Comparative genomics of the genus Desulfitobacterium
Abstract
The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5.5, 4.3 and 3.4 Mbp for D. hafniense, D. dehalogenans and D. dichloroeliminans/metallireducens, respectively. The genomes encode up to seven reductive dehalogenases, the genomes of both D. hafniense DP7 and D. metallireducens 853–15AT did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853–15AT has been reported to carry out organohalide respiration. Unlike reported for the pceABCT gene cluster, the other reductive dehalogenase gene clusters do not show any signs of being genetically mobile. All analyzed desulfitobacterial genomes encode a complete cobalamin synthesis pathway. A menaquinone synthesis pathway was found in all strains except D. dichloroeliminans DCA1T. The detailed analysis of the genome sequence of 12 desulfitobacteria from four different species confirmed that this genus has an extremely large metabolic repertoire.
- Authors:
-
- Wageningen Univ., Wageningen (Netherlands)
- Friedrich Schiller Univ., Jena (Germany)
- Ecole Polytechnique Federale Lausanne (Switzlerland)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Martin Luther Univ., Halle (Germany)
- Wageningen Univ., Wageningen (Netherlands); Helsinki Univ. (Finland)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1543955
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- FEMS Microbiology Ecology (Online)
- Additional Journal Information:
- Journal Name: FEMS Microbiology Ecology (Online); Journal Volume: 93; Journal Issue: 12; Journal ID: ISSN 1574-6941
- Publisher:
- Federation of European Microbiological Societies
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Microbiology
Citation Formats
Kruse, Thomas, Goris, Tobias, Maillard, Julien, Woyke, Tanja, Lechner, Ute, de Vos, Willem, and Smidt, Hauke. Comparative genomics of the genus Desulfitobacterium. United States: N. p., 2017.
Web. doi:10.1093/femsec/fix135.
Kruse, Thomas, Goris, Tobias, Maillard, Julien, Woyke, Tanja, Lechner, Ute, de Vos, Willem, & Smidt, Hauke. Comparative genomics of the genus Desulfitobacterium. United States. https://doi.org/10.1093/femsec/fix135
Kruse, Thomas, Goris, Tobias, Maillard, Julien, Woyke, Tanja, Lechner, Ute, de Vos, Willem, and Smidt, Hauke. Wed .
"Comparative genomics of the genus Desulfitobacterium". United States. https://doi.org/10.1093/femsec/fix135. https://www.osti.gov/servlets/purl/1543955.
@article{osti_1543955,
title = {Comparative genomics of the genus Desulfitobacterium},
author = {Kruse, Thomas and Goris, Tobias and Maillard, Julien and Woyke, Tanja and Lechner, Ute and de Vos, Willem and Smidt, Hauke},
abstractNote = {The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5.5, 4.3 and 3.4 Mbp for D. hafniense, D. dehalogenans and D. dichloroeliminans/metallireducens, respectively. The genomes encode up to seven reductive dehalogenases, the genomes of both D. hafniense DP7 and D. metallireducens 853–15AT did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853–15AT has been reported to carry out organohalide respiration. Unlike reported for the pceABCT gene cluster, the other reductive dehalogenase gene clusters do not show any signs of being genetically mobile. All analyzed desulfitobacterial genomes encode a complete cobalamin synthesis pathway. A menaquinone synthesis pathway was found in all strains except D. dichloroeliminans DCA1T. The detailed analysis of the genome sequence of 12 desulfitobacteria from four different species confirmed that this genus has an extremely large metabolic repertoire.},
doi = {10.1093/femsec/fix135},
journal = {FEMS Microbiology Ecology (Online)},
number = 12,
volume = 93,
place = {United States},
year = {Wed Oct 11 00:00:00 EDT 2017},
month = {Wed Oct 11 00:00:00 EDT 2017}
}
Web of Science
Figures / Tables:
Works referenced in this record:
Siro(haem)amide in Allochromatium vinosum and relevance of DsrL and DsrN, a homolog of cobyrinic acid a,c -diamide synthase, for sulphur oxidation
journal, August 2006
- Lübbe, Yvonne J.; Youn, Hyung-Sun; Timkovich, Russell
- FEMS Microbiology Letters, Vol. 261, Issue 2
Use of Ferric and Ferrous Iron Containing Minerals for Respiration by Desulfitobacterium frappieri
journal, March 2003
- Shelobolina, Evgenya S.; VanPraagh, Catherine Gaw; Lovley, Derek R.
- Geomicrobiology Journal, Vol. 20, Issue 2
Anaerobic Microbial Dehalogenation
journal, October 2004
- Smidt, Hauke; de Vos, Willem M.
