@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}, 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{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{montero_johnson_chou_conners_geouge_tachdjian_nichols_kelly_2007, title={Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge}, volume={73}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.00453-07}, abstractNote={ABSTRACT}, number={15}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Montero, Clemente I. and Johnson, Matthew R. and Chou, Chung-Jung and Conners, Shannon B. and Geouge, Sarah G. and Tachdjian, Sabrina and Nichols, Jason D. and Kelly, Robert M.}, year={2007}, month={Aug}, pages={5058–5065} }
 @article{madding_michel_shockley_conners_epting_johnson_kelly_2007, title={Role of the beta 1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus}, volume={189}, ISSN={["0021-9193"]}, DOI={10.1128/JB.01382-06}, abstractNote={ABSTRACT}, number={2}, journal={JOURNAL OF BACTERIOLOGY}, author={Madding, Lara S. and Michel, Joshua K. and Shockley, Keith R. and Conners, Shannon B. and Epting, Kevin L. and Johnson, Matthew R. and Kelly, Robert M.}, year={2007}, month={Jan}, pages={583–590} }
 @article{montero_lewis_johnson_conners_nance_nichols_kelly_2006, title={Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima}, volume={188}, ISSN={["0021-9193"]}, DOI={10.1128/JB.00470-06}, abstractNote={ABSTRACT}, number={19}, journal={JOURNAL OF BACTERIOLOGY}, author={Montero, Clemente I. and Lewis, Derrick L. and Johnson, Matthew R. and Conners, Shannon B. and Nance, Elizabeth A. and Nichols, Jason D. and Kelly, Robert M.}, year={2006}, month={Oct}, pages={6802–6807} }
 @article{barrangou_azcarate-peril_duong_conners_kelly_klaenhammer_2006, title={Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays}, volume={103}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0511287103}, abstractNote={
            The transport and catabolic machinery involved in carbohydrate utilization by
            Lactobacillus acidophilus
            was characterized genetically by using whole-genome cDNA microarrays. Global transcriptional profiles were determined for growth on glucose, fructose, sucrose, lactose, galactose, trehalose, raffinose, and fructooligosaccharides. Hybridizations were carried out by using a round-robin design, and microarray data were analyzed with a two-stage mixed model ANOVA. Differentially expressed genes were visualized by hierarchical clustering, volcano plots, and contour plots. Overall, only 63 genes (3% of the genome) showed a >4-fold induction. Specifically, transporters of the phospho
            enol
            pyruvate:sugar transferase system were identified for uptake of glucose, fructose, sucrose, and trehalose, whereas ATP-binding cassette transporters were identified for uptake of raffinose and fructooligosaccharides. A member of the LacS subfamily of galactoside-pentose hexuronide translocators was identified for uptake of galactose and lactose. Saccharolytic enzymes likely involved in the metabolism of monosaccharides, disaccharides, and polysaccharides into substrates of glycolysis were also found, including enzymatic machinery of the Leloir pathway. The transcriptome appeared to be regulated by carbon catabolite repression. Although substrate-specific carbohydrate transporters and hydrolases were regulated at the transcriptional level, genes encoding regulatory proteins CcpA, Hpr, HprK/P, and EI were consistently highly expressed. Genes central to glycolysis were among the most highly expressed in the genome. Collectively, microarray data revealed that coordinated and regulated transcription of genes involved in sugar uptake and metabolism is based on the specific carbohydrate provided.
            L. acidophilus
            's adaptability to environmental conditions likely contributes to its competitive ability for limited carbohydrate sources available in the human gastrointestinal tract.
