Methylococcus capsulatus
A Microbial Biorealm page on the genus Methylococcus capsulatus
Classification
Higher order taxa
Kingdom: Cellular Organism
Domain: Bacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Methylococcales
Family: Methylococcaceae (8)
Species
Genus: Methylococcus
Species: capsulatus(8)
Description and significance
Methylococcus capsulatus is a methylotrophic “Gram-negative” bacterium with coccus shape ands live in multiple habitats, however, oxygen is a necessity for such cell to survive. Methylococcus capsulatus is also a thermophilic microbe which optimally live in the temperature of 45 degree Celcius.(4) Genus Methylococcus is more closely related to Euryarchaota than Crenarchaeota.(10) Methylococcus capsulatus is isolated from Methanotrophic bacterium, which serves an unique biological function in earth's environment. Methanotrophic bacteria can oxidize the greenhouse gas, methane, as an energy source for growth (for detailed mechanism refer to section, cell structure and metabolism). This metabolism is called methanotrophy. Methanotrophy lowers the methane level in earth's atmosphere, but does release the less potent greenhouse gas CO2. (2)
(9)
Genome structure
The complete genome of M. capsulatus (Bath) consists of 3,304,697 base pairs with 63.6% of G,C contents. The total number of CDSs (predicted coding sequence) is 3,120 with the average size of 962 base pairs. The number of rRNA operons (16S-23S-5S) in M. capsulatus (Bath) genome is 2, the number of tRNA genes is 46 and the number of sRNA genes is 3. 1,766 proteins of known function and role category and 109 proteins of known function but unknown role category were discovered that serves similar function to M. capsulatus (Bath).(1)
The M. capsulatus genome contains 51 known insertion sequence elements from various families, such as 20 elements from the IS4 family. The majority of such elements are discovered with higher intragenome similarity. This suggests the expansion of these elements, since their introduction into the M. capsulaus genome, repeated cycles of duplication and subsequent deletion, or gene conversion. Twenty elements belonging to the IS4 family of insertion sequences encode a 366-amino-acid transposase with 100% amino acid sequence conservation between copies. One copy (MCA 1197) is found within the soluble methane monooxygenase operon, and this suggests that this element is highly mobile. Other examples of insertion also included disrupted genes encoding tRNA pseudouridine synthase and an exopolysaccharide export protein.(1,5)
Cell structure and metabolism
Methanotrophs have attracted considerable interest over the past 20 years because of their potential in producing bulk chemicals and single-cell protein and for use in biotransformation. Methanotrophs are unique in that they only grow on methane, although some will also grow on methanol.(2) "Methanotrophs are also able to metabolize or co-metabolize xenobiotic compounds, including chlorinated solvents such as trichloroethylene, and hence have potential as bioremediation tools." (2)
There are various metabolic pathways in Methylococcus capsulatus, including the methane oxidation pathway, mechanisms for carbon fixation, and nitrogen fixation, which will be discussed later in this section.
