Methanocaldococcus jannaschii (DSM 2661, ATCC 43067, JCM 10045)

Name: Methanocaldococcus jannaschii (DSM 2661, ATCC 43067, JCM 10045)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6981

Type strain

Strain Designation JAL-1

Culture col. no. DSM 2661 ATCC 43067 JCM 10045 JAL-1 NBRC 100440 1 more

NCBI tax ID(s) 243232 2190

Special Collections DSMZ JCM CIP

Links

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

anaerobe hyperthermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41626

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

@ref 20215

Last LPSN update 2025-12-16 09:48:27

Domain Methanobacteriati

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 (2)

Methanococcus jannaschii
"Methanocaldococcus jannaschii"

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1193	METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)		Medium recipe at MediaDive	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 (°C)	Range
1193	positive	growth	80	hyperthermophilic
67770	positive	growth	80	hyperthermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1193	anaerobe
125439	anaerobe	98.6

Compound production

1193

Compoundhydrogenase

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1193	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM9166v1 assembly for Methanocaldococcus jannaschii DSM 2661	complete	GCA_000091665	243232.20	638154505	243232	98.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Methanocaldococcus jannaschii gene for 16S rRNA, partial sequence, strain: JCM 10045	AB603516	1458		2190
20218	Methanococcus jannaschii 16S ribosomal RNA	M59126	1478		2190

