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Title: 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 853–15A T did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853–15A T 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 metabolicmore » repertoire.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [1]
  1. Wageningen Univ., Wageningen (Netherlands)
  2. Friedrich Schiller Univ., Jena (Germany)
  3. Ecole Polytechnique Federale Lausanne (Switzlerland)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Martin Luther Univ., Halle (Germany)
  6. 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. doi: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. doi: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 = {2017},
month = {10}
}

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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
  • DOI: 10.1128/AEM.01834-09

Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1
journal, January 2005


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
  • DOI: 10.1042/BJ20090151

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations
journal, February 2013


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
  • DOI: 10.1271/bbb.65.1474

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
  • DOI: 10.1073/pnas.1218613110

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
  • DOI: 10.1073/pnas.1932838100

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes
journal, January 2012


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
  • DOI: 10.1002/hlca.200390313

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
  • DOI: 10.1128/JB.02370-14

Use of Bacteria To Stabilize Archaeological Iron
journal, March 2017

  • Comensoli, Lucrezia; Maillard, Julien; Albini, Monica
  • Applied and Environmental Microbiology, Vol. 83, Issue 9
  • DOI: 10.1128/AEM.03478-16

cobA function is required for both de novo cobalamin biosynthesis and assimilation of exogenous corrinoids in Salmonella typhimurium.
journal, January 1990


The nos gene cluster from gram-positive bacterium Geobacillus thermodenitrificans NG80-2 and functional characterization of the recombinant NosZ
journal, December 2008


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
  • DOI: 10.1186/1944-3277-10-15

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
  • DOI: 10.1128/AAC.01408-08

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
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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
  • DOI: 10.1128/AEM.03804-14

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
  • DOI: 10.1099/00207713-44-4-612

Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica
journal, November 2002


ACT: the Artemis comparison tool
journal, June 2005


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
  • DOI: 10.1093/nar/gkr201

EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000


Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
journal, November 2009


Microbial comparative pan-genomics using binomial mixture models
journal, January 2009


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
  • DOI: 10.1007/s002030050308

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
  • DOI: 10.1099/ijs.0.003525-0

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
  • DOI: 10.1074/jbc.M409435200

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
  • DOI: 10.1099/ijs.0.64483-0

Modes and Modulations of Antibiotic Resistance Gene Expression
journal, January 2007

  • Depardieu, F.; Podglajen, I.; Leclercq, R.
  • Clinical Microbiology Reviews, Vol. 20, Issue 1
  • DOI: 10.1128/CMR.00015-06

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
  • DOI: 10.1074/jbc.M413801200

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
  • DOI: 10.1098/rstb.2011.0201

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
  • DOI: 10.1128/AEM.02173-12