Methylobacterium extorquens AM1

 

♦ Strain information

Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. Methylobacterium extorquens AM1 is capable of growth on one-carbon compounds such as methanol. Methanol is oxidized to formaldehyde which is then used metabolically to generate either energy or biomass. These bacteria are commonly found in the environment, especially associated with plants which produce methanol when metabolizing pectin during cell wall synthesis. The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids. [Vuilleumier 2009]

 

♦ Genome information

- NCBI genome:                     http://www.ncbi.nlm.nih.gov/genome/693
- Lineage: Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Methylobacteriaceae; Methylobacterium; Methylobacterium extorquens group; Methylobacterium extorquens (NCBI taxonomy ID: 272630)
 
- NCBI RefSeq accession (1 chromosom, 1 megaplasmid, 3 plasmids):
NC_012808 (chromosome: 5,511,322 bp)
NC_012811 (megaplasmid: 1,261,460 bp)
NC_012807 (plasmid p1META1: 44,195 bp)
NC_012809 (plasmid p2META1: 37,858 bp)
NC_012810 (plasmid p3META1: 24,943 bp)
 
- Genome paper:
Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Médigue C, Lidstrom ME “Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources” PLoS One, 4(5):e5584 (2009)
 
 

♦ Genome browser

- NC_012808 (chromosome: 5,511,322 bp)
 

♦ Antibiotics & secondary metabolites

- NC_012809 (plasmid p2META1) : Not found
- NC_012810 (plasmid p3META1) : Not found

 

♦ Transcriptome structure

- Visualization of high-density data (e.g. RNAseq, ChIP-chip, tiling microarray) against coordinates on the genome

- Following data set can be visualized by Gaggle Genome Browser (Note: this link downloads large data files (~60-190MB)  at initial access) (Java need to be installed on your computer.)   

- GEO accession: GSE42116 (30 samples)
- Tiling array platform: GPL16255 (Marx lab 2012 Harvard University custom Agilent 60-mer array with 15K+ features for Methylobacterium extorquens AM1)
 

♦ Conditional regulons

 

♦ Metabolic network model

 

♦ Gene regulatory network model

 

♦ Phenotype Microarrays

- Phenotype Microarrays testing nearly 2000 cellular phenotypes simultaneously (Biolog PM Technology)