Methylococcus capsulatus: Difference between revisions

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In the article, “Scientists explore genome of methane-breathing microbe” released on September 20th, 2004 by Robert Koenig, the genome sequence of Methylococcus capsulatus was found useful to study “methane-fixing symboints,” because majority of such organisms are usually discovered inside of live animals and cannot be grown on pure culture. 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 the article, “Scientists explore genome of methane-breathing microbe” released on September 20th, 2004 by Robert Koenig, the genome sequence of Methylococcus capsulatus was found useful to study “methane-fixing symboints,” because majority of such organisms are usually discovered inside of live animals and cannot be grown on pure culture. 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.
The genome sequence of Methylococcus capsulatus – a species typical of methane-breathing bacteria commonly found in soils, landfills, sediments and peat bogs – includes a full and at times redundant toolkit of genes for using methane as an energy and carbon source. Such methane-consuming microbes are called methanotrophs.
The genome sequence of Methylococcus capsulatus – a species typical of methane-breathing bacteria commonly found in soils, landfills, sediments and peat bogs – includes a full and at times redundant toolkit of genes for using methane as an energy and carbon source. Such methane-consuming microbes are called methanotrophs.
The study, to be published in the October issue of PLoS Biology and posted online this week, found an unexpected flexibility in M. capsulatus metabolic pathways, hinting that the bacterium is capable of responding to changes in its environment by functioning through different chemical pathways for using methane. That finding, if confirmed by later experiments, may increase the bacterium's potential as a biotech workhorse.
Methanotrophs play an important role in the global energy cycle because they consume methane, a gas that is produced mostly by chemical processes in landfills, in the guts of ruminant livestock such as cows, and by oil and natural 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 such as ruminants and landfills.
The PLoS Biology study found that M. capsulatus has multiple pathways for different stages in the oxidation of methane. They also found genes that suggest metabolic flexibility, including the microbe's likely ability to grow on sugars, to oxidize sulfur, and to live in reduced-oxygen environments.
"We now have a much better picture of the relationship between M. capsulatus and its environment," says Naomi Ward, the paper's first author. "It is important for us to know under what conditions methane can be removed from the ecosystem before it accumulates as a greenhouse gas."
Ward is an Assistant Investigator at The Institute for Genomic Research (TIGR), which led the genomic sequencing and conducted the analysis with scientific collaborators at the University of Bergen in Norway.
While noting that "there is a clear need for experimental validation" of the metabolic pathways suggested by the genome, the study's authors suggest that their analysis "deepens our understanding of methanotroph biology, its relationship to global carbon cycles, and its potential for biotechnological applications."
Johan Lillehaug, the Norwegian scientist who oversaw the University of Bergen's role in the project, says the genome analysis found that M. capsulatus has a novel strategy for scavenging copper, an essential element for regulating methane oxidation. "We found that M. capsulatus is a good model for studying how microbes adapt to varying copper concentrations," he says, noting that M. capsulatus uses two separate systems – at high and low copper concentrations – for oxidizing methane.


==Pathology==
==Pathology==

Revision as of 14:30, 5 June 2007

A Microbial Biorealm page on the genus Methylococcus capsulatus

Classification

Higher order taxa

Kingdom: Bacteria Domain: Proteobacteria Phylum: Gammaproteobacteria Class: Methylococcales Order: Methylococcaceae Family: Methylococcus

Species

  1. Genus: Methylococcus
  1. Species: capsulatus

Description and significance

Methylococcus capsulatus is a methylotrophic “Gram-negative” bacterium with coccus shape, live in multiple habitats, however, oxygen is a necessity for such cell to survive. Methylococcus capsulatus is also a thermophilic microbe which optically live in the temperature of 45C. Methylococcus capsulatus is isolated from Methanotrophic bacterium, which serves a unique biological function in earth's environment. Methanotrophic bacteria is able to generate Green House gas, Methane, as an energy source for growth (detail mechanism refer to section, cell structure and metabolism), and contribute to lower the methane level in earth's atmosphere. Methylococcus capsulatus.jpg

Genome structure

The Complete genome of M. capsulatus (Bath) Genome is consisted with 3,304,697 base pairs along 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). The M. capsulatus genome contains 51 known insertion sequence elements from various families, such as 20 elements are found in IS4 family. 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 suggesting that this element is highly mobile. Other examples of insertion also included disrupted genes encoding tRNA pseudouridine synthase and an exopolysaccharide export protein.