          }, number={10}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barrangou, R and Azcarate-Peril, MA and Duong, T and Conners, SB and Kelly, RM and Klaenhammer, TR}, year={2006}, month={Mar}, pages={3816–3821} }
 @misc{conners_mongodin_johnson_montero_nelson_kelly_2006, title={Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species}, volume={30}, ISSN={["1574-6976"]}, DOI={10.1111/j.1574-6976.2006.00039.x}, abstractNote={High-throughput sequencing of microbial genomes has allowed the application of functional genomics methods to species lacking well-developed genetic systems. For the model hyperthermophile Thermotoga maritima, microarrays have been used in comparative genomic hybridization studies to investigate diversity among Thermotoga species. Transcriptional data have assisted in prediction of pathways for carbohydrate utilization, iron-sulfur cluster synthesis and repair, expolysaccharide formation, and quorum sensing. Structural genomics efforts aimed at the T. maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins. The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes.}, number={6}, journal={FEMS MICROBIOLOGY REVIEWS}, author={Conners, Shannon B. and Mongodin, Emmanuel F. and Johnson, Matthew R. and Montero, Clemente I. and Nelson, Karen E. and Kelly, Robert M.}, year={2006}, month={Nov}, pages={872–905} }
 @article{johnson_conners_montero_chou_shockley_kelly_2006, title={The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture}, volume={72}, ISSN={["0099-2240"]}, DOI={10.1128/aem.72.1.811-818.2006}, abstractNote={ABSTRACT}, number={1}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Johnson, MR and Conners, SB and Montero, CI and Chou, CJ and Shockley, KR and Kelly, RM}, year={2006}, month={Jan}, pages={811–818} }
 @article{lee_shockley_schut_conners_montero_johnson_chou_bridger_wigner_brehm_et al._2006, title={Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus}, volume={188}, ISSN={["1098-5530"]}, DOI={10.1128/JB.188.6.2115-2125.2006}, abstractNote={ABSTRACT}, number={6}, journal={JOURNAL OF BACTERIOLOGY}, author={Lee, HS and Shockley, KR and Schut, GJ and Conners, SB and Montero, CI and Johnson, MR and Chou, CJ and Bridger, SL and Wigner, N and Brehm, SD and et al.}, year={2006}, month={Mar}, pages={2115–2125} }
 @article{price_shannon_sabrina_robert_payne_2005, title={Aflatoxin conducive and non-conducive growth conditions reveal new gene associations with aflatoxin production}, volume={42}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2005.03.009}, abstractNote={Research on aflatoxin (AF) production has traditionally focused on defining the AF biosynthetic pathway with the goal of identifying potential targets for intervention. To understand the effect of nitrogen source, carbon source, temperature, and pH on the regulation of AF biosynthesis, a targeted cDNA microarray consisting of genes associated with AF production over time was employed. Expression profiles for genes involved in AF biosynthesis grouped into five clades. A putative regulon was identified consisting of 20 genes that were induced in the conducive nitrogen and pH treatments and the non-conducive carbon and temperature treatments, as well as four other putative regulons corresponding to each of the four variables studied. Seventeen genes exhibited consistent induction/repression profiles across all the experiments. One of these genes was consistently downregulated with AF production. Overexpression of this gene resulted in repression of AF biosynthesis. The cellular function of this gene is currently unresolved.}, number={6}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Price, MS and Shannon, BCB and Sabrina, TB and Robert, AKB and Payne, GA}, year={2005}, month={Jun}, pages={506–518} }
 @article{conners_montero_comfort_shockley_johnson_chhabra_kelly_2005, title={An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima}, volume={187}, ISSN={["1098-5530"]}, DOI={10.1128/JB.187.21.7267-7282.2005}, abstractNote={ABSTRACT}, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Conners, SB and Montero, CI and Comfort, DA and Shockley, KR and Johnson, MR and Chhabra, SR and Kelly, RM}, year={2005}, month={Nov}, pages={7267–7282} }
 @article{shockley_scott_pysz_conners_johnson_montero_wolfinger_kelly_2005, title={Genorne-wide transcriptional variation within and between steady states for continuous growth of the hyperthermophile Thermotoga maritima}, volume={71}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.71.9.5572-5576.2005}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Shockley, KR and Scott, KL and Pysz, MA and Conners, SB and Johnson, MR and Montero, CI and Wolfinger, RD and Kelly, RM}, year={2005}, month={Sep}, pages={5572–5576} }
 @article{johnson_montero_conners_shockley_bridger_kelly_2005, title={Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima}, volume={55}, ISSN={["1365-2958"]}, DOI={10.1111/j.1365-2958.2004.04419.x}, abstractNote={Summary}, number={3}, journal={MOLECULAR MICROBIOLOGY}, author={Johnson, MR and Montero, CI and Conners, SB and Shockley, KR and Bridger, SL and Kelly, RM}, year={2005}, month={Feb}, pages={664–674} }
 @article{johnson_montero_conners_shockley_pysz_kelly_2004, title={Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms}, volume={32}, ISSN={["1470-8752"]}, DOI={10.1042/BST0320188}, abstractNote={Although much attention has been paid to the genetic, biochemical and physiological aspects of individual hyperthermophiles, how these unique micro-organisms relate to each other and to their natural habitats must be addressed in order to develop a comprehensive understanding of life at high temperatures. Phylogenetic 16 S rRNA-based profiling of samples from various geothermal sites has provided insights into community structure, but this must be complemented with efforts to relate metabolic strategies to biotic and abiotic characteristics in high-temperature habitats. Described here are functional genomics-based approaches, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality.}, number={2004 Apr}, journal={BIOCHEMICAL SOCIETY TRANSACTIONS}, author={Johnson, MR and Montero, CI and Conners, SB and Shockley, KR and Pysz, MA and Kelly, RM}, year={2004}, month={Apr}, pages={188–192} }