- Annual Review of Microbiology, Vol. 58, Issue 1
Reduction of fumarate, mesaconate and crotonate by Mfr, a novel oxygen-regulated periplasmic reductase in Campylobacter jejuni
journal, March 2010
- Guccione, Edward; Hitchcock, Andrew; Hall, Stephen J.
- Environmental Microbiology, Vol. 12, Issue 3
Biochemical and EPR-Spectroscopic Investigation into Heterologously Expressed Vinyl Chloride Reductive Dehalogenase (VcrA) from Dehalococcoides mccartyi Strain VS
journal, March 2015
- Parthasarathy, Anutthaman; Stich, Troy A.; Lohner, Svenja T.
- Journal of the American Chemical Society, Vol. 137, Issue 10
A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols
journal, November 2001
- Pas, Bram; Harmsen, Hermie; Raangs, Gerwin
- Archives of Microbiology, Vol. 176, Issue 5
Tetrachloroethene metabolism of Dehalospirillum multivorans
journal, October 1994
- Neumann, Anke; Scholz-Muramatsu, Heidrun; Diekert, Gabriele
- Archives of Microbiology, Vol. 162, Issue 4
Phenyl methyl ethers: novel electron donors for respiratory growth of Desulfitobacterium hafniense and Desulfitobacterium sp. strain PCE-S
journal, March 2004
- Diekert, Gabriele; Neumann, Anke; Engelmann, Tina
- Archives of Microbiology, Vol. 181, Issue 3
Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009
- Richter, Michael; Rosselló-Móra, Ramon
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
Requirements for CuA and Cu-S Center Assembly of Nitrous Oxide Reductase Deduced from Complete Periplasmic Enzyme Maturation in the Nondenitrifier Pseudomonas putida
journal, February 2003
- Wunsch, P.; Herb, M.; Wieland, H.
- Journal of Bacteriology, Vol. 185, Issue 3
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014
- Kim, M.; Oh, H. -S.; Park, S. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases
journal, March 2014
- Greening, C.; Berney, M.; Hards, K.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 11
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994
- Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
- Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction
journal, January 2012
- Kim, Sang-Hoon; Harzman, Christina; Davis, John K.
- BMC Microbiology, Vol. 12, Issue 1
Anaerobic reduction and oxidation of quinone moieties and the reduction of oxidized metals by halorespiring and related organisms
journal, July 2004
- Luijten, Maurice L. G. C.; Weelink, Sander A. B.; Godschalk, Bas
- FEMS Microbiology Ecology, Vol. 49, Issue 1
SMART 6: recent updates and new developments
journal, January 2009
- Letunic, I.; Doerks, T.; Bork, P.
- Nucleic Acids Research, Vol. 37, Issue Database
SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011
- Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
- Nature Methods, Vol. 8, Issue 10
The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism
journal, July 2014
- Venceslau, S. S.; Stockdreher, Y.; Dahl, C.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 7
Dynamic Control of Electron Transfers in Diflavin Reductases
journal, November 2012
- Aigrain, Louise; Fatemi, Fataneh; Frances, Oriane
- International Journal of Molecular Sciences, Vol. 13, Issue 12
The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine
journal, March 2011
- Gaston, Marsha A.; Zhang, Liwen; Green-Church, Kari B.
- Nature, Vol. 471, Issue 7340
Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S -adenosylmethionine methyltransferase
journal, February 2006
- Qin, Jie; Rosen, Barry P.; Zhang, Yang
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 7
Functional Heterologous Production of Reductive Dehalogenases from Desulfitobacterium hafniense Strains
journal, May 2014
- Mac Nelly, Anita; Kai, Marco; Svatoš, Aleš
- Applied and Environmental Microbiology, Vol. 80, Issue 14
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome"
journal, September 2005
- Tettelin, H.; Masignani, V.; Cieslewicz, M. J.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 39
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, May 2014
- Kim, M.; Oh, H. -S.; Park, S. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase
journal, May 2002
- Hao, B.
- Science, Vol. 296, Issue 5572
Role of quinones in electron transport to oxygen and nitrate in Escherichia coli. Studies with a ubiA− menA− double quinone mutant
journal, July 1977
- Wallace, B. J.; Young, I. G.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 461, Issue 1
The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the ‘termination’ codon, TGA.
journal, June 1986
- Chambers, I.; Frampton, J.; Goldfarb, P.
- The EMBO Journal, Vol. 5, Issue 6
The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems
journal, December 2008
- Simon, Jörg; van Spanning, Rob J. M.; Richardson, David J.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1777, Issue 12
The Genus DehalobacterDehalobacter
book, January 2016
- Maillard, Julien; Holliger, Christof
- Organohalide-Respiring Bacteria
A Combined Transmembrane Topology and Signal Peptide Prediction Method
journal, May 2004
- Käll, Lukas; Krogh, Anders; Sonnhammer, Erik L. L.