Cell structure and metabolism

"Methylococcus capsulatus is a methanotroph (Methane-oxidising bacteria.) Methanotrophs are ubiquitous Gram-negative bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere."

"Methanotrophs are also able to metabolize or co-metabolize xenobiotic compounds, including chlorinated solvents such as trichloroethylene, and hence have potential as bioremediation tools."

Ecology

In the article, “Scientists explore genome of methane-breathing microbe” released on September 20th, 2004 by Robert Koenig, the genome sequence of Methylococcus capsulatus was found useful to study “methane-fixing symboints,” because majority of such organisms are usually discovered inside of live animals and cannot be grown on pure culture. 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. The genome sequence of Methylococcus capsulatus – a species typical of methane-breathing bacteria commonly found in soils, landfills, sediments and peat bogs – includes a full and at times redundant toolkit of genes for using methane as an energy and carbon source. Such methane-consuming microbes are called methanotrophs.

Pathology

The research of disease cause by Methylococcus capsulatus is still in discovering.

Application to Biotechnology

Application to Biotechnology Does this organism produce any useful compounds or enzymes? What are they and how are they used? 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 process is that its reversible, hence, along with the absence of methane, methanotroph will return to its natural level. 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. From the use of Electron paramagnetic resonance spectroscopic parameters corressponding 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/nitrogen ligands with a 2.57A copper to copper interaction, proving for a copper-containing cluster in enzyme pMMO.

Current Research

Arch Microbiol. 2005 Nov 26; :1-16 16311759

Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Frode Berven , Odd Karlsen , Anne Straume , Kristian Flikka , J Murrell , Anne Fjellbirkeland , Johan Lillehaug , Ingvar Eidhammer , Harald Jensen High-resolution two-dimensional gel electrophoresis and mass spectrometry has been used to identify the outer membrane (OM) subproteome of the Gram-negative bacterium Methylococcus capsulatus (Bath). Twenty-eight unique polypeptide sequences were identified from protein samples enriched in OMs. Only six of these polypeptides had previously been identified. The predictions from novel bioinformatic methods predicting beta-barrel outer membrane proteins (OMPs) and OM lipoproteins were compared to proteins identified experimentally. BOMP ( http://www.bioinfo.no/tools/bomp ) predicted 43 beta-barrel OMPs (1.45%) from the 2,959 annotated open reading frames. This was a lower percentage than predicted from other Gram-negative proteomes (1.8-3%). More than half of the predicted BOMPs in M. capsulatus were annotated as (conserved) hypothetical proteins with significant similarity to very few sequences in Swiss-Prot or TrEMBL. The experimental data and the computer predictions indicated that the protein composition of the M. capsulatus OM subproteome was different from that of other Gram-negative bacteria studied in a similar manner. A new program, Lipo, was developed that can analyse entire predicted proteomes and give a list of recognised lipoproteins categorised according to their lipo-box similarity to known Gram-negative lipoproteins ( http://www.bioinfo.no/tools/lipo ). This report is the first using a proteomics and bioinformatics approach to identify the OM subproteome of an obligate methanotroph.

Reference

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Bird, C. W., Lynch, J. M., Pirt, F. J., Reid, W. W., Brooks, C. J. W., and Middleditch, B. S. (1971) Nature

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Edited by Ting Yuan Feng, student of Rachel Larsen at UCSD.Sci. U. S. A.

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