GC content

@ref	GC-content (mol%)	Method
1193	31.0
67770	31	Buoyant density centrifugation (BD)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanocaldococcus jannaschii DSM 2661
NCBI: GCA_000091665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	84.70	no
125439	motility	BacteriaNetⓘ	yes	76.90	no
125439	gram_stain	BacteriaNetⓘ	variable	79.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Restriction modification systems in archaea: A panoramic outlook.	Gulati P, Singh A, Patra S, Bhat S, Verma A.	Heliyon	10.1016/j.heliyon.2024.e27382	2024
	Non-thermodynamic factors affect competition between thermophilic chemolithoautotrophs from deep-sea hydrothermal vents.	Kubik BC, Holden JF.	Appl Environ Microbiol	10.1128/aem.00292-24	2024
Biotechnology	Method for automated high performance closed batch cultivation of gas-utilizing methanogens.	Hofmann W, Orthofer M, Salas Wallach N, Ruddyard A, Ungerank M, Paulik C, Rittmann SKR.	AMB Express	10.1186/s13568-025-01872-y	2025
Enzymology	Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.	de Crecy-Lagard V, Dias R, Sexson N, Friedberg I, Yuan Y, Swairjo MA.	G3 (Bethesda)	10.1093/g3journal/jkaf169	2025
	An AlphaFold Structure Analysis of COQ2 as Key a Component of the Coenzyme Q Synthesis Complex.	Vargas-Perez MLA, Devos DP, Lopez-Lluch G.	Antioxidants (Basel)	10.3390/antiox13040496	2024
	Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.	Burley SK, Bhatt R, Bhikadiya C, Bi C, Biester A, Biswas P, Bittrich S, Blaumann S, Brown R, Chao H, Chithari VR, Craig PA, Crichlow GV, Duarte JM, Dutta S, Feng Z, Flatt JW, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Joy M, Kaelber JT, Khokhriakov I, Lai JS, Lawson CL, Liang Y, Myers-Turnbull D, Peisach E, Persikova I, Piehl DW, Pingale A, Rose Y, Sagendorf J, Sali A, Segura J, Sekharan M, Shao C, Smith J, Trumbull M, Vallat B, Voigt M, Webb B, Whetstone S, Wu-Wu A, Xing T, Young JY, Zalevsky A, Zardecki C.	Nucleic Acids Res	10.1093/nar/gkae1091	2025
Enzymology	The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense gamma-Irradiation.	Madern D, Halgand F, Houee-Levin C, Dufour AB, Coquille S, Ansanay-Alex S, Sacquin-Mora S, Brochier-Armanet C.	Mol Biol Evol	10.1093/molbev/msae231	2024
Genetics	Genetically-modified activation strategy facilitates the discovery of sesquiterpene-derived metabolites from Penicillium brasilianum.	He W, Rong X, Lv H, Zhang L, Bai J, Wang L, Yu L, Zhang L, Zhang T.	Synth Syst Biotechnol	10.1016/j.synbio.2024.12.006	2025
Proteome	Molecular basis of hyper-thermostability in the thermophilic archaeal aldolase MfnB.	Maddock RMA, Marsh CO, Johns ST, Rooms LD, Duke PW, van der Kamp MW, Stach JEM, Race PR.	Extremophiles	10.1007/s00792-024-01359-x	2024
	The structure of the archaeal nuclease RecJ2 implicates its catalytic mechanism and inability to interact with GINS.	Wang WW, Yi GS, Zhou H, Zhao YX, Wang QS, He JH, Yu F, Xiao X, Liu XP.	J Biol Chem	10.1016/j.jbc.2024.107379	2024
	Francisella tularensis universal stress protein contributes to persistence during growth arrest and paraquat-induced superoxide stress.	Girardo B, Yue Y, Lockridge O, Bartling AM, Schopfer LM, Augusto L, Larson MA.	J Bacteriol	10.1128/jb.00377-24	2025
Pathogenicity	Proteome-wide comparison of tertiary protein structures reveals molecular mimicry in Plasmodium-human interactions.	Muthye V, Wasmuth JD.	Front Parasitol	10.3389/fpara.2023.1162697	2023
	Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis.	Bigdeli A, Ghaderi-Zefrehei M, Lesch BJ, Behmanesh M, Arab SS.	PLoS One	10.1371/journal.pone.0308817	2024
Metabolism	Redox Coenzyme F₄₂₀ Biosynthesis in Thermomicrobia Involves Reduction by Stand-Alone Nitroreductase Superfamily Enzymes.	Braga D, Hasan M, Krober T, Last D, Lackner G.	Appl Environ Microbiol	10.1128/aem.00457-20	2020
Metabolism	The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales.	Muller MC, Wagner T.	Int J Mol Sci	10.3390/ijms22168631	2021
	A Genetic System for Methanocaldococcus jannaschii: An Evolutionary Deeply Rooted Hyperthermophilic Methanarchaeon.	Susanti D, Frazier MC, Mukhopadhyay B.	Front Microbiol	10.3389/fmicb.2019.01256	2019