 @misc{pysz_conners_montero_shockley_johnson_ward_kelly_2004, title={Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima}, volume={70}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.70.10.6098-6112.2004}, abstractNote={ABSTRACT}, number={10}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Pysz, MA and Conners, SB and Montero, CI and Shockley, KR and Johnson, MR and Ward, DE and Kelly, RA}, year={2004}, month={Oct}, pages={6098–6112} }
 @article{pysz_ward_shockley_montero_conners_johnson_kelly_2004, title={Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima}, volume={8}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-004-0379-2}, abstractNote={The thermal stress response of the hyperthermophilic bacterium Thermotoga maritima was characterized using a 407-open reading frame-targeted cDNA microarray. Transient gene expression was followed for 90 min, following a shift from 80 degrees C to 90 degrees C. While some aspects of mesophilic heat-shock response were conserved in T. maritima, genome content suggested differentiating features that were borne out by transcriptional analysis. Early induction of predicted heat-shock operons hrcA-grpE-dnaJ (TM0851-TM0850-TM0849), groES-groEL (TM0505-TM0506), and dnaK-sHSP (TM0373-TM0374) was consistent with conserved CIRCE elements upstream of hrcA and groES. Induction of the T. maritima rpoE/ sigW and rpoD/ sigA homologs suggests a mechanism for global heat-shock response in the absence of an identifiable ortholog to a major heat-shock sigma factor. In contrast to heat-shock response in Escherichia coli, the majority of genes encoding ATP-dependent proteases were downregulated, including clpP (TM0695), clpQ (TM0521), clpY (TM0522), lonA (TM1633), and lonB (TM1869). Notably, T. maritima showed indications of a late heat-shock response with the induction of a marR homolog (TM0816), several other putative transcriptional regulators (TM1023, TM1069), and two alpha-glucosidases (TM0434 and TM1068). Taken together, the results reported here indicate that, while T. maritima shares core elements of the bacterial heat-shock response with mesophiles, the thermal stress regulatory strategies of this organism differ significantly. However, it remains to be elucidated whether these differences are related to thermophilicity or phylogenetic placement.}, number={3}, journal={EXTREMOPHILES}, author={Pysz, MA and Ward, DE and Shockley, KR and Montero, CI and Conners, SB and Johnson, MR and Kelly, RM}, year={2004}, month={Jun}, pages={209–217} }
 @article{chhabra_shockley_conners_scott_wolfinger_kelly_2003, title={Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima}, volume={278}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M211748200}, abstractNote={The hyperthermophilic bacteriumThermotoga maritima MSB8 was grown on a variety of carbohydrates to determine the influence of carbon and energy source on differential gene expression. Despite the fact that T. maritima has been phylogenetically characterized as a primitive microorganism from an evolutionary perspective, results here suggest that it has versatile and discriminating mechanisms for regulating and effecting complex carbohydrate utilization. Growth ofT. maritima on monosaccharides was found to be slower than growth on polysaccharides, although growth to cell densities of 108 to 109 cells/ml was observed on all carbohydrates tested. Differential expression of genes encoding carbohydrate-active proteins encoded in the T. maritimagenome was followed using a targeted cDNA microarray in conjunction with mixed model statistical analysis. Coordinated regulation of genes responding to specific carbohydrates was noted. Although glucose generally repressed expression of all glycoside hydrolase genes, other sugars induced or repressed these genes to varying extents. Expression profiles of most endo-acting glycoside hydrolase genes correlated well with their reported biochemical properties, although exo-acting glycoside hydrolase genes displayed less specific expression patterns. Genes encoding selected putative ABC sugar transporters were found to respond to specific carbohydrates, and in some cases putative oligopeptide transporter genes were also found to respond to specific sugar substrates. Several genes encoding putative transcriptional regulators were expressed during growth on specific sugars, thus suggesting functional assignments. The transcriptional response ofT. maritima to specific carbohydrate growth substrates indicated that sugar backbone- and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates. Furthermore, the wide ranging collection of such networks in T. maritima suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrates.}, number={9}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Chhabra, SR and Shockley, KR and Conners, SB and Scott, KL and Wolfinger, RD and Kelly, RM}, year={2003}, month={Feb}, pages={7540–7552} }
 @article{shockley_ward_chhabra_conners_montero_kelly_2003, title={Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus}, volume={69}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.69.4.2365-2371.2003}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Shockley, KR and Ward, DE and Chhabra, SR and Conners, SB and Montero, CI and Kelly, RM}, year={2003}, month={Apr}, pages={2365–2371} }