''Methanocaldococcus jannaschii'' (formerly ''Methanococcus jannaschii'') is a

thermophilic A thermophile is a type of extremophile that thrives at relatively high temperatures, between . Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bact ...

methanogen Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for Adenosine triphosphate, ATP generation in methanogens. A ...

archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

n in the class

Methanococci Methanococci is a class of methanogenic archaea in the phylum Euryarchaeota.See the NCBIbr>webpage on Methanococci Data extracted from the They can be mesophilic, thermophilic A thermophile is a type of extremophile that thrives at relati ...

. It was the first archaeon, and third organism, to have its complete genome

sequenced In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succi ...

. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic

cofactors Cofactor may also refer to: * Cofactor (biochemistry), a substance that needs to be present in addition to an enzyme for a certain reaction to be catalysed * A domain parameter in elliptic curve cryptography, defined as the ratio between the order ...

were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.

History

''Methanocaldococcus jannaschii'' was isolated from a submarine hydrothermal vent at

Woods Hole Oceanographic Institution The Woods Hole Oceanographic Institution (WHOI, acronym pronounced ) is a private, nonprofit research and higher education facility dedicated to the study of marine science and engineering. Established in 1930 in Woods Hole, Massachusetts, it i ...

. The hydrothermal vent was located in the

East Pacific Rise The East Pacific Rise (EPR) is a mid-ocean rise (usually termed an oceanic rise and not a mid-ocean ridge due to its higher rate of spreading that results in less elevation increase and more regular terrain), at a divergent tectonic plate bound ...

, at a depth of 2600 m, near the western coast of Mexico. Surface material was collected at a "

white smoker Hydrothermal vents are fissures on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotsp ...

" chimney which revealed evidence of Methanocaldococcus jannaschii living in this extreme habitat of temperatures from 48 - 94 °C. Like many kinds of

extremophile An extremophile () is an organism that is able to live (or in some cases thrive) in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, press ...

s, ''M. jannaschii'' possess the ability to adapt to high temperatures, high pressure, and moderate salinity.

Sequencing

''Methanocaldococcus jannaschii'' was sequenced by a group at

TIGR TIGR (an acronym of the place-names ''Trieste, Trst'', ''Istria, Istra'', ''Gorizia, Gorica'', and ''Rijeka, Reka''), fully the Revolutionary Organization of the Julian March T.I.G.R. (), was a Militant (word), militant Anti-fascism, anti-fascis ...

led by

Craig Venter John Craig Venter (born October 14, 1946) is an American scientist. He is known for leading one of the first draft sequences of the human genome and led the first team to transfect a cell with a synthetic chromosome. Venter founded Celera Geno ...

using whole-genome

shotgun sequencing In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The Sanger sequencing#Method, chain-termination method of DNA sequencin ...

. ''M. jannaschii'' represented the first member of the Archaea to have its genome sequenced. According to Venter, the unique features of the genome provided strong evidence that there are

three domains of life The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earli ...

. After ''M. jannaschii'' was sequenced using whole-genome random sequencing, several interesting characteristics were determined. Methanocaldococcus has a large circular chromosome that is 1.66 mega base pairs long with a G+C content of 31.4%. The species also has a large circular extra-chromosome and small circular extra-chromosome.

Taxonomy

''Methanocaldoccus jannaschii'' is a member of the genus ''

Methanocaldococcus ''Methanocaldococcus'' formerly known as ''Methanococcus'' is a genus of coccoid methanogen archaea. They are all mesophiles, except the thermophilic ''M. thermolithotrophicus'' and the hyperthermophilic ''M. jannaschii''. The latter was dis ...

'' (previously a part of ''

Methanococcus ''Methanococcus'' is a genus of coccoid methanogens of the family Methanococcaceae. They are all mesophiles, except the thermophilic '' M. thermolithotrophicus'' and the hyperthermophilic '' M. jannaschii''. The latter was discovered at the ba ...

