Archaea-like genes for C1-transfer enzymes in Planctomycetes:: Phylogenetic implications of their unexpected presence in this phylum

The unexpected presence of archaea-like genes for tetrahydromethanopterin (H4MPT)-dependent enzymes in the completely sequenced genome of the aerobic marine planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete Gemmata obscuriglobus strain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes in Planctomycetes and methylotrophic proteobacteria and performed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor of Bacteria and Archaea or were transferred laterally from the archaeal to the bacterial domain and therein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and bacterial H4MPT-dependent Cl-transfer may be proposed: (i) lateral gene transfer (LGT) from Archaea to a common ancestor of Proteobacteria and Planctomycetes seems more likely than the presence of the genes in the common ancestor of Bacteria and Archaea; (ii) a single event of interdomain LGT can be favored over two independent events; and (iii) the archaeal donor of the genes might have been a representative of the Methanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages.