Name: Methanocaldococcus jannaschii JAL-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6981

Type strain:

Species: Methanocaldococcus jannaschii

Strain Designation: JAL-1

Culture col. no.: DSM 2661, ATCC 43067, JCM 10045, CIP 104961, NBRC 100440

Strain history: DSM 2661 <-- J. A. Leigh and W. J. Jones JAL-1.

NCBI tax ID(s): 243232 (strain), 2190 (species)

SI-ID 41626

ATCC 43067, DSM 2661, JCM 10045, CIP 104961, NBRC 100440

Section

Methanocaldococcus jannaschii JAL-1 is an anaerobe, spore-forming, hyperthermophilic archaeon that was isolated from submarine hydrothermal vent.

Gram-negative
spore-forming
anaerobe
hyperthermophilic
16S sequence
Archaea
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Methanococci*
	Order	*Methanococcales*
	Family	*Methanocaldococcaceae*
	Genus	*Methanocaldococcus*
	Species	**Methanocaldococcus jannaschii**
	Full Scientific Name (LPSN)	Methanocaldococcus jannaschii (Jones et al. 1984) Whitman 2002

	Synonym	"Methanocaldococcus* jannaschii"*
	Synonym	Methanococcus jannaschii

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.87

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1193]

Culture medium

METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)

[Ref.: #1193]

Culture medium growth

[Ref.: #1193]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1193]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1193]			growth	80 °C
[Ref.: #67770]			growth	80 °C

[Ref.: #1193]	Temperature range	hyperthermophilic
[Ref.: #67770]	Temperature range	hyperthermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1193]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.619

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.863

[Ref.: #1193]

Name of produced compound

hydrogenase

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	selenocysteine biosynthesis	100	6 of 6
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	coenzyme M biosynthesis	90	9 of 10
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	methanogenesis from CO2	83.33	10 of 12
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	alanine metabolism	48.28	14 of 29
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	peptidoglycan biosynthesis	40	6 of 15
[Ref.: #66794]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	citric acid cycle	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	acetoin degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	non-pathway related	28.95	11 of 38
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	propanol degradation	28.57	2 of 7
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	isoprenoid biosynthesis	26.92	7 of 26
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	cysteine metabolism	22.22	4 of 18
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1193]	Sample type/isolated from	submarine hydrothermal vent
[Ref.: #1193]	Geographic location (country and/or sea, region)	East Pacific Rise
[Ref.: #1193]	Country	International waters

[Ref.: #67770]	Sample type/isolated from	Base of 'white smoker' chimney on the East Pacific Rise
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1193]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Methanocaldococcus jannaschii gene for 16S rRNA, partial sequence, strain: JCM 10045	AB603516	1458	ENA	2190 tax ID	*
[Ref.: #20218]	Methanococcus jannaschii 16S ribosomal RNA	M59126	1478	ENA	2190 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanocaldococcus jannaschii DSM 2661	638154505	complete	JGI IMG/M	243232 tax ID	*
[Ref.: #66792]	Methanocaldococcus jannaschii DSM 2661	GCA_000091665	complete	GenBank	243232 tax ID	*
[Ref.: #66792]	Methanocaldococcus jannaschii DSM 2661	243232.20	complete	PATRIC	243232 tax ID	*
[Ref.: #66792]	Methanocaldococcus jannaschii DSM 2661	243232.26	plasmid	PATRIC	243232 tax ID	*
[Ref.: #66792]	Methanocaldococcus jannaschii DSM 2661	243232.25	plasmid	PATRIC	243232 tax ID	*

[Ref.: #1193]	GC-content	31.0 mol%
[Ref.: #67770]	GC-content	31 mol%	Buoyant density centrifugation (BD)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methanocaldococcus jannaschii DSM 2661 DSM 2661 NCBI: GCA_000091665.1
[Ref.: #69481]	spore-forming	yes	100	no

Availability in culture collections External links

[Ref.: #1193]

Culture collection no.

DSM 2661, ATCC 43067, JCM 10045, CIP 104961, NBRC 100440

[Ref.: #76442]

SI-ID 41626

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	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	*
Metabolism	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	*
Phylogeny	Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon.	Mehta MP, Baross JA	Science	10.1126/science.1134772	2006	*
Phylogeny	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	*
Enzymology	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	*
Phylogeny	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	*
Enzymology	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	*

References

#1193

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2661

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76442

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID41626.1 )

* These data were automatically processed and therefore are not curated

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Methanocaldococcus jannaschii DSM 2661 DSM 2661

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