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Publication Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells(2009-01-01) Yi, HN; Nevin, KP; Kim, BC; Franks, AE; Klimes, A; Tender, LM; Lovley, DRPublication The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens(2009-01-01) Aklujkar, Muktak; Krushkal, Julia; DiBartolo, Genevieve; Lapidus, Alla; Land, Miriam L.; Lovley, Derek R.The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.Publication Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens(2009-01-01) Leang, C; Krushkal, J; Ueki, T; Puljic, M; Sun, J; Juarez, K; Nunez, C; Reguera, G; DiDonato, R; Postier, B; Adkins, RM; Lovley, DRPublication GSEL Version 2, an Online Genome-Wide Query System of Operon Organization and Regulatory Sequence Elements of Geobacter sulfurreducens(2009-01-01) Qu, YH; Brown, P; Barbe, JF; Puljic, M; Merino, E; Adkins, RM; Lovley, DR; Krushkal, JPublication Hierarchical Bayesian meta-analysis models for cross-platform microarray studies(2009-01-01) Conlon, EM; Postier, BL; Methe, BA; Nevin, KP; Lovley, DRPublication Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation(2009-01-01) Wilkins, MJ; VerBerkmoes, NC; Williams, KH; Callister, SJ; Mouser, PJ; Elifantz, H; N'Guessan, AL; Thomas, BC; Nicora, CD; Shah, MB; Abraham, P; Lipton, MS; Lovley, DR; Hettich, RL; Long, PE; Banfield, JFPublication Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens(2009-01-01) Risso, C; Sun, J; Zhuang, K; Mahadevan, R; Deboy, R; Ismail, W; Shrivastava, S; Huot, H; Kothari, S; Daugherty, S; Bui, O; Schilling, CH; Lovley, DR; Methe, BAPublication Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species(2010-01-01) Ueki, T; Lovley, DRPublication Kinetic and mechanistic characterization of the polyhydroxybutyrate synthase from Ralstonia eutropha(2000-01-01) Zhang, SM; Yasuo, T; Lenz, RW; Goodwin, SPublication GEOC 35-Biogeochemical differences in pilot-scale bioremediation treatment plots undergoing iron reduction or sulfate reduction in a uranium-contaminated aquifer(2008-01-01) N'Guessan, AL; Williams, KH; Yabusaki, S; Long, PE; Lovley, DRPublication Electrode-Based Approach for Monitoring In Situ Microbial Activity During Subsurface Bioremediation(2010-01-01) Williams, KH; Nevin, KP; Franks, A; Englert, A; Long, PE; Lovley, DRPublication Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments(2010-01-01) Zhao, J; Fang, YL; Scheibe, TD; Lovley, DR; Mahadevan, RPublication Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes(2010-01-01) Butler, Jessica E.; Young, Nelson D.; Lovley, Derek R.Background Geobacter species grow by transferring electrons out of the cell - either to Fe(III)-oxides or to man-made substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments. Results The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III)-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species. Conclusions These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor.Publication Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer(2010-01-01) N'Guessan, AL; Elifantz, H; Nevin, KP; Mouser, PJ; Methe, B; LWoodard, T; Manley, K; Williams, KH; Wilkins, MJ; Larsen, JT; Long, PE; Lovley, DRPublication Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms(2010-01-01) Franks, AE; Nevin, KP; Glaven, RH; Lovley, DRPublication Stimulating the anaerobic degradation of aromatic hydrocarbons in contaminated sediments by providing an electrode as the electron acceptor(2010-01-01) Zhang, T; Gannon, SM; Nevin, KP; Franks, AE; Lovley, DRPublication Role of Geobacter sulfurreducens Outer Surface c-Type Cytochromes in Reduction of Soil Humic Acid and Anthraquinone-2,6-Disulfonate(2010-01-01) Voordeckers, JW; Kim, BC; Izallalen, M; Lovley, DRPublication Comparative study of the relationship between monomer structure and reactivity for two polyhydroxyalkanoate synthases(2001-01-01) Zhang, S; Kamachi, M; Takagi, Y; Lenz, RW; Goodwin, SPublication De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads(2010-01-01) Nagarajan, H; Butler, JE; Klimes, A; Qiu, Y; Zengler, K; Ward, J; Young, ND; Methe, BA; Palsson, BO; Lovley, DR; Barrett, CLPublication Alignment of the c-Type Cytochrome OmcS along Pili of Geobacter sulfurreducens(2010-01-01) Leang, Ching; Qian, Xinlei; Mester, Tünde; Lovley, Derek R.Immunogold localization revealed that OmcS, a cytochrome that is required for Fe(III) oxide reduction by Geobacter sulfurreducens, was localized along the pili. The apparent spacing between OmcS molecules suggests that OmcS facilitates electron transfer from pili to Fe(III) oxides rather than promoting electron conduction along the length of the pili.