Diversity of Methylotrophy Pathways in the Genus Paracoccus (Alphaproteobacteria)

Paracoccus denitrificans Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of methanol or methylamine. The growing availability of genome sequence data has made it possible to investigate methylotrophy in other Paracoccus species. The examination of a large number of Paracoccus spp. genomes reveals great variability in C-1 metabolism, which have been shaped by different evolutionary mechanisms. Surprisingly, the methylotrophy schemes of many Paracoccus strains appear to have quite different genetic and biochemical bases. Besides the expected 'autotrophic methylotrophs', many strains of this genus possess another C-1 assimilatory pathway, the serine cycle, which seems to have at least three independent origins. Analysis of the co-occurrence of different methylotrophic pathways indicates, on the one hand, evolutionary linkage between the Calvin cycle and the serine cycle, and, on the other hand, that genes encoding some C-1 substrate-oxidizing enzymes occur more frequently in association with one or the other. This suggests that some genetic module combinations form more harmonious enzymatic sets, which act with greater efficiency in the methylotrophic process and thus undergo positive selection.