- Journal of Molecular Biology, Vol. 338, Issue 5
Purification, Cloning, and Sequencing of a 3,5-Dichlorophenol Reductive Dehalogenase from Desulfitobacterium frappieri PCP-1
journal, August 2004
- Thibodeau, J.; Gauthier, A.; Duguay, M.
- Applied and Environmental Microbiology, Vol. 70, Issue 8
Purification and Molecular Characterization of ortho -Chlorophenol Reductive Dehalogenase, a Key Enzyme of Halorespiration in Desulfitobacterium dehalogenans
journal, July 1999
- van de Pas, Bram A.; Smidt, Hauke; Hagen, Wilfred R.
- Journal of Biological Chemistry, Vol. 274, Issue 29
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
journal, April 2012
- Loffler, F. E.; Yan, J.; Ritalahti, K. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Stereoselective Microbial Dehalorespiration with Vicinal Dichlorinated Alkanes
journal, September 2003
- De Wildeman, S.; Diekert, G.; Van Langenhove, H.
- Applied and Environmental Microbiology, Vol. 69, Issue 9
Conversion of phenyl methyl ethers by Desulfitobacterium spp. and screening for the genes involved
journal, October 2014
- Mingo, Felix S.; Studenik, Sandra; Diekert, Gabriele
- FEMS Microbiology Ecology, Vol. 90, Issue 3
Electron transfer by diflavin reductases
journal, April 2004
- Murataliev, Marat B.; Feyereisen, René; Walker, F. Ann
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1698, Issue 1
Two distinct enzyme systems are responsible for tetrachloroethene and chlorophenol reductive dehalogenation in Desulfitobacterium strain PCE1
journal, September 2001
- van de Pas, Bram; Gerritse, Jan; de Vos, Willem
- Archives of Microbiology, Vol. 176, Issue 3
The Physiological Opportunism of Desulfitobacterium hafniense Strain TCE1 towards Organohalide Respiration with Tetrachloroethene
journal, June 2012
- Duret, Aurélie; Holliger, Christof; Maillard, Julien
- Applied and Environmental Microbiology, Vol. 78, Issue 17
Emergence of two types of nondechlorinating variants in the tetrachloroethene-halorespiring Desulfitobacterium sp. strain Y51
journal, August 2005
- Futagami, Taiki; Tsuboi, Yoshinori; Suyama, Akiko
- Applied Microbiology and Biotechnology, Vol. 70, Issue 6
On the function of the various quinone species in Escherichia coli : The role of DMK in the electron transfer chains of
journal, May 2012
- Sharma, Poonam; Teixeira de Mattos, Maarten J.; Hellingwerf, Klaas J.
- FEBS Journal, Vol. 279, Issue 18
A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols
journal, June 2001
- van de Pas, Bram; Harmsen, Hermie; Raangs, Gerwin
- Archives of Microbiology, Vol. 175, Issue 6
HydDB: A web tool for hydrogenase classification and analysis
journal, September 2016
- Søndergaard, Dan; Pedersen, Christian N. S.; Greening, Chris
- Scientific Reports, Vol. 6, Issue 1
Complete Genome Sequence of the Dehalorespiring Bacterium Desulfitobacterium hafniense Y51 and Comparison with Dehalococcoides ethenogenes 195
journal, March 2006
- Nonaka, H.; Keresztes, G.; Shinoda, Y.
- Journal of Bacteriology, Vol. 188, Issue 6
Identification and Characterization of a Novel CprA Reductive Dehalogenase Specific to Highly Chlorinated Phenols from Desulfitobacterium hafniense Strain PCP-1
journal, September 2010
- Bisaillon, A.; Beaudet, R.; Lepine, F.
- Applied and Environmental Microbiology, Vol. 76, Issue 22
Isolation and Characterization of a Novel As(V)-Reducing Bacterium: Implications for Arsenic Mobilization and the Genus Desulfitobacterium
journal, December 2001
- Niggemyer, A.; Spring, S.; Stackebrandt, E.
- Applied and Environmental Microbiology, Vol. 67, Issue 12
Arsenics as bioenergetic substrates
journal, February 2013
- van Lis, Robert; Nitschke, Wolfgang; Duval, Simon
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
Making sense of it all: bacterial chemotaxis
journal, December 2004
- Wadhams, George H.; Armitage, Judith P.
