Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland
Abstract
© 2016 Susanti et al. This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H 2 S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H 2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.
- Authors:
- 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:
- 2282782
- Alternate Identifier(s):
- OSTI ID: 1256945; OSTI ID: 1379032
- Grant/Contract Number:
- AC02-05CH11231; VA-160021
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Desulfurococcus; Sulfur-reducing crenarchaeon; Thermophile; Acidic hot spring
Citation Formats
Susanti, Dwi, Johnson, Eric F., Lapidus, Alla, Han, James, Reddy, T. B. K., Pilay, Manoj, Ivanova, Natalia N., Markowitz, Victor M., Woyke, Tanja, Kyrpides, Nikos C., and Mukhopadhyay, Biswarup. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. United Kingdom: N. p., 2016.
Web. doi:10.1186/s40793-015-0128-4.
Susanti, Dwi, Johnson, Eric F., Lapidus, Alla, Han, James, Reddy, T. B. K., Pilay, Manoj, Ivanova, Natalia N., Markowitz, Victor M., Woyke, Tanja, Kyrpides, Nikos C., & Mukhopadhyay, Biswarup. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. United Kingdom. https://doi.org/10.1186/s40793-015-0128-4
Susanti, Dwi, Johnson, Eric F., Lapidus, Alla, Han, James, Reddy, T. B. K., Pilay, Manoj, Ivanova, Natalia N., Markowitz, Victor M., Woyke, Tanja, Kyrpides, Nikos C., and Mukhopadhyay, Biswarup. Wed .
"Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland". United Kingdom. https://doi.org/10.1186/s40793-015-0128-4.
@article{osti_2282782,
title = {Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland},
author = {Susanti, Dwi and Johnson, Eric F. and Lapidus, Alla and Han, James and Reddy, T. B. K. and Pilay, Manoj and Ivanova, Natalia N. and Markowitz, Victor M. and Woyke, Tanja and Kyrpides, Nikos C. and Mukhopadhyay, Biswarup},
abstractNote = {© 2016 Susanti et al. This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H 2 S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H 2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.},
doi = {10.1186/s40793-015-0128-4},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United Kingdom},
year = {Wed Jan 13 00:00:00 EST 2016},
month = {Wed Jan 13 00:00:00 EST 2016}
}
https://doi.org/10.1186/s40793-015-0128-4
Web of Science
Works referenced in this record:
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 8, Issue 1
Complete Genome Sequence of the Anaerobic, Protein-Degrading Hyperthermophilic Crenarchaeon Desulfurococcus kamchatkensis
journal, December 2008
- Ravin, N. V.; Mardanov, A. V.; Beletsky, A. V.
- Journal of Bacteriology, Vol. 191, Issue 7
Glyceraldehyde-3-Phosphate Ferredoxin Oxidoreductase from Methanococcus maripaludis
journal, August 2007
- Park, M. -O.; Mizutani, T.; Jones, P. R.
- Journal of Bacteriology, Vol. 189, Issue 20
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007
- Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
- BMC Bioinformatics, Vol. 8, Issue 1
Isolation and characterization of flagella and flagellin proteins from the Thermoacidophilic archaea Thermoplasma volcanium and Sulfolobus shibatae.
journal, February 1996
- Faguy, D. M.; Bayley, D. P.; Kostyukova, A. S.
- Journal of Bacteriology, Vol. 178, Issue 3
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014
- Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
- Nucleic Acids Research, Vol. 43, Issue D1
ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008
- Butler, J.; MacCallum, I.; Kleber, M.
- Genome Research, Vol. 18, Issue 5
Mutants in flaI and flaJ of the archaeon Methanococcus voltae are deficient in flagellum assembly: Archaeal flagellum biogenesis in M. voltae
journal, October 2002
- Thomas, Nikhil A.; Mueller, Steffen; Klein, Albrecht
- Molecular Microbiology, Vol. 46, Issue 3
Pyruvate Kinase of the Hyperthermophilic Crenarchaeote Thermoproteus tenax: Physiological Role and Phylogenetic Aspects
journal, April 2000
- Schramm, A.; Siebers, B.; Tjaden, B.
- Journal of Bacteriology, Vol. 182, Issue 7
Phylogenetic position of desulfurococcus amylolyticus
journal, May 2000
- Tourova, T. P.; Kuznetsov, B. B.; Kalganova, T. V.
- Microbiology, Vol. 69, Issue 3
Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka, Russia
journal, September 2012
- Susanti, D.; Johnson, E. F.; Rodriguez, J. R.
- Journal of Bacteriology, Vol. 194, Issue 20
Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens
journal, June 2009
- Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw
- PLoS ONE, Vol. 4, Issue 6
An Intertwined Evolutionary History of Methanogenic Archaea and Sulfate Reduction
journal, September 2012
- Susanti, Dwi; Mukhopadhyay, Biswarup
- PLoS ONE, Vol. 7, Issue 9
Complete genome sequence of Desulfurococcus mucosus type strain (O7/1T)
journal, April 2011
- Wirth, Reinhard; Chertkov, Olga; Held, Brittany
- Standards in Genomic Sciences, Vol. 4, 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
Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus
journal, May 2005
- Perevalova, A. A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 3
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
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
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
journal, January 2009
- MacCallum, Iain; Przybylski, Dariusz; Gnerre, Sante
- Genome Biology, Vol. 10, Issue 10
HMMER web server: interactive sequence similarity searching
journal, May 2011
- Finn, R. D.; Clements, J.; Eddy, S. R.
- Nucleic Acids Research, Vol. 39, Issue suppl
Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic Archaeon Pyrococcus furiosus
journal, January 2001
- Adams, M. W. W.; Holden, J. F.; Menon, A. L.
- Journal of Bacteriology, Vol. 183, Issue 2
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
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
Infernal 1.0: inference of RNA alignments
journal, March 2009
- Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R.
- Bioinformatics, Vol. 25, Issue 10
The archaellum: an old motility structure with a new name
journal, July 2012
- Jarrell, Ken F.; Albers, Sonja-Verena
- Trends in Microbiology, Vol. 20, Issue 7
Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur
journal, November 1994
- Ma, K.; Adams, M. W.
- Journal of Bacteriology, Vol. 176, Issue 21, p. 6509-6517
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
- Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S.
- PLoS ONE, Vol. 7, Issue 12
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
Desulfurococcaceae, the Second Family of the Extremely Thermophilic, Anaerobic, Sulfur-Respiring Thermoproteales
journal, May 1982
- Zillig, W.; Stetter, K. O.; Prangishvilli, D.
- Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I. Abt. Originale C: Allgemeine, angewandte und ökologische Mikrobiologie, Vol. 3, Issue 2
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea
journal, December 2005
- Siebers, Bettina; Schönheit, Peter
- Current Opinion in Microbiology, Vol. 8, Issue 6
Characterization of Flagellum Gene Families of Methanogenic Archaea and Localization of Novel Flagellum Accessory Proteins
journal, December 2001
- Thomas, N. A.; Jarrell, K. F.
- Journal of Bacteriology, Vol. 183, Issue 24