Methylobacterium extorquens DM4
Names | Methylobacterium extorquens DM4 |
---|---|
Accession numbers | NC_012987, NC_012988, NC_012989 |
Background | Methylobacterium extorquens is a pink-pigmented facultative methylotrophic Gram-negative bacterium first isolated in 1960 in Oxford as an airborne contaminant growing on methylamine. The trait common to all Methylobacterium species is the ability to grow on one or several reduced one carbon (C1) compounds other than methane, most prominently methanol. They are often found associated with plants. It has been used as a workhorse to characterize the serine cycle for assimilation of the C1-unit of methylene tetrahydrofolate, a central intermediate in methylotrophic metabolism, and more recently the ethylmalonyl-CoA pathway for glyoxylate regeneration.Methylobacterium strain DM4 was isolated from industrial wastewater sludge in Switzerland, as part of efforts to characterize microorganisms able to degrade the organohalogenated pollutant dichloromethane (DCM). Unlike methanol and methylamine, which are mainly produced naturally, DCM is a highly produced synthetic compound which is rated as potentially carcinogenic for humans. It is highly volatile and water-soluble, making it a widespread contaminant in the environment. Most of the genomic determinants associated with methylotrophy are nearly identical in all strains with exceptions that illustrate the metabolic and genomic versatility of Methylobacterium species. M.extorquens (strain ATCC 14718 / DSM 1338 / AM1, METEA) possesses a unique methylamine dehydrogenase and accessory functions gene cluster (mau), indicating that strain DSM 5838 / DM4 employs an alternative system for growth with methylamine, while the dcm (dichloromethane degradation) gene region is present only in strain DM4. M. extorquens contains large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity (adapted from PMID 19440302). (HAMAP: METED) |
Taxonomy | |
Kingdom: | Bacteria |
Phylum: | Proteobacteria |
Class: | Alphaproteobacteria |
Order: | Rhizobiales |
Family: | Methylobacteriaceae |
Genus: | Methylobacterium |
Species: | extorquens |
Strain | DM4 |
Complete | Yes |
Sequencing centre | (15-JUL-2009) Genoscope - Centre National de Sequencage : BP 191 91006 EVRY cedex - FRANCE (E-mail : seqref@genoscope.cns.fr (19-JUL-2009) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA |
Sequencing quality | Level 6: Finished |
Sequencing depth | NA |
Sequencing method | NA |
Isolation site | Soil contaminated with halogenated (chlorine-containing) hydrocarbons |
Isolation country | Switzerland |
Number of replicons | 3 |
Gram staining properties | Negative |
Shape | Bacilli |
Mobility | Yes |
Flagellar presence | NA |
Number of membranes | 2 |
Oxygen requirements | Aerobic |
Optimal temperature | NA |
Temperature range | Mesophilic |
Habitat | Terrestrial |
Biotic relationship | Free living |
Host name | NA |
Cell arrangement | Pairs, Singles |
Sporulation | Nonsporulating |
Metabolism | NA |
Energy source | Methylotroph |
Diseases | NA |
Pathogenicity | No |
Glycolysis / Gluconeogenesis
Citrate cycle (TCA cycle)
Pentose phosphate pathway
Fatty acid metabolism
Synthesis and degradation of ketone bodies
Purine metabolism
Pyrimidine metabolism
Alanine, aspartate and glutamate metabolism
Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Valine, leucine and isoleucine degradation
Valine, leucine and isoleucine biosynthesis
Lysine biosynthesis
Arginine and proline metabolism
Histidine metabolism
Phenylalanine, tyrosine and tryptophan biosynthesis
Selenocompound metabolism
Cyanoamino acid metabolism
D-Glutamine and D-glutamate metabolism
D-Arginine and D-ornithine metabolism
D-Alanine metabolism
Glutathione metabolism
Streptomycin biosynthesis
Lipopolysaccharide biosynthesis
Peptidoglycan biosynthesis
Pyruvate metabolism
Chloroalkane and chloroalkene degradation
Glyoxylate and dicarboxylate metabolism
Propanoate metabolism
Butanoate metabolism
C5-Branched dibasic acid metabolism
One carbon pool by folate
Methane metabolism
Carbon fixation in photosynthetic organisms
Thiamine metabolism
Riboflavin metabolism
Vitamin B6 metabolism
Nicotinate and nicotinamide metabolism
Pantothenate and CoA biosynthesis
Biotin metabolism
Lipoic acid metabolism
Folate biosynthesis
Porphyrin and chlorophyll metabolism
Terpenoid backbone biosynthesis
Nitrogen metabolism
Sulfur metabolism
Aminoacyl-tRNA biosynthesis
Citrate cycle (TCA cycle)
Pentose phosphate pathway
Fatty acid metabolism
Synthesis and degradation of ketone bodies
Purine metabolism
Pyrimidine metabolism
Alanine, aspartate and glutamate metabolism
Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Valine, leucine and isoleucine degradation
Valine, leucine and isoleucine biosynthesis
Lysine biosynthesis
Arginine and proline metabolism
Histidine metabolism
Phenylalanine, tyrosine and tryptophan biosynthesis
Selenocompound metabolism
Cyanoamino acid metabolism
D-Glutamine and D-glutamate metabolism
D-Arginine and D-ornithine metabolism
D-Alanine metabolism
Glutathione metabolism
Streptomycin biosynthesis
Lipopolysaccharide biosynthesis
Peptidoglycan biosynthesis
Pyruvate metabolism
Chloroalkane and chloroalkene degradation
Glyoxylate and dicarboxylate metabolism
Propanoate metabolism
Butanoate metabolism
C5-Branched dibasic acid metabolism
One carbon pool by folate
Methane metabolism
Carbon fixation in photosynthetic organisms
Thiamine metabolism
Riboflavin metabolism
Vitamin B6 metabolism
Nicotinate and nicotinamide metabolism
Pantothenate and CoA biosynthesis
Biotin metabolism
Lipoic acid metabolism
Folate biosynthesis
Porphyrin and chlorophyll metabolism
Terpenoid backbone biosynthesis
Nitrogen metabolism
Sulfur metabolism
Aminoacyl-tRNA biosynthesis