- Nature Reviews Molecular Cell Biology, Vol. 5, Issue 12
Identification of a Hotdog Fold Thioesterase Involved in the Biosynthesis of Menaquinone in Escherichia coli
journal, April 2013
- Chen, M.; Ma, X.; Chen, X.
- Journal of Bacteriology, Vol. 195, Issue 12
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011
- Tamura, K.; Peterson, D.; Peterson, N.
- Molecular Biology and Evolution, Vol. 28, Issue 10
Purification, cloning and sequencing of an enzyme mediating the reductive dechlorination of 2,4,6-trichlorophenol from Desulfitobacterium frappieri PCP-1
journal, July 2003
- Boyer, Annie; PagÉ-BÉLanger, Rachel; Saucier, Maude
- Biochemical Journal, Vol. 373, Issue 1
A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase
journal, March 2011
- Goris, Tobias; Wait, Annemarie F.; Saggu, Miguel
- Nature Chemical Biology, Vol. 7, Issue 5
Novel Genes of the dsr Gene Cluster and Evidence for Close Interaction of Dsr Proteins during Sulfur Oxidation in the Phototrophic Sulfur Bacterium Allochromatium vinosum
journal, February 2005
- Dahl, C.; Engels, S.; Pott-Sperling, A. S.
- Journal of Bacteriology, Vol. 187, Issue 4
Characterization of an O-Demethylase of Desulfitobacterium hafniense DCB-2
journal, April 2012
- Studenik, S.; Vogel, M.; Diekert, G.
- Journal of Bacteriology, Vol. 194, Issue 13, p. 3317-3326
A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme
journal, July 2020
- Thawai, Chitti; Bunbamrung, Nantiya; Pittayakhajonwut, Pattama
- Scientific Reports, Vol. 10, Issue 1
Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils
journal, February 2016
- Zhang, Xi; Li, Guo-Xiang; Chen, Song-Can
- Genome Announcements, Vol. 4, Issue 1
Characterization of CprK1, a CRP/FNR-Type Transcriptional Regulator of Halorespiration from Desulfitobacterium hafniense
journal, March 2006
- Gabor, K.; Verissimo, C. S.; Cyran, B. C.
- Journal of Bacteriology, Vol. 188, Issue 7
The NiFe Hydrogenases of the Tetrachloroethene-Respiring Epsilonproteobacterium Sulfurospirillum multivorans: Biochemical Studies and Transcription Analysis
journal, March 2017
- Kruse, Stefan; Goris, Tobias; Wolf, Maria
- Frontiers in Microbiology, Vol. 8
Development of a Gene Cloning and Inactivation System for Halorespiring Desulfitobacterium dehalogenans
journal, February 2001
- Smidt, H.; van der Oost, J.; de Vos, W. M.
- Applied and Environmental Microbiology, Vol. 67, Issue 2
Isolation and Characterization of Desulfitobacterium frappieri sp. nov., an Anaerobic Bacterium Which Reductively Dechlorinates Pentachlorophenol to 3-Chlorophenol
journal, October 1996
- Bouchard, B.; Beaudet, R.; Villemur, R.
- International Journal of Systematic Bacteriology, Vol. 46, Issue 4
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
journal, July 2001
- Karlin, Samuel
- Trends in Microbiology, Vol. 9, Issue 7
The genetic basis of tetrathionate respiration in Salmonella typhimurium
journal, April 1999
- Hensel, Michael; Hinsley, Andrew P.; Nikolaus, Thomas
- Molecular Microbiology, Vol. 32, Issue 2
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Artemis: sequence visualization and annotation
journal, October 2000
- Rutherford, K.; Parkhill, J.; Crook, J.
- Bioinformatics, Vol. 16, Issue 10
Translocation of proteins across the cell envelope of Gram-positive bacteria
journal, August 2001
- van Wely, Karel H. M.; Swaving, Jelto; Freudl, Roland
- FEMS Microbiology Reviews, Vol. 25, Issue 4
The twin-arginine translocation (Tat) protein export pathway
journal, June 2012
- Palmer, Tracy; Berks, Ben C.
- Nature Reviews Microbiology, Vol. 10, Issue 7
A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system
journal, November 1997
- Andrews, S. C.; Berks, B. C.; McClay, J.
