Complete genome sequence of Methanothermus fervidus type strain (V24ST)
Abstract
Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24ST is of interest because of its very low substrate ranges, it grows only on H2 + CO2. This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Authors:
-
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- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Helmholtz Centre for Infection Research, Braunschweig (Germany)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Regensburg (Germany)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States). Genome Center
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1511323
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 3; Journal Issue: 3; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Anderson, Iain, Djao, Olivier Duplex Ngatchou, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred, Eichinger, Konrad, Huber, Harald, Wirth, Reinhard, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C. Complete genome sequence of Methanothermus fervidus type strain (V24ST). United States: N. p., 2010.
Web. doi:10.4056/sigs.1283367.
Anderson, Iain, Djao, Olivier Duplex Ngatchou, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred, Eichinger, Konrad, Huber, Harald, Wirth, Reinhard, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, & Kyrpides, Nikos C. Complete genome sequence of Methanothermus fervidus type strain (V24ST). United States. https://doi.org/10.4056/sigs.1283367
Anderson, Iain, Djao, Olivier Duplex Ngatchou, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred, Eichinger, Konrad, Huber, Harald, Wirth, Reinhard, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C. Fri .
"Complete genome sequence of Methanothermus fervidus type strain (V24ST)". United States. https://doi.org/10.4056/sigs.1283367. https://www.osti.gov/servlets/purl/1511323.
@article{osti_1511323,
title = {Complete genome sequence of Methanothermus fervidus type strain (V24ST)},
author = {Anderson, Iain and Djao, Olivier Duplex Ngatchou and Misra, Monica and Chertkov, Olga and Nolan, Matt and Lucas, Susan and Lapidus, Alla and Del Rio, Tijana Glavina and Tice, Hope and Cheng, Jan-Fang and Tapia, Roxanne and Han, Cliff and Goodwin, Lynne and Pitluck, Sam and Liolios, Konstantinos and Ivanova, Natalia and Mavromatis, Konstantinos and Mikhailova, Natalia and Pati, Amrita and Brambilla, Evelyne and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Chang, Yun-Juan and Jeffries, Cynthia D. and Sikorski, Johannes and Spring, Stefan and Rohde, Manfred and Eichinger, Konrad and Huber, Harald and Wirth, Reinhard and Göker, Markus and Detter, John C. and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Klenk, Hans-Peter and Kyrpides, Nikos C.},
abstractNote = {Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24ST is of interest because of its very low substrate ranges, it grows only on H2 + CO2. This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.1283367},
journal = {Standards in Genomic Sciences},
number = 3,
volume = 3,
place = {United States},
year = {Fri Dec 31 00:00:00 EST 2010},
month = {Fri Dec 31 00:00:00 EST 2010}
}
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Figures / Tables:
Figure 1: Phylogenetic tree highlighting the position of M. fervidus V24ST relative to the other type strains within the family Methanothermaceae. The tree was inferred from 1,249 aligned characters of the 16S rRNA gene sequence under the maximum likelihood criterion and rooted in accordance with the current taxonomy. The branchesmore »
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Works referenced in this record:
Hyperthermophilic microorganisms
journal, June 1990
- Stetter, K. O.; Fiala, G.; Huber, G.
- FEMS Microbiology Letters, Vol. 75, Issue 2-3
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
journal, December 2007
- Liolios, K.; Mavromatis, K.; Tavernarakis, N.
- Nucleic Acids Research, Vol. 36, Issue Database
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Biosynthesis of cyclic 2,3-diphosphoglycerate: Isolation and characterization of 2-phosphoglycerate kinase and cyclic 2,3-diphosphoglycerate synthetase from
journal, October 1990
- Lehmacher, Anselm; Vogt, Anne-Barbara; Hensel, Reinhard
- FEBS Letters, Vol. 272, Issue 1-2
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000
- Castresana, J.
- Molecular Biology and Evolution, Vol. 17, Issue 4
Hyperthermophilic procaryotes
journal, May 1996
- Stetter, Karl O.
