publication . Article . 2017

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; ...
Open Access English
  • Published: 01 Feb 2017 Journal: Frontiers in Microbiology, volume 8 (issn: 1664-302X, eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media S.A.
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is deter...
Subjects
free text keywords: phylum, bacterial evolution, genomic analysis, Microbiology, Caldithrix, Original Research, taxonomy, phylogenomics, sequencing
100 references, page 1 of 7

Altschul S. F.Madden T. L.Schäffer A. A.Zhang J.Zhang Z.Miller W. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. 10.1093/nar/25.17.3389 9254694 [OpenAIRE] [PubMed] [DOI]

Amann R. I.Ludwig W.Schleifer K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 143–169.7535888 [OpenAIRE] [PubMed]

Anantharaman V.Aravind L. (2002). MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including molybdenum cofactor sulfurases. FEMS Microbiol. Lett. 207 55–61. 10.1016/s0378-1097(01)00515-8 11886751 [PubMed] [DOI]

Aziz R. K.Bartels D.Best A. A.DeJongh M.Disz T.Edwards R. A. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75 10.1186/1471-2164-9-75 [OpenAIRE] [DOI]

Bailey T. L.Boden M.Buske F. A.Frith M.Grant C. E.Clementi L. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37 W202–W208. 10.1093/nar/gkp335 19458158 [OpenAIRE] [PubMed] [DOI]

Baughn A. D.Garforth S. J.Vilchèze C.Jacobs W. R.Jr. (2009). An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. PLoS Pathog. 5:e1000662 10.1371/journal.ppat.1000662 [OpenAIRE] [DOI]

Bendtsen J. D.Nielsen H.Widdick D.Palmer T.Brunak S. (2005). Prediction of twin-arginine signal peptides. BMC Bioinformatics 6:167 10.1186/1471-2105-6-167 [OpenAIRE] [DOI]

Bennett S. (2004). Solexa Ltd. Pharmacogenomics 5 433–438. 10.1517/14622416.5.4.433 15165179 [PubMed] [DOI]

Bezuidt O.Lima-Mendez G.Reva O. N. (2009). SeqWord gene Island Sniffer: a program to study the lateral genetic exchange among bacteria. World Acad. Sci. Eng. Technol. 58 1169–1174. [OpenAIRE]

Bezuidt O.Pierneef R.Mncube K.Lima-Mendez G.Reva O. N. (2011). Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS ONE 6:e25702 10.1371/journal.pone.0025702 [OpenAIRE] [DOI]

Biegel E.Schmidt S.González J. M.Müller V. (2011). Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci. 68 613–634. 10.1007/s00018-010-0555-8 21072677 [PubMed] [DOI]

Bridger S. L.Clarkson S. M.Stirrett K.DeBarry M. B.Lipscomb G. L.Schut G. J. (2011). Deletion strains reveal metabolic roles for key elemental sulfur-responsive proteins in Pyrococcus furiosus. J. Bacteriol. 193 6498–6504. 10.1128/JB.05445-11 21965560 [OpenAIRE] [PubMed] [DOI]

Buckel W.Thauer R. K. (2013). Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827 94–113. 10.1016/j.bbabio.2012.07.002 22800682 [OpenAIRE] [PubMed] [DOI]

Cantarel B. L.Coutinho P. M.Rancurel C.Bernard T.Lombard V.Henrissat B. (2009). The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37 D233–D238. 10.1093/nar/gkn663 18838391 [OpenAIRE] [PubMed] [DOI]

Caspi R.Altman T.Billington R.Dreher K.Foerster H.Fulcher C. A. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 42 D459–D471. 10.1093/nar/gkt1103 24225315 [OpenAIRE] [PubMed] [DOI]

100 references, page 1 of 7
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is deter...
Subjects
free text keywords: phylum, bacterial evolution, genomic analysis, Microbiology, Caldithrix, Original Research, taxonomy, phylogenomics, sequencing
100 references, page 1 of 7

Altschul S. F.Madden T. L.Schäffer A. A.Zhang J.Zhang Z.Miller W. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. 10.1093/nar/25.17.3389 9254694 [OpenAIRE] [PubMed] [DOI]

Amann R. I.Ludwig W.Schleifer K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 143–169.7535888 [OpenAIRE] [PubMed]

Anantharaman V.Aravind L. (2002). MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including molybdenum cofactor sulfurases. FEMS Microbiol. Lett. 207 55–61. 10.1016/s0378-1097(01)00515-8 11886751 [PubMed] [DOI]

Aziz R. K.Bartels D.Best A. A.DeJongh M.Disz T.Edwards R. A. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75 10.1186/1471-2164-9-75 [OpenAIRE] [DOI]

Bailey T. L.Boden M.Buske F. A.Frith M.Grant C. E.Clementi L. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37 W202–W208. 10.1093/nar/gkp335 19458158 [OpenAIRE] [PubMed] [DOI]

Baughn A. D.Garforth S. J.Vilchèze C.Jacobs W. R.Jr. (2009). An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. PLoS Pathog. 5:e1000662 10.1371/journal.ppat.1000662 [OpenAIRE] [DOI]

Bendtsen J. D.Nielsen H.Widdick D.Palmer T.Brunak S. (2005). Prediction of twin-arginine signal peptides. BMC Bioinformatics 6:167 10.1186/1471-2105-6-167 [OpenAIRE] [DOI]

Bennett S. (2004). Solexa Ltd. Pharmacogenomics 5 433–438. 10.1517/14622416.5.4.433 15165179 [PubMed] [DOI]

Bezuidt O.Lima-Mendez G.Reva O. N. (2009). SeqWord gene Island Sniffer: a program to study the lateral genetic exchange among bacteria. World Acad. Sci. Eng. Technol. 58 1169–1174. [OpenAIRE]

Bezuidt O.Pierneef R.Mncube K.Lima-Mendez G.Reva O. N. (2011). Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS ONE 6:e25702 10.1371/journal.pone.0025702 [OpenAIRE] [DOI]

Biegel E.Schmidt S.González J. M.Müller V. (2011). Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci. 68 613–634. 10.1007/s00018-010-0555-8 21072677 [PubMed] [DOI]

Bridger S. L.Clarkson S. M.Stirrett K.DeBarry M. B.Lipscomb G. L.Schut G. J. (2011). Deletion strains reveal metabolic roles for key elemental sulfur-responsive proteins in Pyrococcus furiosus. J. Bacteriol. 193 6498–6504. 10.1128/JB.05445-11 21965560 [OpenAIRE] [PubMed] [DOI]

Buckel W.Thauer R. K. (2013). Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827 94–113. 10.1016/j.bbabio.2012.07.002 22800682 [OpenAIRE] [PubMed] [DOI]

Cantarel B. L.Coutinho P. M.Rancurel C.Bernard T.Lombard V.Henrissat B. (2009). The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37 D233–D238. 10.1093/nar/gkn663 18838391 [OpenAIRE] [PubMed] [DOI]

Caspi R.Altman T.Billington R.Dreher K.Foerster H.Fulcher C. A. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 42 D459–D471. 10.1093/nar/gkt1103 24225315 [OpenAIRE] [PubMed] [DOI]

100 references, page 1 of 7
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publication . Article . 2017

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; ...