Metabolism	Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer.	Topcuoglu BD, Meydan C, Nguyen TB, Lang SQ, Holden JF.	Appl Environ Microbiol	10.1128/aem.00180-19	2019
Genetics	Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus.	Vailionis JL, Zhao W, Zhang K, Rodionov DA, Lipscomb GL, Tanwee TNN, O'Quinn HC, Bing RG, Kelly RM, Adams MWW, Zhang Y.	Appl Environ Microbiol	10.1128/aem.00563-23	2023
	Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea.	Yi GS, Song Y, Wang WW, Chen JN, Deng W, Cao W, Wang FP, Xiao X, Liu XP.	Genes (Basel)	10.3390/genes8090211	2017
Enzymology	A Reduced F₄₂₀-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon.	Heryakusuma C, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B.	J Bacteriol	10.1128/jb.00078-22	2022
	Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles.	Yu Z, Ma Y, Zhong W, Qiu J, Li J.	Front Microbiol	10.3389/fmicb.2017.01278	2017
Metabolism	tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii.	Yu N, Jora M, Solivio B, Thakur P, Acevedo-Rocha CG, Randau L, de Crecy-Lagard V, Addepalli B, Limbach PA.	J Bacteriol	10.1128/jb.00690-18	2019
Metabolism	Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents.	Stewart LC, Algar CK, Fortunato CS, Larson BI, Vallino JJ, Huber JA, Butterfield DA, Holden JF.	ISME J	10.1038/s41396-019-0382-3	2019
	Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.	Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ.	Sci Adv	10.1126/sciadv.abm9651	2022
	Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612).	Thennarasu S, Polireddy D, Antony A, Yada MR, Algarawi S, Sivakumar N.	Genome Announc	10.1128/genomea.00481-13	2013
	The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study.	Lecocq M, Groussin M, Gouy M, Brochier-Armanet C.	Mol Biol Evol	10.1093/molbev/msaa312	2021
	Characterization of SdGA, a cold-adapted glucoamylase from Saccharophagus degradans.	Wayllace NM, Hedin N, Busi MV, Gomez-Casati DF.	Biotechnol Rep (Amst)	10.1016/j.btre.2021.e00625	2021
	DNA-bridging by an archaeal histone variant via a unique tetramerisation interface.	Ofer S, Blombach F, Erkelens AM, Barker D, Soloviev Z, Schwab S, Smollett K, Matelska D, Fouqueau T, van der Vis N, Kent NA, Thalassinos K, Dame RT, Werner F.	Commun Biol	10.1038/s42003-023-05348-2	2023
Transcriptome	The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1.	de Almeida JPP, Vencio RZN, Lorenzetti APR, Caten FT, Gomes-Filho JV, Koide T.	Genes (Basel)	10.3390/genes10040280	2019
Enzymology	Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis.	Padmanabhan B, Yokoyama S, Bessho Y.	BMC Struct Biol	10.1186/1472-6807-13-10	2013
Enzymology	Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins.	Akanuma S, Yamaguchi M, Yamagishi A.	PLoS One	10.1371/journal.pone.0258821	2021
Phylogeny	KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.	Wang D, Xu J, Yu J.	Biol Direct	10.1186/s13062-015-0083-4	2015
	Characterization of TPP-binding proteins in Methanococci archaeal species.	Harris LK.	Bioinformation	10.6026/97320630012359	2016
Metabolism	Anaerobic coculture of microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C enhances generation of n-alkane-rich biofuels after pyrolysis.	Yamane K, Matsuyama S, Igarashi K, Utsumi M, Shiraiwa Y, Kuwabara T.	Appl Environ Microbiol	10.1128/aem.01685-12	2013
	Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.	Galambos D, Anderson RE, Reveillaud J, Huber JA.	Environ Microbiol	10.1111/1462-2920.14806	2019
Metabolism	PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales.	Shiraishi M, Ishino S, Yoshida K, Yamagami T, Cann I, Ishino Y.	Sci Rep	10.1038/srep25532	2016
Enzymology	Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii.	Padmanabhan B, Strange RW, Antonyuk SV, Ellis MJ, Hasnain SS, Iino H, Agari Y, Bessho Y, Yokoyama S.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s174430910904651x	2009
Enzymology	The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603).	Strange RW, Antonyuk SV, Ellis MJ, Bessho Y, Kuramitsu S, Yokoyama S, Hasnain SS.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309109044923	2009
	Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044).	Rangarajan S, Jeyakanthan J, Mridula P, Sakamoto K, Kitamura Y, Agari Y, Shinkai A, Ebihara A, Kuramitsu S, Yokoyama S, Sekar K.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309108000341	2008
	The RAST Server: rapid annotations using subsystems technology.	Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.	BMC Genomics	10.1186/1471-2164-9-75	2008
	Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.	Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT.	Genes (Basel)	10.3390/genes9030129	2018
Phylogeny	High Frequency of Thermodesulfovibrio spp. and Anaerolineaceae in Association with Methanoculleus spp. in a Long-Term Incubation of n-Alkanes-Degrading Methanogenic Enrichment Culture.	Liang B, Wang LY, Zhou Z, Mbadinga SM, Zhou L, Liu JF, Yang SZ, Gu JD, Mu BZ.	Front Microbiol	10.3389/fmicb.2016.01431	2016
	An alternative path for the evolution of biological nitrogen fixation.	Boyd ES, Hamilton TL, Peters JW.	Front Microbiol	10.3389/fmicb.2011.00205	2011
Metabolism	A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase.	Smollett K, Blombach F, Reichelt R, Thomm M, Werner F.	Nat Microbiol	10.1038/nmicrobiol.2017.21	2017
Enzymology	Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.	Malay AD, Bessho Y, Ellis MJ, Antonyuk SV, Strange RW, Hasnain SS, Shinkai A, Padmanabhan B, Yokoyama S.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309109047046	2009
Metabolism	Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.	Ten-Caten F, Vencio RZN, Lorenzetti APR, Zaramela LS, Santana AC, Koide T.	RNA Biol	10.1080/15476286.2018.1509661	2018
	funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi.	Choi J, Kim KT, Jeon J, Wu J, Song H, Asiegbu FO, Lee YH.	BMC Genomics	10.1186/1471-2164-15-s9-s14	2014
Transcriptome	Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni.	Isokpehi RD, Mahmud O, Mbah AN, Simmons SS, Avelar L, Rajnarayanan RV, Udensi UK, Ayensu WK, Cohly HH, Brown SD, Dates CR, Hentz SD, Hughes SJ, Smith-McInnis DR, Patterson CO, Sims JN, Turner KT, Williams BS, Johnson MO, Adubi T, Mbuh JV, Anumudu CI, Adeoye GO, Thomas BN, Nashiru O, Oliveira G.	Gene Regul Syst Bio	10.4137/grsb.s7491	2011
	Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.	Ver Eecke HC, Butterfield DA, Huber JA, Lilley MD, Olson EJ, Roe KK, Evans LJ, Merkel AY, Cantin HV, Holden JF.	Proc Natl Acad Sci U S A	10.1073/pnas.1206632109	2012
Genetics	Recent Advances in the Identification of Replication Origins Based on the Z-curve Method.	Gao F.	Curr Genomics	10.2174/1389202915999140328162938	2014
Metabolism	Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14.	Menezes S, Gaston KW, Krivos KL, Apolinario EE, Reich NO, Sowers KR, Limbach PA, Perona JJ.	Nucleic Acids Res	10.1093/nar/gkr475	2011
	Recapitulating phylogenies using k-mers: from trees to networks.	Bernard G, Ragan MA, Chan CX.	F1000Res	10.12688/f1000research.10225.2	2016
	Misprediction of Structural Disorder in Halophiles.	Pancsa R, Kovacs D, Tompa P.	Molecules	10.3390/molecules24030479	2019
Enzymology	Characterization of thermophilic archaeal isopentenyl phosphate kinases.	Chen M, Poulter CD.	Biochemistry	10.1021/bi9017957	2010
	Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation.	Liang B, Wang LY, Mbadinga SM, Liu JF, Yang SZ, Gu JD, Mu BZ.	AMB Express	10.1186/s13568-015-0117-4	2015
	Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents.	Topcuoglu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF.	Front Microbiol	10.3389/fmicb.2016.01240	2016
Metabolism	Helix-hairpin-helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues.	Schomacher L, Smolorz S, Ciirdaeva E, Ber S, Kramer W, Fritz HJ.	Nucleic Acids Res	10.1093/nar/gkq270	2010
Metabolism	Discovery of multiple modified F(430) coenzymes in methanogens and anaerobic methanotrophic archaea suggests possible new roles for F(430) in nature.	Allen KD, Wegener G, White RH.	Appl Environ Microbiol	10.1128/aem.02202-14	2014
	Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae.	Da Silva SM, Vang LK, Olson ND, Lund SP, Downey AS, Kelman Z, Salit ML, Lin NJ, Morrow JB.	Biomol Detect Quantif	10.1016/j.bdq.2016.01.001	2016
Metabolism	A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate.	Aziz I, Bibi T, Rashid N, Aono R, Atomi H, Akhtar M.	J Bacteriol	10.1128/jb.00284-18	2018
Metabolism	Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii.	Drevland RM, Waheed A, Graham DE.	J Bacteriol	10.1128/jb.00166-07	2007
Metabolism	The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins.	Hosford CJ, Adams MC, Niu Y, Chappie JS.	J Struct Biol	10.1016/j.jsb.2020.107572	2020
Metabolism	Linking energy production and protein synthesis in hydrogenotrophic methanogens.	Oza JP, Sowers KR, Perona JJ.	Biochemistry	10.1021/bi300106p	2012
Genetics	Identification of replication origins in archaeal genomes based on the Z-curve method.	Zhang R, Zhang CT.	Archaea	10.1155/2005/509646	2005
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
Metabolism	Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120.	Devine E, Holmqvist M, Stensjo K, Lindblad P.	BMC Microbiol	10.1186/1471-2180-9-53	2009
Metabolism	An intertwined evolutionary history of methanogenic archaea and sulfate reduction.	Susanti D, Mukhopadhyay B.	PLoS One	10.1371/journal.pone.0045313	2012
Enzymology	Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3.	Gong B, Shin M, Sun J, Jung CH, Bolt EL, van der Oost J, Kim JS.	Proc Natl Acad Sci U S A	10.1073/pnas.1410806111	2014
Genetics	Inteins as indicators of gene flow in the halobacteria.	Soucy SM, Fullmer MS, Papke RT, Gogarten JP.	Front Microbiol	10.3389/fmicb.2014.00299	2014
	Rfam 12.0: updates to the RNA families database.	Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.	Nucleic Acids Res	10.1093/nar/gku1063	2015
Enzymology	Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase.	Carbone V, Schofield LR, Zhang Y, Sang C, Dey D, Hannus IM, Martin WF, Sutherland-Smith AJ, Ronimus RS.	J Biol Chem	10.1074/jbc.m115.647461	2015
Enzymology	The cyanobacterial NAD kinase gene sll1415 is required for photoheterotrophic growth and cellular redox homeostasis in Synechocystis sp. strain PCC 6803.	Gao H, Xu X.	J Bacteriol	10.1128/jb.05873-11	2012
	Gene order phylogeny and the evolution of methanogens.	Luo H, Sun Z, Arndt W, Shi J, Friedman R, Tang J.	PLoS One	10.1371/journal.pone.0006069	2009
	An Integrative Genomic Island Affects the Adaptations of the Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure.	Li Z, Li X, Xiao X, Xu J.	Front Microbiol	10.3389/fmicb.2016.01927	2016
	Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.	Makarova KS, Galperin MY, Koonin EV.	mBio	10.1128/mbio.01959-17	2017
	Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins.	Demongeot J, Norris V.	Life (Basel)	10.3390/life9020051	2019
Genetics	Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.	Fujishima K, Sugahara J, Tomita M, Kanai A.	PLoS One	10.1371/journal.pone.0001622	2008
	Structures of the sulfite detoxifying F₄₂₀-dependent enzyme from Methanococcales.	Jespersen M, Pierik AJ, Wagner T.	Nat Chem Biol	10.1038/s41589-022-01232-y	2023
	On the representability of complete genomes by multiple competing finite-context (Markov) models.	Pinho AJ, Ferreira PJ, Neves AJ, Bastos CA.	PLoS One	10.1371/journal.pone.0021588	2011
Enzymology	Relationship between Ni(II) and Zn(II) coordination and nucleotide binding by the Helicobacter pylori [NiFe]-hydrogenase and urease maturation factor HypB.	Sydor AM, Lebrette H, Ariyakumaran R, Cavazza C, Zamble DB.	J Biol Chem	10.1074/jbc.m113.502781	2014
Enzymology	Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1).	Kitamura A, Nishimoto M, Sengoku T, Shibata R, Jager G, Bjork GR, Grosjean H, Yokoyama S, Bessho Y.	J Biol Chem	10.1074/jbc.m112.409300	2012
	Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales.	Zink IA, Wimmer E, Schleper C.	Biomolecules	10.3390/biom10111523	2020
	Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold.	Rossbach M, Daumke O, Klinger C, Wittinghofer A, Kaufmann M.	BMC Struct Biol	10.1186/1472-6807-5-7	2005