- Microbiology, Vol. 143, Issue 11
The InterPro protein families database: the classification resource after 15 years
journal, November 2014
- Mitchell, Alex; Chang, Hsin-Yu; Daugherty, Louise
- Nucleic Acids Research, Vol. 43, Issue D1
Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
journal, April 2013
- Hug, Laura A.; Maphosa, Farai; Leys, David
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Functional characterization of the trigger factor protein PceT of tetrachloroethene-dechlorinating Desulfitobacterium hafniense Y51
journal, April 2009
- Morita, Yasuyuki; Futagami, Taiki; Goto, Masatoshi
- Applied Microbiology and Biotechnology, Vol. 83, Issue 4
The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics
journal, April 2013
- Rupakula, Aamani; Kruse, Thomas; Boeren, Sjef
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O2-tolerance?
journal, September 2012
- Pandelia, Maria-Eirini; Lubitz, Wolfgang; Nitschke, Wolfgang
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1817, Issue 9
A periplasmic flavoprotein in Wolinella succinogenes that resembles the fumarate reductase of Shewanella putrefaciens
journal, April 1998
- Simon, Jörg; Gross, Roland; Klimmek, Oliver
- Archives of Microbiology, Vol. 169, Issue 5
Clustal W and Clustal X version 2.0
journal, September 2007
- Larkin, M. A.; Blackshields, G.; Brown, N. P.
- Bioinformatics, Vol. 23, Issue 21, p. 2947-2948
Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity
journal, April 2013
- Yan, Jun; Im, Jeongdae; Yang, Yi
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T
journal, October 2012
- Pester, M.; Brambilla, E.; Alazard, D.
- Journal of Bacteriology, Vol. 194, Issue 22
Analysis of a 2,4,6-trichlorophenol-dehalogenating enrichment culture and isolation of the dehalogenating member Desulfitobacterium frappieri strain TCP-A
journal, March 2001
- Breitenstein, Antje; Saano, Aimo; Salkinoja-Salonen, Mirja
- Archives of Microbiology, Vol. 175, Issue 2
Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols
journal, July 2011
- Bisaillon, Ariane; Beaudet, Réjean; Lépine, François
- Applied and Environmental Microbiology, Vol. 77, Issue 17
Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism
journal, January 2002
- Kröger, Achim; Biel, Simone; Simon, Jörg
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1553, Issue 1-2
Growth substrate dependent localization of tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans
journal, June 2006
- John, Markus; Schmitz, Roland P. H.; Westermann, Martin
- Archives of Microbiology, Vol. 186, Issue 2
Diversity of Cobalamin Riboswitches in the Corrinoid-Producing Organohalide Respirer Desulfitobacterium hafniense
journal, September 2013
- Choudhary, P. K.; Duret, A.; Rohrbach-Brandt, E.
- Journal of Bacteriology, Vol. 195, Issue 22
Complete genome sequence of Dehalobacter restrictus PER-K23T
journal, July 2013
- Kruse, Thomas; Maillard, Julien; Goodwin, Lynne
- Standards in Genomic Sciences, Vol. 8, Issue 3
Cytochrome c-dependent methacrylate reductase from Geobacter sulfurreducens AM-1
journal, July 1999
- Mikoulinskaia, Oxana; Akimenko, Vasily; Galouchko, Alexander
- European Journal of Biochemistry, Vol. 263, Issue 2
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
journal, June 2015
- Müller, Jochen A.; Fullerton, Heather; Zinder, Stephen H.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 6
Transcriptional Regulation of the cpr Gene Cluster in ortho-Chlorophenol-Respiring Desulfitobacterium dehalogenans
journal, October 2000
- Smidt, H.; van Leest, M.; van der Oost, J.
- Journal of Bacteriology, Vol. 182, Issue 20
CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics
journal, April 2013
- Vesth, Tammi; Lagesen, Karin; Acar, Öncel
- PLoS ONE, Vol. 8, Issue 4
Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer
journal, May 2015
- Arkhipova, Oksana V.; Meer, Margarita V.; Mikoulinskaia, Galina V.
- PLOS ONE, Vol. 10, Issue 5
Characterization of a flavocytochrome that is induced during the anaerobic respiration of Fe3+ by Shewanella frigidimarina NCIMB400
journal, August 1999
- Dobbin, Paul S.; Butt, Julea N.; Powell, Anne K.
- Biochemical Journal, Vol. 342, Issue 2
IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 42, Issue D1
The Desulfitobacterium genus
journal, September 2006
- Villemur, Richard; Lanthier, Martin; Beaudet, Réjean
- FEMS Microbiology Reviews, Vol. 30, Issue 5
Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S
journal, December 1997
- Miller, Evelyn; Wohlfarth, Gert; Diekert, G.
