Methanocaldococcus jannaschii
| Methanocaldococcus jannaschii | |
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| Species: | M. jannaschii
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| Methanocaldococcus jannaschii | |
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Methanocaldococcus jannaschii (formerly Methanococcus jannaschii) is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon, and third organism, to have its complete genome sequenced.[1] The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism,[2] as were several other archaeal-specific metabolic pathways.
History
[edit]Methanocaldococcus jannaschii was isolated from a submarine hydrothermal vent at Woods Hole Oceanographic Institution.[3] The hydrothermal vent was located in the East Pacific Rise, at a depth of 2600 m, near the western coast of Mexico. Surface material was collected at a "white smoker" chimney which revealed evidence of Methanocaldococcus jannaschii living in this extreme habitat of temperatures from 48 - 46 °C. Like many kinds of extremophiles, M. jannaschii possess the ability to adapt to high temperatures, high pressure, and moderate salinity.[4]
Sequencing
[edit]Methanocaldococcus jannaschii was sequenced by a group at TIGR led by Craig Venter[5] using whole-genome shotgun sequencing. 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.[5] 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.[6]
Taxonomy
[edit]Methanocaldoccus jannaschii is a member of the genus Methanocaldococcus (previously a part of Methanococcus) and is therefore sometimes referred to as a "class I" methanogen (e.g. [1]).
Biology and biochemistry
[edit]Methanocaldococcus jannaschii is a thermophilic methanogen, meaning it grows by making methane as a metabolic byproduct. It is only capable of growth on carbon dioxide and hydrogen as primary energy sources, unlike many other methanococci (such as Methanococcus maripaludis) which can also use formate as a primary energy source.[3] The genome includes many hydrogenases, such as a 5,10-methenyltetrahydromethanopterin hydrogenase,[7] a ferredoxin hydrogenase (eha), and a coenzyme F420 hydrogenase.[8]
Proteomic studies showed that M. jannaschii contains a large number of inteins: 19 were discovered by one study.[9]
Many novel metabolic pathways have been worked out in M. jannaschii, including the pathways for synthesis of many methanogenic cofactors,[2] riboflavin,[10] and novel amino acid synthesis pathways.[citation needed] Many information processing pathways have also been studied in this organism, such as an archaeal-specific DNA polymerase family.[11] Information about single-pass transmembrane proteins from M. jannaschii was compiled in Membranome database.[citation needed]
Relevance and Research
[edit]Due to the amount of information that was gained from sequencing, 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 mechanisms. Research on mutagenesis has focused on seeing if these enzymes, which are typically optimal at high temperatures, can be just as active in low temperatures.[12] M. jannaschii has been a model system for in vivo genetic studies.[13] Since M. jannaschii is an extremophile several astrobiology research projects have begun looking into methane producing bacteria.[14]
References
[edit]- ^ Carol J. Bult; Owen White; Gary J. Olsen; Lixin Zhou; Robert D. Fleischmann; Granger G. Sutton; Judith A. Blake; Lisa M. FitzGerald; Rebecca A. Clayton; Jeannine D. Gocayne; Anthony R. Kerlavage; Brian A. Dougherty; Jean-Francois Tomb; Mark D. Adams; Claudia I. Reich; Ross Overbeek; Ewen F. Kirkness; Keith G. Weinstock; Joseph M. Merrick; Anna Glodek; John L. Scott; Neil S. M. Geoghagen; Janice F. Weidman; Joyce L. Fuhrmann; Dave Nguyen; Teresa R. Utterback; Jenny M. Kelley; Jeremy D. Peterson; Paul W. Sadow; Michael C. Hanna; Matthew D. Cotton; Kevin M. Roberts; Margaret A. Hurst; Brian P. Kaine; Mark Borodovsky; Hans-Peter Klenk; Claire M. Fraser; Hamilton O. Smith; Carl R. Woese; J. Craig Venter (1996). "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii". Science. 273 (5278): 1058–1073. Bibcode:1996Sci...273.1058B. doi:10.1126/science.273.5278.1058. PMID 8688087. S2CID 41481616.
- ^ a b Robert H. White (2001). "Biosynthesis of the methanogenic cofactors". Vitamins and Hormones. 61: 299–337. doi:10.1016/s0083-6729(01)61010-0. ISBN 978-0-12-709861-6. PMID 11153270.
- ^ a b W. J. Jones; J. A. Leigh; F. Mayer; C. R. Woese; R. S. Wolfe (1983). "Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent". Archives of Microbiology. 136 (4): 254–261. doi:10.1007/BF00425213. S2CID 33277659.
- ^ Tsoka, Sophia; Simon, David; Ouzounis, Christos A. (2004). "Automated metabolic reconstruction forMethanococcus jannaschii". Archaea. 1 (4): 223–229. doi:10.1155/2004/324925. ISSN 1472-3646. PMC 2685575. PMID 15810431.
- ^ a b Nicholas Wade (23 August 1996). "Deep sea yields a clue to life's origin". New York Times.
