Strain identifier
BacDive ID: 6981
Type strain: 
Species: Methanocaldococcus jannaschii
Strain Designation: JAL-1
Strain history: DSM 2661 <-- J. A. Leigh and W. J. Jones JAL-1.
NCBI tax ID(s): 243232 (strain), 2190 (species)
version 8.1 (current version)
General
@ref: 1193
BacDive-ID: 6981
DSM-Number: 2661
keywords: genome sequence, 16S sequence, Archaea, anaerobe, spore-forming, hyperthermophilic, Gram-negative
description: Methanocaldococcus jannaschii JAL-1 is an anaerobe, spore-forming, hyperthermophilic archaeon that was isolated from submarine hydrothermal vent.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 243232 | strain |
| 2190 | species |
strain history
| @ref | history |
|---|---|
| 1193 | <- J. W. Jones, University of Illinois, Urbana, USA; JAL-1 <- J. A. Leigh {1982} |
| 67770 | DSM 2661 <-- J. A. Leigh and W. J. Jones JAL-1. |
doi: 10.13145/bacdive6981.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanococci
- order: Methanococcales
- family: Methanocaldococcaceae
- genus: Methanocaldococcus
- species: Methanocaldococcus jannaschii
- full scientific name: Methanocaldococcus jannaschii (Jones et al. 1984) Whitman 2002
synonyms
@ref synonym 20215 Methanocaldococcus jannaschii 20215 Methanococcus jannaschii
@ref: 1193
domain: Archaea
phylum: Euryarchaeota
class: Methanococci
order: Methanococcales
family: Methanocaldococcaceae
genus: Methanocaldococcus
species: Methanocaldococcus jannaschii
full scientific name: Methanocaldococcus jannaschii (Jones et al. 1984) Whitman 2002
strain designation: JAL-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.87
Culture and growth conditions
culture medium
- @ref: 1193
- name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)
- growth: yes
- link: https://mediadive.dsmz.de/medium/282
- composition: Name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282) Composition: MgCl2 x 6 H2O 4.05138 g/l NaHCO3 0.988142 g/l Na2S x 9 H2O 0.494071 g/l L-Cysteine HCl x H2O 0.494071 g/l KCl 0.326087 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l ZnSO4 x 7 H2O 0.00177866 g/l CoSO4 x 7 H2O 0.00177866 g/l CaCl2 x 2 H2O 0.000988142 g/l FeSO4 x 7 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l CuSO4 x 5 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l Thiamine HCl 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1193 | positive | growth | 80 | hyperthermophilic | |
| 67770 | positive | growth | 80 | hyperthermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1193 | anaerobe | |
| 69480 | anaerobe | 99.619 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | no | 99.863 |
compound production
- @ref: 1193
- compound: hydrogenase
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country |
|---|---|---|---|
| 1193 | submarine hydrothermal vent | East Pacific Rise | International waters |
| 67770 | Base of 'white smoker' chimney on the East Pacific Rise |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 1193
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methanocaldococcus jannaschii gene for 16S rRNA, partial sequence, strain: JCM 10045 | AB603516 | 1458 | ena | 2190 |
| 20218 | Methanococcus jannaschii 16S ribosomal RNA | M59126 | 1478 | ena | 2190 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanocaldococcus jannaschii DSM 2661 | 638154505 | complete | img | 243232 |
| 66792 | Methanocaldococcus jannaschii DSM 2661 | GCA_000091665 | complete | ncbi | 243232 |
| 66792 | Methanocaldococcus jannaschii DSM 2661 | 243232.20 | complete | patric | 243232 |
| 66792 | Methanocaldococcus jannaschii DSM 2661 | 243232.26 | plasmid | patric | 243232 |
| 66792 | Methanocaldococcus jannaschii DSM 2661 | 243232.25 | plasmid | patric | 243232 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1193 | 31.0 | |
| 67770 | 31 | Buoyant density centrifugation (BD) |
Genome-based predictions
predictions
- trait: spore-forming
- prediction: yes
- confidence: 100
- training_data: no
External links
@ref: 1193
culture collection no.: DSM 2661, ATCC 43067, JCM 10045, CIP 104961, NBRC 100440
straininfo link
- @ref: 76442
- straininfo: 41626
