Methylobacterium extorquens DM4

TEM image (75,000x) of Methylobacterium dichloromethanicum DM4 growing with dichloromethane (DCM), immunolabelled using the protein A-gold technique with a DCM dehalogenase specific antibody, and showing the cytoplasmic localization of this biodegradative enzyme, whose expression is induced by DCM (photo R. Hermann).

Microbes growing on one-carbon compounds have long captured the interest of scientists. How do these organisms make multi-carbon compounds from molecules without C-C bonds? Among those, aerobic alpha-proteobacteria of the Methylobacterium genus have been much favoured objects of investigation, as much for their distinctive red colour as for their intriguing core metabolic pathways that feature both bacterial - and archaeal - like genes, their ability to escape the toxicity of formaldehyde as a key metabolic intermediate, and the promise of making organic molecules of biotechnological value from low-cost materials such as methanol.

A first complete genome sequence of the reference strain of the Methylobacterium genus, M. extorquens AM1 has now been completed in the US American partner laboratory (Chistoserdova et al., 2003).

The specific interest in sequencing the genome of a pollutant-resistant bacterium of the same genus is to drive forward detailed investigations of the genomic basis of biological adaptations to toxic halogenated organic compounds. In microorganisms, these adaptations feature two main aspects:

• the ability to degrade toxic compounds, often used by the corresponding microorganisms as sole source of a life-essential element for growth, and/or
• the ability to withstand high concentrations of toxic compounds, e.g. through membrane strengthening and/or compound excretion, or inactivation.

Several well characterised Methylobacterium species grow with halogenated methanes (i.e. dichloromethane or chloromethane) as the sole carbon source. The dichloromethane degrading strain Methylobacterium extorquens DM4* whose genome has now been sequenced was isolated from soil from a treatment plant for halogenated hydrocarbon waste in the late seventies, following the inclusion of dichloromethane in the first list of priority pollutant by the EPA. It has now been investigated intensively at the physiological, enzymatic and genetic level for more than two decades (Vuilleumier, 2002). Strain DM4 provides an attractive paradigm, stripped down to its bare essentials (one carbon and one or two halogen substituents), for addressing many aspects of microbial degradation of halogenated toxic organic compounds. Do specific membrane proteins for pollutant transport in and out of the microbial cell exist? How is the hydrochloric acid produced intracellularly during the degradation of halogenated pollutants excreted? Do microorganisms that degrade genotoxic halogenated organic compounds feature adaptations of their DNA repair machinery?

The availability of the genome sequence of the DM4 strain, and its comparison to the available sequence of the Methylobacterium type strain which is unable to degrade dichloromethane, should provide new elements of answers to these and other related questions, and thus bears the promise of yielding significant new findings on the adaptations of microbes to pollutants at the genetic level.

*First named Methylobacterium dichloromethanicum, the sequenced strain belongs to the Methylobacterium extorquens species.