- FEMS Microbiology Reviews, Vol. 18, Issue 2-3
Thermoadaptation of methanogenic bacteria by intracellular ion concentration
journal, January 1988
- Hensel, Reinhard; König, Helmut
- FEMS Microbiology Letters, Vol. 49, Issue 1
The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions
journal, January 2010
- Leahy, Sinead C.; Kelly, William J.; Altermann, Eric
- PLoS ONE, Vol. 5, Issue 1
Purification and characterization of d-glyceraldehyde-3-phosphate dehydrogenase from the thermophilic archaebacterium Methanothermus fervidus
journal, May 1987
- Fabry, Stefan; Hensel, Reinhard
- European Journal of Biochemistry, Vol. 165, Issue 1
The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP+ at 2.1 Å resolution
journal, March 2000
- Charron, C.; Talfournier, F.; Isupov, M. N.
- Journal of Molecular Biology, Vol. 297, Issue 2
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
[6] Triose-phosphate isomerase from Pyrococcus woesei and Methanothermus fervidus
book, January 2001
- Schramm, Alexander; Kohlhoff, Michael; Hensel, Reinhard
- Hyperthermophilic enzymes Part B
Complete genome sequence of Kytococcus sedentarius type strain (541T)
journal, July 2009
- Sims, David; Brettin, Thomas; Detter, John C.
- Standards in Genomic Sciences, Vol. 1, Issue 1
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 6
journal, April 1981
- None, None
- International Journal of Systematic Bacteriology, Vol. 31, Issue 2, p. 215-218
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
journal, September 2008
- Yarza, Pablo; Richter, Michael; Peplies, Jörg
- Systematic and Applied Microbiology, Vol. 31, Issue 4
A Rapid Bootstrap Algorithm for the RAxML Web Servers
journal, October 2008
- Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques
- Systematic Biology, Vol. 57, Issue 5
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 8
journal, April 1982
- Trujillo, Martha E.
- International Journal of Systematic Bacteriology, Vol. 32, Issue 2, p. 266-268
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis
journal, December 2005
- Fricke, W. F.; Seedorf, H.; Henne, A.
- Journal of Bacteriology, Vol. 188, Issue 2
HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones.
journal, August 1990
- Sandman, K.; Krzycki, J. A.; Dobrinski, B.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 15
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
journal, August 1996
- Bult, C. J.; White, O.; Olsen, G. J.
- Science, Vol. 273, Issue 5278
A novel ether core lipid with H-shaped C80-isoprenoid hydrocarbon chain from the hyperthermophilic methanogen Methanothermus fervidus
journal, February 1998
- Morii, Hiroyuki; Eguchi, Tadashi; Nishihara, Masateru
- Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, Vol. 1390, Issue 3
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
journal, November 1997
- Klenk, Hans-Peter; Clayton, Rebecca A.; Tomb, Jean-Francois
- Nature, Vol. 390, Issue 6658
Genes encoding the 7S RNA and tRNASer are linked to one of the two rRNA operons in the genome of the extremely thermophilic archaebacterium Methanothermus fervidus
journal, May 1990
- Haas, Elizabeth S.; Brown, James W.; Daniels, Charles J.
- Gene, Vol. 90, Issue 1
The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79
journal, January 2005
- Judicial Commission of the International Committee on Systematics of Prokaryotes,
- International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 1, p. 517-518
Multiple sequence alignment using partial order graphs
journal, March 2002
- Lee, C.; Grasso, C.; Sharlow, M. F.
- Bioinformatics, Vol. 18, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010
- Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
- Nature Methods, Vol. 7, Issue 6
Methanothermus sociabilis sp. nov., a Second Species within the Methanothermaceae Growing at 97°C
journal, July 1986
- Lauerer, Gerta; Kristjansson, Jakob K.; Langworthy, Thomas A.
- Systematic and Applied Microbiology, Vol. 8, Issue 1-2
Methanogens: reevaluation of a unique biological group.
journal, January 1979
- Balch, W. E.; Fox, G. E.; Magrum, L. J.
- Microbiological Reviews, Vol. 43, Issue 2
Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses.
journal, January 1993
- Koga, Y.; Nishihara, M.; Morii, H.
- Microbiological Reviews, Vol. 57, Issue 1
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Methanogens: reevaluation of a unique biological group.
journal, January 1979
- Balch, W. E.; Fox, G. E.; Magrum, L. J.
- Microbiological Reviews, Vol. 43, Issue 2
Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses
journal, March 1993
- Koga, Y.; Nishihara, M.; Morii, H.
- Microbiological Reviews, Vol. 57, Issue 1
Works referencing / citing this record:
Autocatalytic chemical networks preceded proteins and RNA in evolution
posted_content, July 2019
- Xavier, Joana C.; Hordijk, Wim; Kauffman, Stuart
- BioRxiv
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