@article{lewis_notey_chandrayan_loder_lipscomb_adams_kelly_2015, title={A mutant ('lab strain') of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology}, volume={19}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-014-0712-3}, abstractNote={A mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targeted gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.}, number={2}, journal={EXTREMOPHILES}, author={Lewis, Derrick L. and Notey, Jaspreet S. and Chandrayan, Sanjeev K. and Loder, Andrew J. and Lipscomb, Gina L. and Adams, Michael W. W. and Kelly, Robert M.}, year={2015}, month={Mar}, pages={269–281} }
 @article{dam_kataeva_yang_zhou_yin_chou_poole_westpheling_hettich_giannone_et al._2011, title={Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725}, volume={39}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkq1281}, abstractNote={Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of ∼80°C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.}, number={8}, journal={NUCLEIC ACIDS RESEARCH}, author={Dam, Phuongan and Kataeva, Irina and Yang, Sung-Jae and Zhou, Fengfeng and Yin, Yanbin and Chou, Wenchi and Poole, Farris L., II and Westpheling, Janet and Hettich, Robert and Giannone, Richard and et al.}, year={2011}, month={Apr}, pages={3240–3254} }
 @article{muddiman_andrews_lewis_notey_kelly_2010, title={Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-3955-6}, abstractNote={The proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream experiments. Following efficient secretome purification, GeLC-MS(2) analysis and prediction servers suggested probable protein secretion to complement experimental data. In an effort to define the extracellular proteome of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus, several techniques were considered regarding sample processing to achieve the most in-depth analysis of secreted proteins. Order of operation experiments, all including the C(18) bead technique, demonstrated that two levels of sample purification were necessary to effectively desalt the sample and provide sufficient protein identifications. Five sample preparation combinations yielded 71 proteins and the majority described, as enzymatic and putative uncharacterized proteins, anticipate consolidated bioprocessing applications. Nineteen proteins were predicted by Phobius, SignalP, SecretomeP, or TatP for extracellular secretion, and 11 contained transmembrane domain stretches suggested by Phobius and transmembrane hidden Markov model. The sample preparation technique demonstrating the most effective outcome for C. saccharolyticus secreted proteins in this study, involved acetone precipitation followed by the C(18) bead method in which 2.4% (63 proteins) of the predicted proteome was identified, including proteins suggested to have secretion and transmembrane moieties.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David and Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert}, year={2010}, month={Sep}, pages={377–389} }
 @article{andrews_lewis_notey_kelly_muddiman_2010, title={Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2 (vol 398, pg 377, 2010)}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-4102-0}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert and Muddiman, David}, year={2010}, month={Oct}, pages={1837–1837} }
 @article{muddiman_andrews_lewis_notey_kelly_2010, title={Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting}, volume={398}, ISSN={["1618-2642"]}, DOI={10.1007/s00216-010-3929-8}, abstractNote={Probing the intracellular proteome of Thermotoga maritima and Caldicellulosiruptor saccharolyticus in pure and co-culture affords a global investigation into the machinery and mechanisms enduring inside the bacterial thermophilic cell at the time of harvest. The second of a two part study, employing GeLC-MS2 a variety of proteins were confidently identified with <1% false discovery rate, and spectral counts for label-free relative quantification afforded indication of the dynamic proteome as a function of environmental stimuli. Almost 25% of the T. maritima proteome and 10% of the C. saccharolyticus proteome were identified. Through comparison of growth temperatures for T. maritima, a protein associated with chemotaxis was uniquely present in the sample cultivated at the non-optimal growth temperature. It is suspected that movement was induced due to the non-optimal condition as the organism may need to migrate in the culture to locate more nutrients. The inventory of C. saccharolyticus proteins identified in these studies and attributed to spectral counting, demonstrated that two CRISPR-associated proteins had increased expression in the pure culture versus the co-culture. Further focusing on this relationship, a C. saccharolyticus phage-shock protein was identified in the co-culture expanding a scenario that the co-culture had decreased antiviral resistance and accordingly an infection-related protein was present. Alterations in growth conditions of these bacterial thermophilic microorganisms offer a glimpse into the intricacy of microbial behavior and interaction.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David and Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert}, year={2010}, month={Sep}, pages={391–404} }
 @article{andrews_lewis_notey_kelly_muddiman_2010, title={Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting (vol 398, pg 391, 2010)}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-4050-8}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert and Muddiman, David}, year={2010}, month={Oct}, pages={1839–1839} }
 @article{blumer-schuette_lewis_kelly_2010, title={Phylogenetic, Microbiological, and Glycoside Hydrolase Diversities within the Extremely Thermophilic, Plant Biomass-Degrading Genus Caldicellulosiruptor}, volume={76}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01400-10}, abstractNote={ABSTRACT}, number={24}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Blumer-Schuette, Sara E. and Lewis, Derrick L. and Kelly, Robert M.}, year={2010}, month={Dec}, pages={8084–8092} }
 @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}, 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} }
 @article{chou_shockley_conners_lewis_comfort_adams_kelly_2007, title={Impact of substrate glycoside linkage. and elemental sulfur on bioenergetics, of and hydrogen production by the hyperthermophilic Archaeon Pyrococcus furiosus}, volume={73}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00597-07}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Chou, Chung-Jung and Shockley, Keith R. and Conners, Shannon B. and Lewis, Derrick L. and Comfort, Donald A. and Adams, Michael W. W. and Kelly, Robert M.}, year={2007}, month={Nov}, pages={6842–6853} }
 @article{kataeva_foston_yang_pattathil_biswal_poole_basen_rhaesa_thomas_azadi_et al., title={Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature}, volume={6}, number={7}, journal={Energy & Environmental Science}, author={Kataeva, I. and Foston, M. B. and Yang, S. J. and Pattathil, S. and Biswal, A. K. and Poole, F. L. and Basen, M. and Rhaesa, A. M. and Thomas, T. P. and Azadi, P. and et al.}, pages={2186–2195} }