Model system: Methylotrophy
Methylotrophy is the capacity to aerobically utilize single-carbon (C1) compounds as a sole source of carbon and energy. This consists of three stages: 1.) oxidation of C1 compounds to formaldehyde, 2.) dissimilation of formaldehyde to CO2, and 3.) assimilation of formaldehyde into biomass. What is remarkable about this capacity is that nearly all such C1 compounds are oxidized to formaldehyde as a central metabolite, which itself can be burned for energy or drawn into assimilatory metabolism.
This presents an intriguing problem: fast growth requires a high flux through formaldehyde, but the pool must remain low or else it would pickle the cell. It has been calculated that if formaldehyde production went unchecked by utilization for just one minute, the cell would fill to over 100 mM formaldehyde. Thus, methylotrophs must maintain a healthy balance of production/consumption, while also efficiently proportioning carbon to assimilatory and dissimilatory metabolism? (See ref 12 in publications for the most recent picture as to how this is accomplished.)
So why study methylotrophy?
There are multiple aspects to methylotrophy that make it a wonderful model system. On the practical side, methylotrophs play a key role in the global cycling of C1 compounds (such as methane) and offer intriguiging biotechnological opportunities for the production of commodity chemicals from methanol. As mentioned above their physiology revolving around the internal production and consumption of a toxic intermediate, formaldehyde, is fascinating and involves the action of multiple unique metabolic modules that are not commonly present in other organisms.
It is the apparent evolutionary history of methylotrophy, however, that is perhaps the most compelling reason to pursue these organisms for our studies. First, methylotrophy clearly does not have a monophyletic origin. Examination of a phylogenetic tree of bacteria shows that methylotrophs are found in multiple clades of bacteria with non-methylotrophic sister taxa. However, the genes required for methylotrophic growth are highly conserved amongst methylotrophs, are found in large gene clusters, and have phylogenies that are often incongruent with that of the “organismal” 16S rDNA tree. These observations are consistent with methylotrophic lineages having arose multiple times, apparently as a consequence of horizontal gene transfer (HGT, genetic exchange between microbes -sometimes from different clades entirely) of methylotrophy gene clusters.
Methylobacterium extorquens AM1
M. extorquens AM1 is the best-understood methylotroph. It is an alpha-proteobacterium closely related to rhizobia and is a facultative methylotroph (can grow on C1 and multicarbon substrates). The figure to the right of a clover leafprint applied to a methanol-containing plate illustrates its niche as a leaf epiphyte (and yes, leaves really do make methanol – lots of it).
Approximately 100 methylotrophy genes have been identified thus far in Methylobacterium and the genome sequence (~8 MB) is nearly completed. Furthermore, a stoichiometric model of central metabolism has beeng generated and tested, expression microarrays and proteomic methods have been developed, and a series of genetic tools have been developed. These advances have made Methylobacterium a powerful model organsim.