Phylogenetic analysis of erythritol catabolic loci within the Rhizobiales and Proteobacteria
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Date
2013-02-23
Authors
Geddes, Barney A
Hausner, Georg
Oresnik, Ivan J
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Abstract
Abstract
Background
The ability to use erythritol as a sole carbon source is not universal among
the Rhizobiaceae. Based on the relatedness to the catabolic genes in
Brucella it has been suggested that the eryABCD operon
may have been horizontally transferred into Rhizobium. During work
characterizing a locus necessary for the transport and catabolism of
erythritol, adonitol and L-arabitol in Sinorhizobium meliloti, we
became interested in the differences between the erythritol loci of S.
meliloti and R. leguminosarum. Utilizing the Ortholog
Neighborhood Viewer from the DOE Joint Genome Institute database it appeared
that loci for erythritol and polyol utilization had distinct arrangements
that suggested these loci may have undergone genetic rearrangements.
Results
A data set was established of genetic loci containing erythritol/polyol
orthologs for 19 different proteobacterial species. These loci were analyzed
for genetic content and arrangement of genes associated with erythritol,
adonitol and L-arabitol catabolism. Phylogenetic trees were constructed for
core erythritol catabolic genes and contrasted with the species phylogeny.
Additionally, phylogenetic trees were constructed for genes that showed
differences in arrangement among the putative erythritol loci in these
species.
Conclusions
Three distinct erythritol/polyol loci arrangements have been identified that
reflect metabolic need or specialization. Comparison of the phylogenetic
trees of core erythritol catabolic genes with species phylogeny provides
evidence that is consistent with these loci having been horizontally
transferred from the alpha-proteobacteria into both the beta and
gamma-proteobacteria. ABC transporters within these loci adopt 2 unique
genetic arrangements, and although biological data suggests they are
functional erythritol transporters, phylogenetic analysis suggests they may
not be orthologs and probably should be considered analogs. Finally,
evidence for the presence of paralogs, and xenologs of erythritol catabolic
genes in some of the genomes included in the analysis is provided.
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Citation
BMC Microbiology. 2013 Feb 23;13(1):46