- ^ Bult, Carol J.; White, Owen; Olsen, Gary J.; Zhou, Lixin; Fleischmann, Robert D.; Sutton, Granger G.; Blake, Judith A.; FitzGerald, Lisa M.; Clayton, Rebecca A.; Gocayne, Jeannine D.; Kerlavage, Anthony R.; Dougherty, Brian A.; Tomb, Jean-Francois; Adams, Mark D.; Reich, Claudia I. (1996-08-23). "Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii". Science. 273 (5278): 1058–1073. doi:10.1126/science.273.5278.1058. ISSN 0036-8075.
- ^ Erica J. Lyon; Seigo Shima; Gerrit Buurman; Shantanu Chowdhuri; Alfred Batschauer; Klaus Steinbach; Rudolf K. Thauer (January 2004). "UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea". European Journal of Biochemistry. 271 (1): 195–204. doi:10.1046/j.1432-1033.2003.03920.x. PMID 14686932.
- ^ Rudolf K. Thauer; Anne-Kristin Kaster; Meike Goenrich; Michael Schick; Takeshi Hiromoto; Seigo Shima (2010). "Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage". Annual Review of Biochemistry. 79: 507–536. doi:10.1146/annurev.biochem.030508.152103. PMID 20235826.
- ^ Wenhong Zhu; Claudia I. Reich; Gary J. Olsen; Carol S. Giometti; John R. Yates III (2004). "Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis". Journal of Proteome Research. 3 (3): 538–548. doi:10.1021/pr034109s. PMID 15253435.
- ^ Ilka Haase; Simone Mörtl; Peter Köhler; Adelbert Bacher; Markus Fischer (2003). "Biosynthesis of riboflavin in Archaea: 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii". European Journal of Biochemistry. 270 (5): 1025–1032. doi:10.1046/j.1432-1033.2003.03478.x. PMID 12603336.
- ^ Yoshizumi Ishino; Kayoko Komori; Isaac K. O. Cann; Yosuke Koga (1998). "A novel DNA polymerase family found in Archaea". Journal of Bacteriology. 180 (8): 2232–2236. doi:10.1128/JB.180.8.2232-2236.1998. PMC 107154. PMID 9555910.
- ^ Vieille, Claire; Zeikus, Gregory J. (March 2001). "Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability". Microbiology and Molecular Biology Reviews. 65 (1): 1–43. doi:10.1128/mmbr.65.1.1-43.2001. ISSN 1092-2172. PMC 99017. PMID 11238984.
- ^ Tumbula, Debra L.; Whitman, William B. (July 1999). "Genetics of Methanococcus: possibilities for functional genomics in Archaea". Molecular Microbiology. 33 (1): 1–7. doi:10.1046/j.1365-2958.1999.01463.x. ISSN 0950-382X.
- ^ Maus, Deborah; Heinz, Jacob; Schirmack, Janosch; Airo, Alessandro; Kounaves, Samuel P.; Wagner, Dirk; Schulze-Makuch, Dirk (2020-01-08). "Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars Analog Environments". Scientific Reports. 10 (1): 6. doi:10.1038/s41598-019-56267-4. ISSN 2045-2322. PMC 6949245. PMID 31913316.
Further reading
[edit]- Gao, Yongxiang (November 2013). "Crystallization and preliminary X-ray diffraction analysis of MJ0458, an adenylate kinase from Methanocaldococcus jannaschii". Acta Crystallographica Section F. 69 (11): 1272–1274. doi:10.1107/S1744309113026638. PMC 3818051. PMID 24192367.
- Wang, Yu; Xu, Huimin; White, Robert H. (August 2014). "Beta-alanine biosynthesis in Methanocaldococcus jannaschii". American Society for Microbiology. 196 (15): 2869–2875. doi:10.1128/JB.01784-14. PMC 4135672. PMID 24891443.
- Allen, Kyle D.; Xu, Huimin; White, Robert H. (September 2014). "Identification of a unique radical S-adenosylmethionine methylase likely involved in methanopterin biosynthesis in Methanocaldococcus jannaschii". Journal of Bacteriology. 196 (18): 3315–3323. doi:10.1128/JB.01903-14. PMC 4135684. PMID 25002541.
- Lee, Eun Hye; Lee, Kitaik; Hwang, Kwang Yeon (13 December 2013). "Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii". Acta Crystallographica Section D. 70 (4): 922–931. doi:10.1107/S1399004713033762. PMID 24699638.
- Jeffrey M. Dick, Everett L. Shock: The Release of Energy During Protein Synthesis at Ultramafic-Hosted Submarine Hydrothermal Ecosystems. In: AGU Journal of Geophysical Research: Biogeosciences, Volume 126, Issue 11, e2021JG006436. doi:10.1029/2021JG006436. First published: 30 October 2021. See also: New Possibilities for Life in the Strange, Dark World at the Bottom of Earth's Ocean – And Perhaps in Oceans on Other Planets on SciTechDaily. November 28, 2021. Source: Arizona State University