'') and is therefore sometimes referred to as a "class I" methanogen (e.g

.

Biology and biochemistry

''Methanocaldococcus jannaschii'' is a thermophilic

, meaning it grows by methanogenesis, making methane as a metabolic byproduct. It is only capable of growth on

carbon dioxide Carbon dioxide is a chemical compound with the chemical formula . It is made up of molecules that each have one carbon atom covalent bond, covalently double bonded to two oxygen atoms. It is found in a gas state at room temperature and at norma ...

and

hydrogen Hydrogen is a chemical element; it has chemical symbol, symbol H and atomic number 1. It is the lightest and abundance of the chemical elements, most abundant chemical element in the universe, constituting about 75% of all baryon, normal matter ...

as primary energy sources, unlike many other methanococci (such as ''

Methanococcus maripaludis ''Methanococcus maripaludis'' is a species of methanogenic archaea found in marine environments, predominantly salt marshes. ''M. maripaludis'' is a non-pathogenic, gram-negative, weakly motile, non-spore-forming, and strictly anaerobic mesophil ...

'') which can also use

formate Formate (IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless. Fundamentals When dissolved in water, formic acid co ...

as a primary energy source. The genome includes many

hydrogenase A hydrogenase is an enzyme that Catalysis, catalyses the reversible Redox, oxidation of molecular hydrogen (H2), as shown below: Hydrogen oxidation () is coupled to the reduction of electron acceptors such as oxygen, nitrate, Ferric, ferric i ...

s, such as a 5,10-methenyltetrahydromethanopterin hydrogenase, a

ferredoxin hydrogenase Ferredoxins (from Latin ''ferrum'': iron + redox, often abbreviated "fd") are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied t ...

(eha), and a

coenzyme F420 hydrogenase In enzymology, a coenzyme F420 hydrogenase () is an enzyme that catalyzes the chemical reaction :H2 + coenzyme F420 \rightleftharpoons reduced coenzyme F420 Thus, the two substrates of this enzyme are H2 and coenzyme F420, whereas its product ...

Proteomic Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

studies showed that ''M. jannaschii'' contains a large number of

inteins Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (called exteins) on ...

: 19 were discovered by one study. Many novel metabolic pathways have been worked out in ''M. jannaschii'', including the pathways for synthesis of many methanogenic cofactors,

riboflavin Riboflavin, also known as vitamin B2, is a vitamin found in food and sold as a dietary supplement. It is essential to the formation of two major coenzymes, flavin mononucleotide and flavin adenine dinucleotide. These coenzymes are involved in ...

, and novel amino acid synthesis pathways. Many information processing pathways have also been studied in this organism, such as an archaeal-specific

DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create t ...

family. Information about single-pass transmembrane proteins from ''M. jannaschii'' was compiled in

Membranome database Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from ''Homo sapiens'', ''Arabidopsis thaliana'', ''Dictyostelium discoideum'', ''Saccharomyces cerevisiae'', '' ...

Relevance and Research

Due to the amount of information that was gained from

sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...

, several research interests have developed. One area of interest is the hyperthermophilic enzymes that ''Methanococcus jannaschii'' produces in hopes of understanding enzyme evolution or even enzyme

catalytic mechanism Enzyme catalysis is the increase in the rate of a process by an "enzyme", a biological molecule. Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, calle ...

s. Research on

mutagenesis Mutagenesis () is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using lab ...

has focused on seeing if these enzymes, which are typically optimal at high temperatures, can be just as active in low temperatures. ''M. jannaschii'' has been a model system for in vivo genetic studies. Since ''M. jannaschii'' is an extremophile several astrobiology research projects have begun looking into methane producing bacteria.

References

External links

Microbe wiki entry for ''Methano(caldo)coccus jannaschii''

UCSD genome browser entry for ''Methanocaldococcus jannaschii''

KEGG entry for ''Methanocaldococcus jannaschii''

Type strain of ''Methanocaldococcus jannaschii'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q6823580 Euryarchaeota Archaea described in 1983