	Unsupervised statistical clustering of environmental shotgun sequences.	Kislyuk A, Bhatnagar S, Dushoff J, Weitz JS.	BMC Bioinformatics	10.1186/1471-2105-10-316	2009
Phylogeny	CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.	Grissa I, Vergnaud G, Pourcel C.	Nucleic Acids Res	10.1093/nar/gkn228	2008
	Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.	Chai J, Kora G, Ahn TH, Hyatt D, Pan C.	BMC Evol Biol	10.1186/s12862-014-0207-y	2014
Genetics	Tracing lifestyle adaptation in prokaryotic genomes.	Altermann E.	Front Microbiol	10.3389/fmicb.2012.00048	2012
Genetics	Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.	Perez-Rueda E, Janga SC.	Mol Biol Evol	10.1093/molbev/msq033	2010
Metabolism	Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils.	Pold G, Pold G, Billings AF, Blanchard JL, Burkhardt DB, Frey SD, Melillo JM, Schnabel J, van Diepen LT, DeAngelis KM.	Appl Environ Microbiol	10.1128/aem.02012-16	2016
Metabolism	Regulation of universal stress protein genes by quorum sensing and RpoS in Burkholderia glumae.	Kim H, Goo E, Kang Y, Kim J, Hwang I.	J Bacteriol	10.1128/jb.06396-11	2012
	Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii.	Zhang J, Olsen GJ.	RNA	10.1261/rna.1715209	2009
	Novel archaeal adhesion pilins with a conserved N terminus.	Esquivel RN, Xu R, Pohlschroder M.	J Bacteriol	10.1128/jb.00572-13	2013
Genetics	Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.	Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM.	Front Microbiol	10.3389/fmicb.2015.01192	2015
	Oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways.	Slesak I, Slesak H, Kruk J.	Astrobiology	10.1089/ast.2011.0704	2012
	The very early evolution of protein translocation across membranes.	Harris AJ, Goldman AD.	PLoS Comput Biol	10.1371/journal.pcbi.1008623	2021
Pathogenicity	DPAGT1 Inhibitors of Capuramycin Analogues and Their Antimigratory Activities of Solid Tumors.	Mitachi K, Kansal RG, Hevener KE, Gillman CD, Hussain SM, Yun HG, Miranda-Carboni GA, Glazer ES, Clemons WM, Kurosu M.	J Med Chem	10.1021/acs.jmedchem.0c00545	2020
	Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.	Krupovic M, Gonnet M, Hania WB, Forterre P, Erauso G.	PLoS One	10.1371/journal.pone.0049044	2013
	Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.	Rodriguez-Rivas J, Marsili S, Juan D, Valencia A.	Proc Natl Acad Sci U S A	10.1073/pnas.1611861114	2016
Metabolism	Distribution of glucan-branching enzymes among prokaryotes.	Suzuki E, Suzuki R.	Cell Mol Life Sci	10.1007/s00018-016-2243-9	2016
Metabolism	Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes.	Naganuma T, Nomura N, Yao M, Mochizuki M, Uchiumi T, Tanaka I.	J Biol Chem	10.1074/jbc.m109.068098	2010
Pathogenicity	Identification of rcnA (yohM), a nickel and cobalt resistance gene in Escherichia coli.	Rodrigue A, Effantin G, Mandrand-Berthelot MA.	J Bacteriol	10.1128/jb.187.8.2912-2916.2005	2005
	An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea.	Atkinson GC, Hauryliuk V, Tenson T.	BMC Evol Biol	10.1186/1471-2148-11-22	2011
	MetaGene: prokaryotic gene finding from environmental genome shotgun sequences.	Noguchi H, Park J, Takagi T.	Nucleic Acids Res	10.1093/nar/gkl723	2006
	Study of inter- and intra-individual variations in the salivary microbiota.	Lazarevic V, Whiteson K, Hernandez D, Francois P, Schrenzel J.	BMC Genomics	10.1186/1471-2164-11-523	2010
	Similar gene estimates from circular and linear standards in quantitative PCR analyses using the prokaryotic 16S rRNA gene as a model.	Oldham AL, Duncan KE.	PLoS One	10.1371/journal.pone.0051931	2012
Enzymology	De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy.	Mills DJ, Vitt S, Strauss M, Shima S, Vonck J.	Elife	10.7554/elife.00218	2013
Metabolism	The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.	Hove-Jensen B, Brodersen DE, Manav MC.	Microbiol Mol Biol Rev	10.1128/mmbr.00040-18	2019
Transcriptome	Environment specific substitution tables for thermophilic proteins.	Mizuguchi K, Sele M, Cubellis MV.	BMC Bioinformatics	10.1186/1471-2105-8-s1-s15	2007
Genetics	PIRSF family classification system for protein functional and evolutionary analysis.	Nikolskaya AN, Arighi CN, Huang H, Barker WC, Wu CH.	Evol Bioinform Online		2007
Phylogeny	Isolation and characterization of endophytic bacteria isolated from the leaves of the common bean (Phaseolus vulgaris).	de Oliveira Costa LE, de Queiroz MV, Borges AC, de Moraes CA, de Araujo EF.	Braz J Microbiol	10.1590/s1517-838220120004000041	2012
	Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12.	Sun J, Tuncay K, Haidar AA, Ensman L, Stanley F, Trelinski M, Ortoleva P.	Algorithms Mol Biol	10.1186/1748-7188-2-2	2007
Metabolism	An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.	Sato T, Fujihashi M, Miyamoto Y, Kuwata K, Kusaka E, Fujita H, Miki K, Atomi H.	J Biol Chem	10.1074/jbc.m113.457259	2013
Phylogeny	TIGRFAMs and Genome Properties in 2013.	Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.	Nucleic Acids Res	10.1093/nar/gks1234	2013
Metabolism	Metallo-GTPase HypB from Helicobacter pylori and its interaction with nickel chaperone protein HypA.	Xia W, Li H, Yang X, Wong KB, Sun H.	J Biol Chem	10.1074/jbc.m111.287581	2012
Phylogeny	Development of two PCR-based techniques for detecting helical and coccoid forms of Helicobacter pylori.	Shahamat M, Alavi M, Watts JE, Gonzalez JM, Sowers KR, Maeder DW, Robb FT.	J Clin Microbiol	10.1128/jcm.42.8.3613-3619.2004	2004
Genetics	Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus.	Tang KH, Barry K, Chertkov O, Dalin E, Han CS, Hauser LJ, Honchak BM, Karbach LE, Land ML, Lapidus A, Larimer FW, Mikhailova N, Pitluck S, Pierson BK, Blankenship RE.	BMC Genomics	10.1186/1471-2164-12-334	2011
	Efficient computation of absent words in genomic sequences.	Herold J, Kurtz S, Giegerich R.	BMC Bioinformatics	10.1186/1471-2105-9-167	2008
Genetics	The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.	Arakawa K, Tomita M.	Evol Bioinform Online		2007
Metabolism	Phylogenomic reconstruction of archaeal fatty acid metabolism.	Dibrova DV, Galperin MY, Mulkidjanian AY.	Environ Microbiol	10.1111/1462-2920.12359	2014
Genetics	Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins.	Lopez-Ramirez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Alvarez G.	J Mol Evol	10.1007/s00239-011-9441-8	2011
	Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.	Brochier-Armanet C, Forterre P.	Archaea	10.1155/2006/582916	2007
	Correlation between sequence conservation and the genomic context after gene duplication.	Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.	Nucleic Acids Res	10.1093/nar/gki913	2005
Metabolism	Functional characterization of two structurally novel diacylglycerol acyltransferase2 isozymes responsible for the enhanced production of stearate-rich storage lipid in Candida tropicalis SY005.	Dey P, Chakraborty M, Kamdar MR, Maiti MK.	PLoS One	10.1371/journal.pone.0094472	2014
Metabolism	Acetamido sugar biosynthesis in the Euryarchaea.	Namboori SC, Graham DE.	J Bacteriol	10.1128/jb.01970-07	2008
Genetics	A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.	D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.	BMC Genomics	10.1186/s12864-015-2194-9	2016
	Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.	Zhang J, Li E, Olsen GJ.	Nucleic Acids Res	10.1093/nar/gkp213	2009
Metabolism	Reconstructing the mosaic glycolytic pathway of the anaerobic eukaryote Monocercomonoides.	Liapounova NA, Hampl V, Gordon PM, Sensen CW, Gedamu L, Dacks JB.	Eukaryot Cell	10.1128/ec.00258-06	2006
Enzymology	Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes.	Raedts J, Kengen SW, van der Oost J.	Glycoconj J	10.1007/s10719-011-9324-7	2011
Metabolism	Homologue structure of the SLAC1 anion channel for closing stomata in leaves.	Chen YH, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, Rost B, Love J, Siegelbaum SA, Hendrickson WA.	Nature	10.1038/nature09487	2010
Genetics	Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.	Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC.	ISME J	10.1038/ismej.2010.162	2011
Metabolism	DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.	Cheng H, Grishin NV.	Protein Sci	10.1110/ps.051364905	2005
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
