@article{lee_crosby_rubinstein_laemthong_bing_straub_adams_kelly_2020, title={The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in 'Caldi World'}, volume={24}, ISSN={["1433-4909"]}, url={https://doi.org/10.1007/s00792-019-01116-5}, DOI={10.1007/s00792-019-01116-5}, abstractNote={Terrestrial hot springs near neutral pH harbor extremely thermophilic bacteria from the genus Caldicellulosiruptor, which utilize the carbohydrates of lignocellulose for growth. These bacteria are technologically important because they produce novel, multi-domain glycoside hydrolases that are prolific at deconstructing microcrystalline cellulose and hemicelluloses found in plant biomass. Among other interesting features, Caldicellulosiruptor species have successfully adapted to bind specifically to lignocellulosic substrates via surface layer homology (SLH) domains associated with glycoside hydrolases and unique binding proteins (tāpirins) present only in these bacteria. They also utilize a parallel pathway for conversion of glyceraldehyde-3-phosphate into 3-phosphoglycerate via a ferredoxin-dependent oxidoreductase that is conserved across the genus. Advances in the genetic tools for Caldicellulosiruptor bescii, including the development of a high-temperature kanamycin-resistance marker and xylose-inducible promoter, have opened the door for metabolic engineering applications and some progress along these lines has been reported. While several species of Caldicellulosiruptor can readily deconstruct lignocellulose, improvements in the amount of carbohydrate released and in the production of bio-based chemicals are required to successfully realize the biotechnological potential of these organisms.}, number={1}, journal={EXTREMOPHILES}, author={Lee, Laura L. and Crosby, James R. and Rubinstein, Gabriel M. and Laemthong, Tunyaboon and Bing, Ryan G. and Straub, Christopher T. and Adams, Michael W. W. and Kelly, Robert M.}, year={2020}, month={Jan}, pages={1–15} }
 @article{lee_hart_lunin_alahuhta_bomble_himmel_blumer-schuette_adams_kelly_2019, title={Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species}, volume={85}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01983-18}, abstractNote={
            The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed.
            Caldicellulosiruptor
            species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called tāpirins, are involved in the way that
            Caldicellulosiruptor
            species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here.
          }, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Lee, Laura L. and Hart, William S. and Lunin, Vladimir V. and Alahuhta, Markus and Bomble, Yannick J. and Himmel, Michael E. and Blumer-Schuette, Sara E. and Adams, Michael W. W. and Kelly, Robert M.}, year={2019}, month={Feb} }
 @article{rudershausen_m. lee_lombardo_merrell_buckel_2019, title={Survival and Habitat of Yellow‐Phase American Eels in North Carolina Tidal Creeks}, volume={148}, ISSN={0002-8487 1548-8659}, url={http://dx.doi.org/10.1002/tafs.10190}, DOI={10.1002/tafs.10190}, abstractNote={Abstract}, number={5}, journal={Transactions of the American Fisheries Society}, publisher={Wiley}, author={Rudershausen, Paul J. and M. Lee, Laura and Lombardo, Steven M. and Merrell, Jeffery H. and Buckel, Jeffrey A.}, year={2019}, month={Aug}, pages={978–990} }
 @article{conway_crosby_hren_southerland_lee_lunin_alahuhta_himmel_bomble_adams_et al._2018, title={Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species}, volume={64}, ISSN={["1547-5905"]}, DOI={10.1002/aic.16354}, abstractNote={Biological hydrolysis of microcrystalline cellulose is an uncommon feature in the microbial world, especially among bacteria and archaea growing optimally above 70°C (the so‐called extreme thermophiles). In fact, among this group only certain species in the genus Caldicellulosiruptor are capable of rapid and extensive cellulose degradation. Four novel multidomain glycoside hydrolases (GHs) from Caldicellulosiruptor morganii and Caldicellulosiruptor danielii were produced recombinantly in Caldicellulosiruptor bescii and characterized. These GHs are structurally organized with two or three catalytic domains flanking carbohydrate binding modules from Family 3. Collectively, these enzymes represent GH families 5, 9, 10, 12, 44, 48, and 74, and hydrolyze crystalline