@article{bielen_verhaart_vanfossen_blumer-schuette_stams_oost_kelly_kengen_2013, title={A thermophile under pressure: Transcriptional analysis of the response of Caldicellulosiruptor saccharolyticus to different H-2 partial pressures}, volume={38}, ISSN={["1879-3487"]}, DOI={10.1016/j.ijhydene.2012.11.082}, abstractNote={Increased hydrogen (H2) levels are known to inhibit H2 formation in Caldicellulosiruptor saccharolyticus. To investigate this organism's strategy for dealing with elevated H2 levels the effect of the hydrogen partial pressure (PH2) on fermentation performance was studied by growing cultures under high and low PH2 in a glucose limited chemostat setup. Transcriptome analysis revealed the upregulation of genes involved in the disposal of reducing equivalents under high PH2, like lactate dehydrogenase and alcohol dehydrogenase as well as the NADH-dependent and ferredoxin-dependent hydrogenases. These findings are in line with the observed shift in fermentation profiles from acetate production to the production of acetate, lactate and ethanol under high PH2. Moreover, differential transcription was observed for genes involved in carbon metabolism, fatty acid biosynthesis and several transport systems. In addition, presented transcription data provide evidence for the involvement of the redox sensing Rex protein in gene regulation under high PH2 cultivation conditions.}, number={4}, journal={INTERNATIONAL JOURNAL OF HYDROGEN ENERGY}, author={Bielen, Abraham A. M. and Verhaart, Marcel R. A. and VanFossen, Amy L. and Blumer-Schuette, Sara E. and Stams, Alfons J. M. and Oost, John and Kelly, Robert M. and Kengen, Serve W. M.}, year={2013}, month={Feb}, pages={1837–1849} }
 @article{vanfossen_ozdemir_zelin_kelly_2011, title={Glycoside Hydrolase Inventory Drives Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus}, volume={108}, ISSN={["1097-0290"]}, DOI={10.1002/bit.23093}, abstractNote={AbstractThe genome of Caldicellulosiruptor saccharolyticus encodes a range of glycoside hydrolases (GHs) that mediate plant biomass deconstruction by this bacterium. Two GH‐based genomic loci that appear to be central to the hydrolysis of hemicellulosic and cellulosic substrates were examined. XynB‐XynF (Csac_2404‐Csac_2411) encodes intracellular and extracellular GHs that are active towards xylan and xylan side‐chains, as well as carboxymethyl cellulose (CMC). XynD (Csac_2409) and XynE (Csac_2410) were produced recombinantly and confirmed to be xylanases. XynF (Csac_2411) was produced in two separate polypeptides, each with one GH43 catalytic domain displaying α‐L‐arabinofuranosidase activity. CelA‐ManB (Csac_1076‐Csac_1080) encodes four multi‐domain, extracellular GHs, including CelB (Csac_1078), a 118 kDa extracellular enzyme not present in the other genome‐sequenced member of this genus, Caldicellulosiruptor bescii (formerly Anaerocellum thermophilum). CelB contains both GH10 and GH5 domains, separated by a family 3 carbohydrate‐binding module (CBM3). CelB encoded in Csac_1078 differed from the version originally reported (Saul et al., 1990, Appl Environ Microbiol 56:3117–3124) with respect to linker regions. CelB hydrolyzed xylan and CMC, as well as barley β‐glucan, glucomannan, and arabinoxylan. For all substrates tested, intact CelB was significantly more active than either the individual GH5 and GH10 domains or the two discrete domains together, indicating that the multi‐domain architecture is essential for complex carbohydrate hydrolysis. Transcriptomes for C. saccharolyticus grown at 70°C on glucose, xylose, xyloglucan, switchgrass, and poplar revealed that certain GHs were particularly responsive to growth on switchgrass and poplar and that CelB was in the top decile of all transcripts during growth on the plant biomass. Biotechnol. Bioeng. 2011; 108:1559–1569. © 2011 Wiley Periodicals, Inc.}, number={7}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={VanFossen, Amy L. and Ozdemir, Inci and Zelin, Samantha L. and Kelly, Robert M.}, year={2011}, month={Jul}, pages={1559–1569} }
 @article{vanfossen_verhaart_kengen_kelly_2009, title={Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01959-09}, abstractNote={ABSTRACT
          
            Coutilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H
            2
            -producing, extremely thermophilic bacterium
            Caldicellulosiruptor saccharolyticus
            growing on individual monosaccharides (arabinose, fructose, galactose, glucose, mannose, and xylose), mixtures of these sugars, as well as on xylan and xylogluco-oligosacchrides.
            C. saccharolyticus
            grew at approximately the same rate (
            t
            d
            , ∼95 min) and to the same final cell density (1 × 10
            8
            to 3 × 10
            8
            cells/ml) on all sugars and sugar mixtures tested. In the monosaccharide mixture, although simultaneous consumption of all monosaccharides was observed, not all were utilized to the same extent (fructose > xylose/arabinose > mannose/glucose/galactose). Transcriptome contrasts for monosaccharide growth revealed minimal changes in some cases (e.g., 32 open reading frames [ORFs] changed ≥2-fold for glucose versus galactose), while substantial changes occurred for cases involving mannose (e.g., 353 ORFs changed ≥2-fold for glucose versus mannose). Evidence for catabolite repression was not noted for either growth on multisugar mixtures or the corresponding transcriptomes. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for most of the 24 putative carbohydrate ATP-binding cassette transporters and single phosphotransferase system identified in
            C. saccharolyticus
            . Although most transporter genes responded to individual monosaccharides and polysaccharides, the genes Csac_0692 to Csac_0694 were upregulated only in the monosaccharide mixture. The results presented here affirm the broad growth substrate preferences of
            C. saccharolyticus
            on carbohydrates representative of lignocellulosic biomass and suggest that this bacterium holds promise for biofuel applications.
          }, number={24}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={VanFossen, Amy L. and Verhaart, Marcel R. A. and Kengen, Serve M. W. and Kelly, Robert M.}, year={2009}, month={Dec}, pages={7718–7724} }
 @article{comfort_chou_conners_vanfossen_kelly_2008, title={Functional-genomics-based identification and characterization of open reading frames encoding alpha-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01920-07}, abstractNote={ABSTRACT
          
            Bioinformatics analysis and transcriptional response information for
            Pyrococcus furiosus
            grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.
          }, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Comfort, Donald A. and Chou, Chung-Jung and Conners, Shannon B. and VanFossen, Amy L. and Kelly, Robert M.}, year={2008}, month={Feb}, pages={1281–1283} }
 @article{werken_verhaart_vanfossen_willquist_lewis_nichols_goorissen_mongodin_nelson_niel_et al._2008, title={Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.00968-08}, abstractNote={ABSTRACT
          
            Caldicellulosiruptor saccharolyticus
            is an extremely thermophilic, gram-positive anaerobe which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO
            2
            , and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to coutilize glucose and xylose make this bacterium an attractive candidate for microbial bioenergy production. Here, the complete genome sequence of
            C. saccharolyticus
            , consisting of a 2,970,275-bp circular chromosome encoding 2,679 predicted proteins, is described. Analysis of the genome revealed that
            C. saccharolyticus
            has an extensive polysaccharide-hydrolyzing capacity for cellulose, hemicellulose, pectin, and starch, coupled to a large number of ABC transporters for monomeric and oligomeric sugar uptake. The components of the Embden-Meyerhof and nonoxidative pentose phosphate pathways are all present; however, there is no evidence that an Entner-Doudoroff pathway is present. Catabolic pathways for a range of sugars, including rhamnose, fucose, arabinose, glucuronate, fructose, and galactose, were identified. These pathways lead to the production of NADH and reduced ferredoxin. NADH and reduced ferredoxin are subsequently used by two distinct hydrogenases to generate hydrogen. Whole-genome transcriptome analysis revealed that there is significant upregulation of the glycolytic pathway and an ABC-type sugar transporter during growth on glucose and xylose, indicating that
            C. saccharolyticus
            coferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks is a highly desirable feature of this lignocellulose-utilizing, biofuel-producing bacterium.
          }, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Werken, Harmen J. G. and Verhaart, Marcel R. A. and VanFossen, Amy L. and Willquist, Karin and Lewis, Derrick L. and Nichols, Jason D. and Goorissen, Heleen P. and Mongodin, Emmanuel F. and Nelson, Karen E. and Niel, Ed W. J. and et al.}, year={2008}, month={Nov}, pages={6720–6729} }
 @article{vanfossen_lewis_nichols_kelly_2008, title={Polysaccharide Degradation and Synthesis by Extremely Thermophilic Anaerobes}, volume={1125}, ISBN={["978-1-57331-705-4"]}, ISSN={["0077-8923"]}, DOI={10.1196/annals.1419.017}, abstractNote={Extremely thermophilic fermentative anaerobes (growth Topt ≥ 70°C) have the capacity to use a variety of carbohydrates as carbon and energy sources. As such, a wide variety of glycoside hydrolases and transferases have been identified in these microorganisms. The genomes of three model extreme thermophiles—an archaeon Pyrococcus furiosus (Topt = 98°C), and two bacteria, Thermotoga maritima (Topt = 80°C) and Caldicellulosiruptor saccharolyticus (Topt = 70°C)—encode numerous carbohydrate‐active enzymes, many of which have been characterized biochemically in their native or recombinant forms. In addition to their voracious appetite for polysaccharide degradation, polysaccharide production has also been noted for extremely thermophilic fermentative anaerobes; T. maritima generates exopolysaccharides that aid in biofilm formation, a process that appears to be driven by intraspecies and interspecies interactions.}, number={1}, journal={Annals of the New York Academy of Sciences}, author={VanFossen, A.L. and Lewis, D.L. and Nichols, J.D. and Kelly, R.M.}, year={2008}, month={Mar}, pages={322–337} }