Methane oxidation pathway: Methanotrophs are unique in their possession of methane monooxygenases (MMOs), which catalyze the first step of methane oxidation. M. capsulatus is known to generate both a particulate membrane-bound form, pMMO, and a soluble form, sMMO, and these two enzymes have been well studied because their ability to perform methane oxidation.(6,7)
Carbon cycle: Carbon cycle is a process of turning the atmospheric carbon dioxide produced from combustion and respiration of all aerobes into anaerobic sediments via photo-and chemoautotrophy. Later, methanogens will generate methane from such organism. With the presence of heat and pressure, petroleum, coal, and peat can also be produced.(11)
Nitrogen fixation: "M. capsulatus is able to fix atmospheric nitrogen, conferring an advantage in environments where fixed nitrogen is limiting, and the structural genes for nitrogenase,nifH, nifD, and nifK, were previously shown to be contiguous, as they are in other nitrogen fixers."(7) This region include the genes nifE, nifN, and nifX, which are involved in synthesis of the nitrogenase iron-molybdenum cofactor; this organization has been found in Chlorobium tepidum and some nitrogen-fixing methanogenic Archaea. Two 2Fe-2S ferredoxins and genes identified as conserved hypotheticals are interspersed with the nif genes in the same orientation. The conserved hypothetical genes share the highest sequence similarity with genes from other organisms capable of nitrogen fixation, suggesting that they also have a role in this process.(7)
Ecology
The genome sequence of Methylococcus capsulatus was found useful to study “methane-fixing symboints,” because the majority of such organisms are usually discovered inside of live-animals and cannot be grown on pure culture.(2) Inherited the characteristic of Methanotrophs, M. capsulatus contributes to the earth's ecosystem greatly by consuming methane, a product derived from chemical process of landfills and in the guts of ruminant livestock and also by many oil and gas processing plants.In recent years, environmental scientists have shown increasing interest in methanotrophs because their use of methane as a sole source of carbon and energy could possibly be harnessed to play an important role in efforts to reduce methane emissions that are generated by biological sources.(7)
Pathology
Methylococcus capsulatus is not known to cause any diseases.
Application to Biotechnology
Methanotrophs produce an enzyme called methane monooxygenase (pMMO) that is not highly specific and can degrade TCE (trichloroethylene) and other compounds in addition to methane. Such enzyme are usually present in a small amount, to obtain an appropriate amount of this organism, the energy source, methane was pumped into the contaminated soils. As a necessity to perform hydrocarbon oxidation, oxygen was also pumped into soil for pMMO generation. One advantage for such mechanism is that, its reversible, hence, along with the absence of methane, methanotroph will return to its natural level. (3)
Methylococcus capculatus is perhaps the best studied and most useful methanotroph in the present microbiology world. pMMO is a membrane bound enzyme that can be purified from Methylococcus capculatus. This enzyme, as mentioned earlier, catalyzes the chemical process of oxidizing methane to methanol in methanotrophs, however, more surprising facts was found that enzyme pMMO is a dimer with both mononuclear copper and a copper-containing cluster. The purified enzyme, pMMO has a molecular mass of nearly 200 kDa along with an α2β2γ2 polypeptide arrangement. Each 200kDa were discovered to have approximately 4.8 copper ions and 1.5 iron ions. This experiment could only be done with great amount of pMMO enzyme, therefore, tremendous quantity of methane was conserved on agar plates to cultivate such enzyme. (3) From the use of Electron paramagnetic resonance spectroscopic parameters corresponding to 40 to 60% of the total copper are consisted of a mononuclear type 2 copper site. X-ray absorption indicate that purified pMMO is a mixture of Cu(I) and Cu(II) oxidation states. Finally, this experiment leads to a result showing the x-ray absorption fine structure data are best fit with oxygen or nitrogen ligands with a 2.57A copper to copper interaction, proving for a copper-containing cluster in enzyme pMMO.(3)