cellulose, glucan, xylan, and mannan, the primary carbohydrates in plant biomass. Degradation of microcrystalline cellulose by cocktails of GHs from three Caldicellulosiruptor species demonstrated that synergistic interactions enable mixtures of multiple enzymes to outperform single enzymes, suggesting a community mode of action for lignocellulose utilization in thermal environments. © 2018 American Institute of Chemical Engineers AIChE J, 64: 4218–4228, 2018}, number={12}, journal={AICHE JOURNAL}, author={Conway, Jonathan M. and Crosby, James R. and Hren, Andrew P. and Southerland, Robert T. and Lee, Laura L. and Lunin, Vladimir V. and Alahuhta, Petri and Himmel, Michael E. and Bomble, Yannick J. and Adams, Michael W. W. and et al.}, year={2018}, month={Dec}, pages={4218–4228} }
 @article{zurawski_khatibi_akinosho_straub_compton_conway_lee_ragauskas_davison_adams_et al._2017, title={Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00969-17}, abstractNote={ABSTRACT}, number={17}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Zurawski, Jeffrey V. and Khatibi, Piyum A. and Akinosho, Hannah O. and Straub, Christopher T. and Compton, Scott H. and Conway, Jonathan M. and Lee, Laura L. and Ragauskas, Arthur J. and Davison, Brian H. and Adams, Michael W. W. and et al.}, year={2017}, month={Sep} }
 @article{williams-rhaesa_poole_dinsmore_lipscomb_rubinstein_scott_conway_lee_khatibi_kelly_et al._2017, title={Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00444-17}, abstractNote={ABSTRACT}, number={14}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Williams-Rhaesa, Amanda M. and Poole, Farris L., II and Dinsmore, Jessica T. and Lipscomb, Gina L. and Rubinstein, Gabriel M. and Scott, Israel M. and Conway, Jonathan M. and Lee, Laura L. and Khatibi, Piyum A. and Kelly, Robert M. and et al.}, year={2017}, month={Jul} }
 @misc{counts_zeldes_lee_straub_adams_kelly_2017, title={Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms}, volume={9}, ISSN={["1939-005X"]}, DOI={10.1002/wsbm.1377}, abstractNote={The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs—basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology‐based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377}, number={3}, journal={WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE}, author={Counts, James A. and Zeldes, Benjamin M. and Lee, Laura L. and Straub, Christopher T. and Adams, Michael W. W. and Kelly, Robert M.}, year={2017}, month={May} }
 @article{conway_pierce_le_harper_wright_tucker_zurawski_lee_blumer-schuette_kelly_2016, title={Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species}, volume={291}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m115.707810}, abstractNote={The genome of the extremely thermophilic bacterium Caldicellulosiruptor kronotskyensis encodes 19 surface layer (S-layer) homology (SLH) domain-containing proteins, the most in any Caldicellulosiruptor species genome sequenced to date. These SLH proteins include five glycoside hydrolases (GHs) and one polysaccharide lyase, the genes for which were transcribed at high levels during growth on plant biomass. The largest GH identified so far in this genus, Calkro_0111 (2,435 amino acids), is completely unique to C. kronotskyensis and contains SLH domains. Calkro_0111 was produced recombinantly in Escherichia coli as two pieces, containing the GH16 and GH55 domains, respectively, as well as putative binding and spacer domains. These displayed endo- and exoglucanase activity on the β-1,3-1,6-glucan laminarin. A series of additional truncation mutants of Calkro_0111 revealed the essential architectural features required for catalytic function. Calkro_0402, another of the SLH domain GHs in C. kronotskyensis, when produced in E. coli, was active on a variety of xylans and β-glucans. Unlike Calkro_0111, Calkro_0402 is highly conserved in the genus Caldicellulosiruptor and among other biomass-degrading Firmicutes but missing from Caldicellulosiruptor bescii. As such, the gene encoding Calkro_0402 was inserted into the C. bescii genome, creating a mutant strain with its S-layer extensively decorated with Calkro_0402. This strain consequently degraded xylans more extensively than wild-type C. bescii. The results here provide new insights into the architecture and role of SLH domain GHs and demonstrate that hemicellulose degradation can be enhanced through non-native SLH domain GHs engineered into the genomes of Caldicellulosiruptor species.}, number={13}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Conway, Jonathan M. and Pierce, William S. and Le, Jaycee H. and Harper, George W. and Wright, John H. and Tucker, Allyson L. and Zurawski, Jeffrey V. and Lee, Laura L. and Blumer-Schuette, Sara E. and Kelly, Robert M.}, year={2016}, month={Mar}, pages={6732–6747} }