- Archives of Microbiology, Vol. 168, Issue 6
An unusual tandem-domain rhodanese harbouring two active sites identified in Desulfitobacterium hafniense: Unusual rhodanese protein in Desulfitobacterium
journal, July 2012
- Prat, Laure; Maillard, Julien; Rohrbach-Brandt, Emmanuelle
- FEBS Journal, Vol. 279, Issue 15
Physiological Adaptation of Desulfitobacterium hafniense Strain TCE1 to Tetrachloroethene Respiration
journal, April 2011
- Prat, Laure; Maillard, Julien; Grimaud, Régis
- Applied and Environmental Microbiology, Vol. 77, Issue 11
Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth
journal, June 2002
- Bentley, R.; Chasteen, T. G.
- Microbiology and Molecular Biology Reviews, Vol. 66, Issue 2
Desulfitobacterium hafniense sp. nov., an Anaerobic, Reductively Dechlorinating Bacterium
journal, April 1996
- Christiansen, N.; Ahring, B. K.
- International Journal of Systematic Bacteriology, Vol. 46, Issue 2
Global transcriptome analysis of the tetrachloroethene-dechlorinating bacterium Desulfitobacterium hafniense Y51 in the presence of various electron donors and terminal electron acceptors
journal, August 2011
- Peng, Xue; Yamamoto, Shogo; Vertès, Alain A.
- Journal of Industrial Microbiology & Biotechnology, Vol. 39, Issue 2
The Many Faces of Vitamin B12: Catalysis by Cobalamin-Dependent Enzymes
journal, June 2003
- Banerjee, Ruma; Ragsdale, Stephen W.
- Annual Review of Biochemistry, Vol. 72, Issue 1, p. 209-247
vanI : a novel d -Ala- d -Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense : Vancomycin resistance in
journal, July 2014
- Kruse, Thomas; Levisson, Mark; de Vos, Willem M.
- Microbial Biotechnology, Vol. 7, Issue 5
Redundancy and specificity of multiple trigger factor chaperones in Desulfitobacteria
journal, May 2011
- Maillard, J.; Genevaux, P.; Holliger, C.
- Microbiology, Vol. 157, Issue 8
Fine-Tuning Our Knowledge of the Anaerobic Route to Cobalamin (Vitamin B12)
journal, August 2006
- Roessner, C. A.; Scott, A. I.
- Journal of Bacteriology, Vol. 188, Issue 21
Arsenic and Selenium in Microbial Metabolism
journal, October 2006
- Stolz, John F.; Basu, Partha; Santini, Joanne M.
- Annual Review of Microbiology, Vol. 60, Issue 1
Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates
journal, September 2015
- Goris, Tobias; Schiffmann, Christian L.; Gadkari, Jennifer
- Scientific Reports, Vol. 5, Issue 1
Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression
journal, December 2008
- Gabor, K.; Hailesellasse Sene, K.; Smidt, H.
- Microbiology, Vol. 154, Issue 12
Periplasmic Electron Transfer via the c-Type Cytochromes MtrA and FccA of Shewanella oneidensis MR-1
journal, October 2009
- Schuetz, B.; Schicklberger, M.; Kuermann, J.
- Applied and Environmental Microbiology, Vol. 75, Issue 24
Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes - origin and evolution of the dissimilatory sulfate-reduction pathway
journal, July 2007
- Meyer, B.; Kuever, J.
- Microbiology, Vol. 153, Issue 7
Sequence of the gene encoding flavocytochrome c from Shewanella putrefaciens: a tetraheme flavoenzyme that is a soluble fumarate reductase related to the membrane-bound enzymes from other bacteria
journal, December 1992
- Pealing, Sara L.; Black, Ann C.; Manson, Forbes D. C.
- Biochemistry, Vol. 31, Issue 48
Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1
journal, January 2005
- Maillard, Julien; Regeard, Christophe; Holliger, Christof
- Environmental Microbiology, Vol. 7, Issue 1
Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough
journal, May 2009
- Lobo, Susana A. L.; Brindley, Amanda; Warren, Martin J.
- Biochemical Journal, Vol. 420, Issue 2
Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations
journal, February 2013
- Simon, Jörg; Klotz, Martin G.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
Cloning, sequencing and overexpression of cob A which encodes ATP:corrinoid adenosyltranferase in Salmonella typhimurium
journal, July 1993
- Suh, Sang-Jin; Escalante-Semerena, J. C.
- Gene, Vol. 129, Issue 1
Isolation and Characterization of Desulfitobacterium sp. strain Y51 Capable of Efficient Dehalogenation of Tetrachloroethene and Polychloroethanes
journal, January 2001
- Suyama, Akiko; Iwakiri, Ryo; Kai, Keiichirou
- Bioscience, Biotechnology, and Biochemistry, Vol. 65, Issue 7
Carbon source-dependent expansion of the genetic code in bacteria
journal, November 2012
- Prat, L.; Heinemann, I. U.; Aerni, H. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 51
Complete genome sequence and analysis of Wolinella succinogenes
journal, September 2003
- Baar, C.; Eppinger, M.; Raddatz, G.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 20
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes
journal, January 2012
- Dos Santos, Patricia C.; Fang, Zhong; Mason, Steven W.
