The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1.

Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H(2) -evolving and H(2) -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown.

[1]  P. Junier,et al.  Effect of Competing Electron Acceptors on the Reduction of U(VI) by Desulfotomaculum reducens , 2010 .

[2]  Eleanor J. Schofield,et al.  Metal reduction by spores of Desulfotomaculum reducens. , 2009, Environmental microbiology.

[3]  L. Krumholz,et al.  Thioredoxin Is Involved in U(VI) and Cr(VI) Reduction in Desulfovibrio desulfuricans G20 , 2009, Journal of bacteriology.

[4]  R. Amann,et al.  Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide , 2009, Environmental microbiology.

[5]  C. Vonrhein,et al.  The Crystal Structure of Desulfovibrio vulgaris Dissimilatory Sulfite Reductase Bound to DsrC Provides Novel Insights into the Mechanism of Sulfate Respiration* , 2008, Journal of Biological Chemistry.

[6]  Dylan Chivian,et al.  Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth , 2008, Science.

[7]  Paul Richardson,et al.  The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). , 2008, Environmental microbiology.

[8]  P. Long,et al.  Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction. , 2008, Environmental science & technology.

[9]  Jizhong Zhou,et al.  Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis , 2008, Antonie van Leeuwenhoek.

[10]  T. Phelps,et al.  Microbial uranium immobilization independent of nitrate reduction. , 2007, Environmental microbiology.

[11]  J. Meyer,et al.  [FeFe] hydrogenases and their evolution: a genomic perspective , 2007, Cellular and Molecular Life Sciences.

[12]  H. Park,et al.  Ferric iron reduction by Desulfovibrio vulgaris Hildenborough wild type and energy metabolism mutants , 2007, Antonie van Leeuwenhoek.

[13]  Laurie N. DiDonato,et al.  Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens , 2007, BMC Microbiology.

[14]  S. Spring,et al.  Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments. , 2006, International journal of systematic and evolutionary microbiology.

[15]  K. Weber,et al.  Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction , 2006, Nature Reviews Microbiology.

[16]  Alice Dohnalkova,et al.  Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  M. Teixeira,et al.  Characterization of the Desulfovibrio desulfuricans ATCC 27774 DsrMKJOP complex--a membrane-bound redox complex involved in the sulfate respiratory pathway. , 2006, Biochemistry.

[18]  F. Brockman,et al.  Desulfotomaculum and Methanobacterium spp. Dominate a 4- to 5-Kilometer-Deep Fault , 2005, Applied and Environmental Microbiology.

[19]  Michael N Fienen,et al.  Mass-transfer limitations for nitrate removal in a uranium-contaminated aquifer. , 2005, Environmental science & technology.

[20]  Jizhong Zhou,et al.  Global Transcriptional Profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) Reduction , 2005, Applied and Environmental Microbiology.

[21]  T. Mehta,et al.  Extracellular electron transfer via microbial nanowires , 2005, Nature.

[22]  Gerrit Voordouw,et al.  Physiological and Gene Expression Analysis of Inhibition of Desulfovibrio vulgaris Hildenborough by Nitrite , 2004, Journal of bacteriology.

[23]  H. Cypionka,et al.  Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake , 2004, Archives of Microbiology.

[24]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[25]  P. Vignais,et al.  Molecular biology of microbial hydrogenases. , 2004, Current issues in molecular biology.

[26]  Rekha Seshadri,et al.  The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough , 2004, Nature Biotechnology.

[27]  R. Hedderich,et al.  Two distinct heterodisulfide reductase-like enzymes in the sulfate-reducing archaeon Archaeoglobus profundus. , 2004, European journal of biochemistry.

[28]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[29]  D. R. Bond,et al.  Electron Transfer by Desulfobulbus propionicus to Fe(III) and Graphite Electrodes , 2004, Applied and Environmental Microbiology.

[30]  Joseph M Suflita,et al.  Periplasmic Cytochrome c3 of Desulfovibrio vulgaris Is Directly Involved in H2-Mediated Metal but Not Sulfate Reduction , 2004, Applied and Environmental Microbiology.