 @article{zurawski_conway_lee_simpson_izquierdo_blumer-schuette_nookaew_adams_kelly_2015, title={Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization}, volume={81}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01622-15}, abstractNote={ABSTRACT}, number={20}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Zurawski, Jeffrey V. and Conway, Jonathan M. and Lee, Laura L. and Simpson, Hunter J. and Izquierdo, Javier A. and Blumer-Schuette, Sara and Nookaew, Intawat and Adams, Michael W. W. and Kelly, Robert M.}, year={2015}, month={Oct}, pages={7159–7170} }
 @article{blumer-schuette_alahuhta_conway_lee_zurawski_giannone_hettich_lunin_himmel_kelly_2015, title={Discrete and Structurally Unique Proteins (Tapirins) Mediate Attachment of Extremely Thermophilic Caldicellulosiruptor Species to Cellulose}, volume={290}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m115.641480}, abstractNote={Background: Lignocellulose-degrading microorganisms utilize binding modules associated with glycosidic enzymes to attach to polysaccharides. Results: Structurally unique, discrete proteins (tāpirins) bind to cellulose with a high affinity. Conclusion: Tāpirins represent a new class of proteins used by Caldicellulosiruptor species to attach to cellulose. Significance: The tāpirins establish a new paradigm for how cellulolytic bacteria adhere to cellulose. A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to deconstruct lignocellulose. These extracellular proteins are used to attach to, modify, and hydrolyze the complex polysaccharides present in plant cell walls. Cellulolytic enzymes, often containing carbohydrate-binding modules, are key to this process; however, these enzymes are not solely responsible for attachment. Few mechanisms of attachment have been discovered among bacteria that do not form large polypeptide structures, called cellulosomes, to deconstruct biomass. In this study, bioinformatics and proteomics analyses identified unique, discrete, hypothetical proteins (“tāpirins,” origin from Māori: to join), not directly associated with cellulases, that mediate attachment to cellulose by species in the noncellulosomal, extremely thermophilic bacterial genus Caldicellulosiruptor. Two tāpirin genes are located directly downstream of a type IV pilus operon in strongly cellulolytic members of the genus, whereas homologs are absent from the weakly cellulolytic Caldicellulosiruptor species. Based on their amino acid sequence, tāpirins are specific to these extreme thermophiles. Tāpirins are also unusual in that they share no detectable protein domain signatures with known polysaccharide-binding proteins. Adsorption isotherm and trans vivo analyses demonstrated the carbohydrate-binding module-like affinity of the tāpirins for cellulose. Crystallization of a cellulose-binding truncation from one tāpirin indicated that these proteins form a long β-helix core with a shielded hydrophobic face. Furthermore, they are structurally unique and define a new class of polysaccharide adhesins. Strongly cellulolytic Caldicellulosiruptor species employ tāpirins to complement substrate-binding proteins from the ATP-binding cassette transporters and multidomain extracellular and S-layer-associated glycoside hydrolases to process the carbohydrate content of lignocellulose.}, number={17}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Blumer-Schuette, Sara E. and Alahuhta, Markus and Conway, Jonathan M. and Lee, Laura L. and Zurawski, Jeffrey V. and Giannone, Richard J. and Hettich, Robert L. and Lunin, Vladimir V. and Himmel, Michael E. and Kelly, Robert M.}, year={2015}, month={Apr}, pages={10645–10656} }
 @article{conway_zurawski_lee_blumer-schuette_kelly, title={Lignocellulosic biomass deconstruction by the extremely thermophilic genus caldicellulosiruptor}, journal={Thermophilic Microorganisms}, author={Conway, J. M. and Zurawski, J. V. and Lee, L. L. and Blumer-Schuette, S. E. and Kelly, R. M.}, pages={91–119} }