Phylogeny of bacterial methylotrophy genes reveals robustness in Methylobacterium mxaF sequences and mxa operon construction

Abstract

mxaF, the structural gene for the methanol dehydrogenase (MDH enzyme), encodes for alpha subunit of the MDH enzyme. This member of the mxa family is required for production of a functional MDH enzyme. Methylobacterium species, pink-pigmented facultatively methylotrophic bacteria (PPFMs), are plant colonizing, methylotrophic bacteria that utilize methanol as a carbon and energy source during phyllosphere and rhizosphere growth. In a previous study that examined the phylogeny of soil and blueberry skin biofilm isolates, mxaF sequence was found to be a more useful indicator of species distinction within the Methylobacterium genus than 16S rRNA gene sequence and that it was not influenced by several environmental properties, including pH. Here, the phylogeny of methylotrophy genes including mxaF is examined to assess the potential for use of mxaF sequence as a biomarker for the Methylobacterium genus. A phylogenetic comparison of 311 archived PPFM and non-PPFM GenBank bacterial sequences of mxaF, xoxF, and generically annotated PQQ-dependent dehydrogenase genes in the methanol/ethanol family was conducted, including 270 mxaF, mxaF′ and mxaF-like sequences. In addition, construction of operons within the mxa gene family was compared using GenBank completed genome sequences to investigate potential horizontal gene transfer (HGT) events within the mxa methylotrophy system. mxaF sequence and mxa gene family operon construction was found to be highly conserved within the genus Methylobacterium as compared to other bacterial genera. The data reveal evidence of HGT events between Methylobacterium species and other bacterial genera as well as the potential for mxaF sequence to be used as a taxonomic indicator for environmental Methylobacterium strains.