	Carboxylic ester hydrolases from hyperthermophiles.	Levisson M, van der Oost J, Kengen SW.	Extremophiles	10.1007/s00792-009-0260-4	2009
Metabolism	Archaea signal recognition particle shows the way.	Zwieb C, Bhuiyan S.	Archaea	10.1155/2010/485051	2010
Metabolism	Distribution analysis of hydrogenases in surface waters of marine and freshwater environments.	Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, Schwarz C, Gutekunst K, Vanselow KH, Schmitz R, LaRoche J, Schulz R, Appel J.	PLoS One	10.1371/journal.pone.0013846	2010
	Is the genetic landscape of the deep subsurface biosphere affected by viruses?	Anderson RE, Brazelton WJ, Baross JA.	Front Microbiol	10.3389/fmicb.2011.00219	2011
Metabolism	Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.	Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ.	J Biol Chem	10.1074/jbc.m110.163154	2010
Metabolism	Glutamine versus ammonia utilization in the NAD synthetase family.	De Ingeniis J, Kazanov MD, Shatalin K, Gelfand MS, Osterman AL, Sorci L.	PLoS One	10.1371/journal.pone.0039115	2012
Enzymology	ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea.	Verhees CH, Tuininga JE, Kengen SW, Stams AJ, van der Oost J, de Vos WM.	J Bacteriol	10.1128/jb.183.24.7145-7153.2001	2001
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Metabolism	Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.	Gao B, Gupta RS.	BMC Genomics	10.1186/1471-2164-8-86	2007
Metabolism	Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue.	Suloway CJ, Rome ME, Clemons WM.	EMBO J	10.1038/emboj.2011.433	2012
Metabolism	The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.	Reher M, Fuhrer T, Bott M, Schonheit P.	J Bacteriol	10.1128/jb.01281-09	2010
Enzymology	Modelling the evolution of the archeal tryptophan synthase.	Merkl R.	BMC Evol Biol	10.1186/1471-2148-7-59	2007
	Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.	Castillo R, Saier MH.	Int J Microbiol	10.1155/2010/187373	2010
	Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.	Ashby MK.	Archaea	10.1155/2006/562404	2006
	A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule).	Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK.	DNA Res	10.1093/dnares/dsp021	2009
	Iron homeostasis in the Rhodobacter genus.	Zappa S, Bauer CE.	Adv Bot Res	10.1016/b978-0-12-397923-0.00010-2	2013
Metabolism	Triosephosphate isomerase: a highly evolved biocatalyst.	Wierenga RK, Kapetaniou EG, Venkatesan R.	Cell Mol Life Sci	10.1007/s00018-010-0473-9	2010
Phylogeny	Comparative genomic analyses of the bacterial phosphotransferase system.	Barabote RD, Saier MH.	Microbiol Mol Biol Rev	10.1128/mmbr.69.4.608-634.2005	2005
Genetics	Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.	Koonin EV, Wolf YI.	Nucleic Acids Res	10.1093/nar/gkn668	2008
Metabolism	Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.	Lo CC, Bonner CA, Xie G, D'Souza M, Jensen RA.	Microbiol Mol Biol Rev	10.1128/mmbr.00024-09	2009
Genetics	Metabiotics Signature through Genome Sequencing and In Vitro Inhibitory Assessment of a Novel Lactococcus lactis Strain UTNCys6-1 Isolated from Amazonian Camu-Camu Fruits.	Tenea GN.	Int J Mol Sci	10.3390/ijms24076127	2023
Metabolism	A SLC6 transporter cloned from the lion's mane jellyfish (Cnidaria, Scyphozoa) is expressed in neurons.	Bouchard C, Boudko DY, Jiang RHY.	PLoS One	10.1371/journal.pone.0218806	2019
	Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3.	Diale MO, Kayitesi E, Serepa-Dlamini MH.	Front Genet	10.3389/fgene.2021.672149	2021
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
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
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
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
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

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;
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methanocaldococcus jannaschii (DSM 2661, ATCC 43067, JCM 10045)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000091665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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