- BMC Genomics, Vol. 13, Issue 1
The Cofactor of Tetrachloroethene Reductive Dehalogenase ofDehalospirillum multivorans Is Norpseudo-B12, a New Type of a Natural Corrinoid
journal, November 2003
- Kräutler, Bernhard; Fieber, Wolfgang; Ostermann, Sigrid
- Helvetica Chimica Acta, Vol. 86, Issue 11
Genomic, Proteomic, and Biochemical Analysis of the Organohalide Respiratory Pathway in Desulfitobacterium dehalogenans
journal, December 2014
- Kruse, Thomas; van de Pas, Bram A.; Atteia, Ariane
- Journal of Bacteriology, Vol. 197, Issue 5
Use of Bacteria To Stabilize Archaeological Iron
journal, March 2017
- Comensoli, Lucrezia; Maillard, Julien; Albini, Monica
- Applied and Environmental Microbiology, Vol. 83, Issue 9
cobA function is required for both de novo cobalamin biosynthesis and assimilation of exogenous corrinoids in Salmonella typhimurium.
journal, January 1990
- Escalante-Semerena, J. C.; Suh, S. J.; Roth, J. R.
- Journal of Bacteriology, Vol. 172, Issue 1
The nos gene cluster from gram-positive bacterium Geobacillus thermodenitrificans NG80-2 and functional characterization of the recombinant NosZ
journal, December 2008
- Liu, Xueqian; Gao, Chunxu; Zhang, Aixiang
- FEMS Microbiology Letters, Vol. 289, Issue 1
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S
journal, February 2015
- Goris, Tobias; Hornung, Bastian; Kruse, Thomas
- Standards in Genomic Sciences, Vol. 10, Issue 1
Noncanonical Vancomycin Resistance Cluster from Desulfitobacterium hafniense Y51
journal, May 2009
- Kalan, L.; Ebert, S.; Kelly, T.
- Antimicrobial Agents and Chemotherapy, Vol. 53, Issue 7
Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli.
journal, July 1986
- Zinoni, F.; Birkmann, A.; Stadtman, T. C.
- Proceedings of the National Academy of Sciences, Vol. 83, Issue 13
Arsenic Methylation and Volatilization by Arsenite S -Adenosylmethionine Methyltransferase in Pseudomonas alcaligenes NBRC14159
journal, February 2015
- Zhang, Jun; Cao, Tingting; Tang, Zhu
- Applied and Environmental Microbiology, Vol. 81, Issue 8
Isolation and Characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an Anaerobic Bacterium Which Reductively Dechlorinates Chlorophenolic Compounds
journal, October 1994
- Utkin, I.; Woese, C.; Wiegel, J.
- International Journal of Systematic Bacteriology, Vol. 44, Issue 4
Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica
journal, November 2002
- Berks, Ben C.; Hinsley, Andrew P.
- Microbiology, Vol. 148, Issue 11
ACT: the Artemis comparison tool
journal, June 2005
- Carver, T. J.; Rutherford, K. M.; Berriman, M.
- Bioinformatics, Vol. 21, Issue 16
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011
- Letunic, I.; Bork, P.
- Nucleic Acids Research, Vol. 39, Issue suppl
EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000
- Rice, Peter; Longden, Ian; Bleasby, Alan
- Trends in Genetics, Vol. 16, Issue 6
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
journal, November 2009
- McMurdie, Paul J.; Behrens, Sebastian F.; Müller, Jochen A.
- PLoS Genetics, Vol. 5, Issue 11
Microbial comparative pan-genomics using binomial mixture models
journal, January 2009
- Snipen, Lars; Almøy, Trygve; Ussery, David W.
- BMC Genomics, Vol. 10, Issue 1
Desulfitobacterium sp. strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene or ortho -chlorinated phenols
journal, February 1996
- Gerritse, J.; Renard, Veronique; Gomes, T. M. Pedro
- Archives of Microbiology, Vol. 165, Issue 2
Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons
journal, August 2009
- Kunapuli, U.; Jahn, M. K.; Lueders, T.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 3
Regulation of Anaerobic Dehalorespiration by the Transcriptional Activator CprK
journal, September 2004
- Pop, Stelian M.; Kolarik, Ryan J.; Ragsdale, Stephen W.
