Methanopyrus kandleri

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A Microbial Biorealm page on the genus Methanopyrus kandleri

Classification

Higher order taxa

cellular organisms

Doomain: Archaea

Phylum: Euryarchaeota

Class: Methanopyri

Order: Methanopyrales

Family: Methanopyraceae

Genus: Methanopyrus


Species

NCBI: Taxonomy

Methanopyrus kandleri

Description and significance

Methanopyrus kandleri is a Gram positive, rod-shaped, anaerobic methanogen that is classified as an archaeon (2,7,8). M. kandleri, is also one of the most exceptional extremophiles known today. Not only is it a hyperthermophile, but it is also a thriving halophile. It can survive in temperatures up to 110 degrees Celsius which makes it the most temperature resistant species of all the other methanogens (4,6). M. kandleri's hyperthermophilic properties are matched by its halophillic tendencies. Intracellular salt content of trianionic cDPG (cyclic 2,3-diphosphoglycerate) and K+ have been measured at concentrations as high as 1.1M and 3M, respectively (3). Its ability to live in these harsh environments is thought to be credited towards its methanogenic metabolism (4).


Genome structure

The entire genome of M. kandleri has been sequenced by Fidelity Systems in Maryland using a customized sequencing method made specifically for this archaeon called direct genomic sequencing. This process has four phases: the skimming shotgun phase, the direct sequencing phase, the gap closure and assembly verification phase, and finally the computational genome analysis (2). This method actually took advantage of a very unique topoisomerase V found only in M. kandleri to help sequence this genome (5). For more on topoisomerase V, see Cell Structure and metabolism or Current Research. By this method, the genome was determined to be a single chromosome that was 1,694,969 base pairs (bp) long. This method proved to work very well since there was only about 1 error per 40 kb (2). The sequence showed very high levels of guanine and cytosine content, which is most likely an adaptation to the extreme environments it lives in (6). Nucleotides 1694501-747 were believed to contain the origin of replication for this chromosome. In this genome, 1,692 protein-coding genes and 39 structural RNA genes were found. These proteins have the highest ratio between negatively and positively charged amino acids and therefore M. kandleri has the lowest isoelectric point in all archaeon (2). M. kandleri is said to have a very high number of orphan genes (5). Although the 16S rRNA and EF-1alpha sequences phylogenically placed M. kandleri relatively far away from the other species of methanogens, the complete sequencing of the genome showed the similarities between the members of this monophyly group (2,6,7). For more on the classification of this organism, see Current Research.


Cell structure and metabolism

M. kandleri is a gram positive archaeon, which means that it has only one cell membrane that is surrounded by a thick cell wall (2). Because M. kandleri is a hyperthermophile as well as a halophile, many structural changes must take place in order to survive. One example of these changes can be seen in the cell membrane of this organism. The cell membranes show an unusual archaeic characteristic of having unsaturated lipids; specifically terpenoid lipids which are primative lipids thought to be the origin of phytantyl diethers, found in all other archaea (2,5). Although it was believed that only eukaryotes contained proteins called histones that condense DNA, it was recently discovered that methanogens also had a protein that does this. The histone found in M. kandleri, called HMK, differs from those found in both eukaryotes and other methanogens. HMK is twice as long as other methanogenic histones, but is believed to bind DNA similar to those of eukaryotes based on spatial similarities (10). Another structural rarity can be seen in the reliance of enzymes on intracellular salt content. This salt concentration greatly affects activity and thermostability of enzymes; specifically enzymes involved in methanogenic processes. The two enzymes proven to show sensetivity to salt concentrations are formylmethanofuran:tetrahydromethanopterin formyltransferase and N5,N10-methenyltetrahydromethanopterin cyclohydrolase. In order to protect itself from osmolysis due to high intracellular salt concentrations, M. kandleri is surrounded by a pseudomurien sacculus (2,3,8). The enzyme topoisomerase V is the most rare topoisomerase known and is only found in M. kandleri. When first discovered it was believed to be related to topoisomerase I, but when it was closely examined it was determined that they were in a class of their own (2,5,11). Another extremely rare enzyme found in M. kandleri is a two-subunit reverse gyrase (2,12).

M. kandleri is a methanogen which means that it produces methane from dihydrogen and carbon dioxide in its environment. It is considered a chemolithoautotroph since it does not use a carbon source other than carbon dioxide. It is also a strict anaerobe which means that it does not use oxygen as its final electron acceptor. Because the methanogenic metabolism of this species is not temperature sensetive, it is able to live in high temperature environments. Because of these high temperatures many of the metabolic enzymes have adapted in many ways as discussed above (2,4, 8,13).


Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

There are no known diseases caused by M. kandleri in any species.

Application to Biotechnology

There has only been one discovery s to how M. Kandleri can be used in the biotechnology field. That is the use of DNA topoisomerase V, an enzyme unique only to M. kandleri, in DNA sequencing. It is such a good choice for this application because of its ability to be active at high temperatures and high salt concentrations. It is also able to handle uneven nucleotide compositions and complex repeat structures unlike other topoisomerases. This enzyme was first used in the ThermoFidelase sequencing kit to determine the sequence of M. kandlei itself.

The helix-hairpin-helix (HhH)2 tandem repeats on the C-terminal tail that make up the DNA binding domain of topoisomerase V are also of interest to may scientists. This HhH2 domain is so interesting because it provides both an apurinic and apyrimidic site that can allow this enzyme to nick the DNA at the phosphodiester bond and remove a single nucleotide. This is important because in vitro the main cause of DNA damage is depurination. Although this HhH2 domain can be found on other enzymes, it is almost never found as abundantly as on topoisomerase V. The strategy for utilizing this domain in vitro is to add them to enzymes like Taq and Pfu DNA polymerases in order to increase their effectiveness and thermostability.


Current Research

Enter summaries of the most recent research here--at least three required

References

(1) NCBI: Methanopyrus kandleri, Accessed August 27, 2007, "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2320&lvl=3&lin=f&keep=1&srchmode=1&unlock"

(2) Alexei I. Slesarev, Katja V. Mezhevaya, Kira S. Makarova, Nikolai N. Polushin, Olga V. Shcherbinina, Vera V. Shakhova, Galina I. Belova, L. Aravind, Darren A. Natale, Igor B. Rogozin, Roman L. Tatusov, Yuri I. Wolf, Karl O. Stetter, Andrei G. Malykh, Eugene V. Koonin, and Sergei A. Kozyavkin. "The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens," Proc Natl Acad Sci U S A, 2002 April 2; 99(7): 4644–4649.

(3) Shima S, Thauer RK, Ermler U. “Hyperthermophilic and salt-dependent formyltransferase from Methanopyrus kandleri,” Biochem Soc Trans, 2004 Apr; 32(Pt 2): 269-72.

(4) Ricardo Cavicchioli. “Cold-adapted archaea,” Nature Reviews Microbiology 4, May 2006; 331-343 .

(5) Patrick Forterre. "DNA topoisomerase V: a new fold of mysterious origin," Trends in Biotechnology, June 2006; Volume 24, Issue 6, Pages 245-247

(6) Jork Nolling, Amy Elfner, John R. Palmer, Vanessa J. Steigerwald, Todd D. Pihl, James A. Lake, John N. Reeve. "Phylogeny of Methanopyrus Kandleri Based on Methyl Coenzyme M Reductase Operons;" International Journal of Systematic Bacteriology, Oct. 1996; Vol. 46, No.4, p. 1170-1173.

(7) Maria C. Rivera, and James A. Lake. "The Phylogeny of Methanopyrus kandleri," International Journal of Systematic Bacteriology, Jan. 1996; Vol. 46, No. 1, p. 348-351.

(8) Shima S, Herault DA, Berkessel A, Thauer RK. " Activation and thermostabilization effects of cyclic 2,3-diphosphoglycerate on enzymes from the hypothermophilic Methanopyrus kandleri," Arch Microbio., 1998 Nov; 170(6): 469-72.

(9) Krah R, O'Dea MH, Gellert M. "Reverse gyrase from Methanopyrus kandleri. Reconstitution of an active extremozyme from its two recombinant subunits," J Biol Chem., May 23 1997; 272(21):13986-90.

(10) Fahrner RL, Cascio D, Lake JA, Slesarev A. "An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone," Protein Sci., Oct. 2001; 10(10):2002-7.

(11) Alexei I. Slesarev, James A. Lake, Karl O. Stetter, Martin Gellert, and Sergei A. Kozyavkin. "Purification and Characterization of DNA Topoisomerase V," The Journal of Biological Chemistry, Feb 4 1994; p. 3295-3303.

(12) Regis Krah, Mary H. O'Dea, and Martin Gellert. "Reverse Gyrase from Methanopyrus kandleri," The American Society for Biochemistry and Molecular Biology, Inc., May 23, 1997; p. 13986-13990.

(13) Beile Gao and Radhey S Gupta. "Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis," BMC Genomics, March 29 2007.

Edited by Brandon Leonard, a student of Rachel Larsen