[31]  T. Hansen,et al.  Immunocytochemical localization of APS reductase and bisulfite reductase in three Desulfovibrio species , 1988, Archives of Microbiology.

[32]  J A Eisen,et al.  Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments , 2003, Science.

[33]  F. Brockman,et al.  Temporal Shifts in the Geochemistry and Microbial Community Structure of an Ultradeep Mine Borehole Following Isolation , 2003 .

[34]  M. Teixeira,et al.  A novel membrane-bound respiratory complex from Desulfovibrio desulfuricans ATCC 27774. , 2003, Biochimica et biophysica acta.

[35]  R. Hedderich,et al.  Physiological role of the F420-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis , 2003, Archives of Microbiology.

[36]  P. Long,et al.  Characterization of Microbial Activities and U Reduction in a Shallow Aquifer Contaminated by Uranium Mill Tailings , 2003, Microbial Ecology.

[37]  G. Voordouw.  Carbon Monoxide Cycling by Desulfovibrio vulgaris Hildenborough , 2002, Journal of bacteriology.

[38]  J. Wall,et al.  Uranium Reduction by Desulfovibrio desulfuricans Strain G20 and a Cytochrome c3 Mutant , 2002, Applied and Environmental Microbiology.

[39]  Kelly P. Nevin,et al.  Mechanisms for Fe(III) Oxide Reduction in Sedimentary Environments , 2002 .

[40]  J. Meyer,et al.  Classification and phylogeny of hydrogenases. , 2001, FEMS microbiology reviews.

[41]  S. Macnaughton,et al.  Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site , 2001, Applied and Environmental Microbiology.

[42]  A. Beliaev,et al.  MtrC, an outer membrane decahaem c cytochrome required for metal reduction in Shewanella putrefaciens MR‐1 , 2001, Molecular microbiology.

[43]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[44]  G. Gottschalk,et al.  The F420H2 Dehydrogenase fromMethanosarcina mazei Is a Redox-driven Proton Pump Closely Related to NADH Dehydrogenases* , 2000, The Journal of Biological Chemistry.

[45]  Dianne K. Newman,et al.  A role for excreted quinones in extracellular electron transfer , 2000, Nature.

[46]  K. Aoki,et al.  Characterization by denaturing gradient gel electrophoresis of bacterial communities in deep groundwater at the Kamaishi Mine, Japan. , 2000, The Journal of general and applied microbiology.

[47]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[48]  B. Jørgensen,et al.  Psychrophilic sulfate-reducing bacteria isolated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica s , 1999, International journal of systematic bacteriology.

[49]  D. White.  The Physiology and Biochemistry of Prokaryotes , 1999 .

[50]  M. Adams,et al.  The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization. , 1999, Biochimica et biophysica acta.

[51]  U. Deppenmeier,et al.  Energy Conservation by the H2:Heterodisulfide Oxidoreductase from Methanosarcina mazei Gö1: Identification of Two Proton-Translocating Segments , 1999, Journal of bacteriology.

[52]  G. Olsen,et al.  CRITICA: coding region identification tool invoking comparative analysis. , 1999, Molecular biology and evolution.

[53]  Anna Obraztsova,et al.  Sulfate-reducing bacterium grows with Cr(VI), U(VI), Mn(IV), and Fe(III) as electron acceptors , 1998 .

[54]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[55]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[56]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[57]  O Gascuel,et al.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.

[58]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[59]  O. Meyer,et al.  Molecular characterization of the gene cluster coxMSL encoding the molybdenum-containing carbon monoxide dehydrogenase of Oligotropha carboxidovorans , 1995, Journal of bacteriology.

[60]  R. Thauer,et al.  Purification of a two-subunit cytochrome-b-containing heterodisulfide reductase from methanol-grown Methanosarcina barkeri. , 1994, European journal of biochemistry.

[61]  R. Thauer,et al.  H2: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Composition and properties. , 1994, European journal of biochemistry.

[62]  F. Widdel,et al.  Gram-Negative Mesophilic Sulfate-Reducing Bacteria , 1992 .

[63]  J. M. Odom,et al.  Hydrogen cycling as a general mechanism for energy coupling in the sulfate‐reducing bacteria, Desulfovibrio sp. , 1981 .