
Olson DG, Lynd LR. Transformation of Clostridium thermocellum by electroporation. Methods enzymol. 1st ed. Waltham: Academic Press; 2012. p. 317–30.
Google Scholar
Guss AM, Olson DG, Caiazza NC, Lynd LR. Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. Biotechnol Biofuels. 2012;5:30.
Article
CAS
Google Scholar
Dumitrache A, Akinosho H, Rodriguez M, Meng X, Yoo CG, Natzke J, et al. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure. Biotechnol Biofuels. 2016;9:31.
Article
Google Scholar
Sander K, Wilson CM, Rodriguez M, Klingeman DM, Rydzak T, Davison BH, et al. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation. Biotechnol Biofuels. 2015;8:211.
Article
Google Scholar
Dumitrache A, Wolfaardt GM, Allen DG, Liss SN, Lynd LR. Tracking the cellulolytic activity of Clostridium thermocellum biofilms. Biotechnol Biofuels. 2013;6:175.
Article
Google Scholar
Wilson CM, Klingeman DM, Schlachter C, Syed MH, Wu C, Guss AM, et al. LacI transcriptional regulatory networks in Clostridium thermocellum DSM1313. Appl Environ Microbiol. 2017;83:e02751–816.
Article
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 5 Feb 2016.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq-A python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420–35.
Article
Google Scholar