- Journal of Biological Chemistry, Vol. 279, Issue 48
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
journal, January 2007
- Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter
- International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1
The Role of the Novel Fem Protein VanK in Vancomycin Resistance in Streptomyces coelicolor
journal, January 2005
- Hong, Hee-Jeon; Hutchings, Matthew I.; Hill, Lionel M.
- Journal of Biological Chemistry, Vol. 280, Issue 13
The bacterial Sec-translocase: structure and mechanism
journal, April 2012
- Lycklama a. Nijeholt, Jelger A.; Driessen, Arnold J. M.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1592
Impact of Vitamin B 12 on Formation of the Tetrachloroethene Reductive Dehalogenase in Desulfitobacterium hafniense Strain Y51
journal, September 2012
- Reinhold, Anika; Westermann, Martin; Seifert, Jana
- Applied and Environmental Microbiology, Vol. 78, Issue 22
Insights into organohalide respiration and the versatile catabolism of S ulfurospirillum multivorans gained from comparative genomics and physiological studies : Genome sequence of
journal, September 2014
- Goris, Tobias; Schubert, Torsten; Gadkari, Jennifer
- Environmental Microbiology, Vol. 16, Issue 11
Influence of Different Electron Donors and Acceptors on Dehalorespiration of Tetrachloroethene by
Desulfitobacterium frappieri
TCE1
journal, December 1999
- Gerritse, Jan; Drzyzga, Oliver; Kloetstra, Geert
- Applied and Environmental Microbiology, Vol. 65, Issue 12
Isolation and characterization of an anaerobic chlorophenol-transforming bacterium
journal, September 1992
- Madsen, T.; Licht, D.
- Applied and Environmental Microbiology, Vol. 58, Issue 9
Tetrachloroethene Dehalogenase from
Dehalospirillum multivorans
: Cloning, Sequencing of the Encoding Genes, and Expression of the
pceA
Gene in
Escherichia coli
journal, August 1998
- Neumann, Anke; Wohlfarth, Gert; Diekert, Gabriele
- Journal of Bacteriology, Vol. 180, Issue 16
Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate
journal, October 1996
- Sanford, R. A.; Cole, J. R.; Löffler, F. E.
- Applied and Environmental Microbiology, Vol. 62, Issue 10
Random Transposition by Tn
916
in
Desulfitobacterium dehalogenans
Allows for Isolation and Characterization of Halorespiration-Deficient Mutants
journal, November 1999
- Smidt, Hauke; Song, Donglin; van der Oost, John
- Journal of Bacteriology, Vol. 181, Issue 22
Works referencing / citing this record:
Guided cobamide biosynthesis for heterologous production of reductive dehalogenases
journal, December 2018
- Schubert, Torsten; Reuß, Stephan H.; Kunze, Cindy
- Microbial Biotechnology, Vol. 12, Issue 2
An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research
journal, January 2018
- Türkowsky, Dominique; Jehmlich, Nico; Diekert, Gabriele
- FEMS Microbiology Ecology, Vol. 94, Issue 3
The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC
journal, April 2018
- Buttet, Géraldine F.; Willemin, Mathilde S.; Hamelin, Romain
- Frontiers in Microbiology, Vol. 9
Guided cobamide biosynthesis for heterologous production of reductive dehalogenases
journal, December 2018
- Schubert, Torsten; Reuß, Stephan H.; Kunze, Cindy
- Microbial Biotechnology, Vol. 12, Issue 2
Organohalide-respiring Desulfoluna species isolated from marine environments
journal, January 2020
- Peng, Peng; Goris, Tobias; Lu, Yue
- The ISME Journal, Vol. 14, Issue 3
The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC
journal, April 2018
- Buttet, Géraldine F.; Willemin, Mathilde S.; Hamelin, Romain
- Frontiers in Microbiology, Vol. 9
Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut
journal, July 2018
- Atashgahi, Siavash; Shetty, Sudarshan A.; Smidt, Hauke
- Frontiers in Physiology, Vol. 9
Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill
journal, August 2018
- Lechner, Ute; Türkowsky, Dominique; Dinh, Thi Thu Hang
- Microbial Biotechnology, Vol. 11, Issue 6
Organohalide-respiring Desulfoluna species isolated from marine environments
journal, January 2020
- Peng, Peng; Goris, Tobias; Lu, Yue
- The ISME Journal, Vol. 14, Issue 3
Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill
journal, August 2018
- Lechner, Ute; Türkowsky, Dominique; Dinh, Thi Thu Hang
- Microbial Biotechnology, Vol. 11, Issue 6
Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut
journal, July 2018
- Atashgahi, Siavash; Shetty, Sudarshan A.; Smidt, Hauke
- Frontiers in Physiology, Vol. 9