Database Authors
Christos Ouzounis1, Ismini Baltsavia1, Ron Caspi2, Anamika Kothari2
1Centre for Research and Technology Hellas, 2SRI International
Summary Methanocaldococcus jannaschii (formerly Methanococcus jannaschii) is a thermophilic methanogenic archaeon. It was originally isolated by a research team from the Woods Hole Oceanographic Institution using the manned submersible ALVIN from a sediment sample collected from the base of a "white smoker" chimney located at 21°N on the East Pacific Rise, at a depth of 2600 meters. It was named after the late Woods Hole marine microbiologist Holger Jannasch [Jones83].

The organism, which is a strict anaerobe, grows at pressures of up to more than 200 atmospheres and over a temperature range of 48°C to 94°C, with an optimum temperature near 85°C. The cells are flagellated, with two waved-bundles of flagella, each containing a high number of flagella arranged in subgroups, and both inserted close to the same cell pole [Jones83].

Methanocaldococcus jannaschii was the first archaeon to have its complete genome sequenced [Bult96]. Unlike many other Methanococci, it is only capable of growth on carbon dioxide and hydrogen as primary energy sources. Being the first archaeon to be fully sequenced, the organism has been used in many studies of novel archaeal metabolic and information processing pathways.

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 26.5 and MetaCyc [Caspi20] version 26.5 on 06-Oct-2022, based on genome annotation performed by Drs. Christos Ouzounis and Ismini Baltsavia from the Centre for Research and Technology Hellas in Thessaloniki, Greece, and improved by subsequent manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome1,8151,72145491,664,970RefSeq:NC_000909
plasmid pDSM2661_154510358,407RefSeq:NC_001732
plasmid pDSM2661_213130016,550RefSeq:NC_001733
Total:1,8821,78545521,739,927
Genes without a physical map position:1
Ortholog data available?Yes
Database Contents
Genes1,883
Pathways151
Enzymatic Reactions896
Transport Reactions26
Polypeptides1,786
Protein Complexes94
Enzymes531
Transporters94
Compounds734
Transcription Units1,259
tRNAs37
Protein Features6,272
GO Terms15,453
Database Version29.0
Taxonomic Lineage cellular organisms
Archaea
Euryarchaeota
Methanomada group
Methanococci
Methanococcales
Methanocaldococcaceae
Methanocaldococcus
Methanocaldococcus jannaschii
Methanocaldococcus jannaschii DSM 2661
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603984
NCBI BioProjectPRJNA224116
NCBI-Taxonomy243232
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Bult96: Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC (1996). "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Science 273(5278);1058-73. PMID: 8688087

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Jones83: Jones W J, Leigh J A, Mayer F, Woese C R, Wolfe R S (1983). "Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent." Archives of Microbiology 136(4);254-261.

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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