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9734046 | Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. | Jeanthon C, L'Haridon S, Reysenbach AL, Vernet M, Messner P, Sleytr UB, Prieur D | Int J Syst Bacteriol | 10.1099/00207713-48-3-913 | 1998 | Anti-Bacterial Agents/pharmacology, Base Sequence, DNA, Ribosomal/chemistry, Methanococcus/classification/growth & development/*isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics | Genetics |
| Enzymology | 9862122 | The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. | Shi L, Potts M, Kennelly PJ | FEMS Microbiol Rev | 10.1111/j.1574-6976.1998.tb00369.x | 1998 | Amino Acid Sequence, Archaeal Proteins/*genetics, Archaeoglobus fulgidus/enzymology/genetics, Bacillus subtilis/enzymology/genetics, Bacterial Proteins/*genetics, Borrelia burgdorferi Group/enzymology/genetics, Cyanobacteria/enzymology/genetics, Escherichia coli/enzymology/genetics, Haemophilus influenzae/enzymology/genetics, Helicobacter pylori/enzymology/genetics, Methanobacterium/enzymology/genetics, Methanococcus/enzymology/genetics, Molecular Sequence Data, Mycoplasma/enzymology/genetics, Open Reading Frames/*genetics, Phosphoprotein Phosphatases/*genetics, Protein Serine-Threonine Kinases/*genetics, Protein-Tyrosine Kinases/*genetics, Sequence Alignment | Genetics |
| Phylogeny | 10319479 | Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. | Jeanthon C, L'Haridon S, Reysenbach AL, Corre E, Vernet M, Messner P, Sleytr UB, Prieur D | Int J Syst Bacteriol | 10.1099/00207713-49-2-583 | 1999 | Base Composition, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Methanococcus/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water Microbiology | Genetics |
| Phylogeny | 17170307 | Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon. | Mehta MP, Baross JA | Science | 10.1126/science.1134772 | 2006 | Amino Acid Sequence, Archaea/classification/genetics/*isolation & purification/*metabolism, Archaeal Proteins/chemistry/genetics/metabolism, Base Sequence, *Ecosystem, Genes, Archaeal, Genes, rRNA, Geologic Sediments/microbiology, *Hot Temperature, Molecular Sequence Data, Nitrogen/metabolism, *Nitrogen Fixation/genetics, Nitrogenase/chemistry/*genetics/metabolism, Operon, Oxidation-Reduction, Oxidoreductases/chemistry/genetics/metabolism, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Volcanic Eruptions | Metabolism |
| Metabolism | 18438658 | Characterization of a dITPase from the hyperthermophilic archaeon Thermococcus onnurineus NA1 and its application in PCR amplification. | Kim YJ, Ryu YG, Lee HS, Cho Y, Kwon ST, Lee JH, Kang SG | Appl Microbiol Biotechnol | 10.1007/s00253-008-1467-5 | 2008 | Amino Acid Sequence, Archaeal Proteins/chemistry/genetics/*metabolism, Cloning, Molecular, DNA-Directed DNA Polymerase/metabolism, Deoxyribonucleotides/metabolism/pharmacology, Inosine Triphosphate/metabolism/pharmacology, Kinetics, Molecular Sequence Data, Nucleic Acid Synthesis Inhibitors, *Polymerase Chain Reaction/drug effects, Pyrophosphatases/chemistry/genetics/*metabolism, Sequence Alignment, Thermococcus/chemistry/*enzymology/genetics | Enzymology |
| Enzymology | 19851023 | Cloning, purification and preliminary X-ray crystallographic analysis of a hypothetical protein, MJ0754, from Methanococcus jannaschii DSM 2661. | Lee EH, Nam KH, Hwang KY | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309109036562 | 2009 | Archaeal Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Methanococcus/*chemistry | |
| Enzymology | 24443971 | Role of tRNA orthogonality in an expanded genetic code. | Javahishvili T, Manibusan A, Srinagesh S, Lee D, Ensari S, Shimazu M, Schultz PG | ACS Chem Biol | 10.1021/cb4005172 | 2014 | Amino Acids/chemistry/genetics, Genetic Code/*genetics, Methanocaldococcus/enzymology/genetics, RNA, Transfer/chemistry/*genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1193 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2661) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2661 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 76442 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41626.1 | StrainInfo: A central database for resolving microbial strain identifiers |