Current Research
The Research of "Quantitative Proteomic Analysis of Metabolic Regulation by Copper Ions in Methylococcus capsulatus" conducted by Department of Chemistry, National Taiwan University. This research focuses on copper ions that switch the oxidation of methane by soluble methane monooxygenase to particulate methane monooxygenase in Methylococcus capsulatus (Bath). This research leads toward the understanding of changes in cellular metabolism related to the transcriptional and metabolic switch. (13)
The research of "Methylococcus capsulatus (Bath) is a dimer with both mononuclear copper and a copper-containing cluster" conducted by Northwestern University. This research focuses on the existence of copper ions inside the enzyme pMMO, which is purified from the organism of M. capsulatus.(3)
The research titled "Temperature Affects Fatty Acids In Methylococcus capsulatus" conducted by Jahnke, Linda L. talks about the correlation between temperature and monounsaturated fatty acids which derived from methane-oxidizing M. capsulatus bacterium. (14)
Reference
1.Naomi Ward,1,2 Qivind Larsen,3 James Sakwa,1 Live Bruseth,4 Hoda Khouri,1 A. Scott Durkin,1 George Dimitrov,1 Lingxia Jiang,1 David Scanlan,1 Katherine H Kang,1 Matt Lewis,1 Karen E Nelson,1 Barbara Methé,1 Martin Wu,1 John F Heidelberg,1 Ian T Paulsen,1,5 Derrick Fouts,1 Jacques Ravel,1 Hervé Tettelin,1 Qinghu Ren,1 Tim Read,1 Robert T DeBoy,1 Rekha Seshadri,1 Steven L Salzberg,1,9 Harald B Jensen,4 Nils Kåre Birkeland,3 William C Nelson,1 Robert J Dodson,1 Svenn H Grindhaug,7 Ingeborg Holt,6 Ingvar Eidhammer,7 Inge Jonasen,7 Susan Vanaken,1 Terry Utterback,1 Tamara V Feldblyum,1 Claire M Fraser,1,8 Johan R Lillehaug,4 and Jonathan A Eisen. “Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) ” pp. 358- 418 2004 October 2nd
2.Brock, T. D Methylococcus capsulatus is a methane-oxidising bacterium that has great potential in bioremediation Vol. 5 pp.9-33. June 1st 2002. (2)
3.Raquel L. Lieberman, Deepak, Shrestha, Peter E. Doan, Brian M. Hoffman, Timothy L. Stemmler and Amy C. Rosenzweig. “Purified particulate methane monooxygenase from ”Methylococcus capsulatus (Bath) is a dimer with both mononuclear copper and a copper-containing cluster” Vol. 100 pp. 3820-3825 April 1, 2003. (3)
4.Kylie J. Walters, George T. Gassner, Stephen J, Lippard, Gerhard Wager. “Structure of the soluble methane monooxygenase regulatory protein B” Vol. 96 pp. 7877-7882, July 1999(4)
5.Ilker Uz, M. E. Rasche, T. Townsend, A.V. Ogram, A. S. Lindner. “Characterization of methanogenic and methanotrophic assemblages in landfill samples” pp. S202-S205 November 2003 (5)
6.J.B Yavitt, D.M. Downey, G.E.Lang, A.J.Sexston. “Methane consumption in Two Temperate Forest Soils” Vol. 9 pp.39-52, Jan 1990 (6)
7.Martin Bender, Ralf Conrad. “Microbial Oxidation of Methane, Ammonium and Carbon Monoxide and Turnover of Nitrous Oxide and Nitric Oxide in Soils”Vol. 27. pp97-112, 1994 (7)
8.Govorukhina, N.I., Kletsova, L.V., Tsygankov, Yu.D. Trotsenko, Yu.A., and Netrusov, A.I. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=414&lvl=3&lin=f&keep=1&srchmode=1&unlock(8)
9.DOE-Public, http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=21 (9)
10.Moselio Schaechter, John L. Ingraham, Frederic C. Neidhardt. “Microbe” pp.207-208, 2006(10)
11.Moselio Schaechter, John L. Ingraham, Frederic C. Neidhardt. “Microbe” pp.360-362, 2006(11)
12.Moselio Schaechter, John L. Ingraham, Frederic C. Neidhardt. “Microbe” pp.469-470, 2006(12)
13.Wei-Chun Kao, Yat-Ren Chen, Eugene C. Yi, Hookeun Lee, Qiang Tian, Keh-Ming Wu, Shih-Feng Tsai, Steve S.-F. Yu, Yu-Ju Chen, Ruedi Aebersold, Sunney I. Chan. "Quantitative Proteomic Analysis of Metabolic Regulation by Copper Ions in Methylococcus capsulatus" September 22, 2005 Manuscript M408013200 (13)
14.Jahnke, Linda L."Temperature Affects Fatty Acids In Methylococcus Capsulatus", Nasa Technology Report Server, Document ID 19930000093, 2005 September 30th. (14)
Edited by Ting Yuan Feng, student of Rachel Larsen and Kit Pogliano
KMG
