Structure and Evolution of Chlorate Reduction Composite Transposons

Abstract

The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.

Phenotypic and Genotypic Description of Sedimenticola selenatireducens Strain CUZ, a Marine (Per)Chlorate-Respiring Gammaproteobacterium, and Its Close Relative the Chlorate-Respiring Sedimenticola Strain NSS

“…Given the high 16S rRNA gene sequence similarity between these strains, it is somewhat surprising that they have distinct approaches to chlorate metabolism. However, both the (per)chlorate reduction gene complex (i.e., the PRI) and the chlorate reduction gene complex are associated with transposases (29,39), supporting mounting evidence that these complexes are transferred horizontally (11). Recent horizontal gene transfer may explain why these closely related species nonetheless have distinct approaches to (per)chlorate metabolism.…”

“…Although both Clr and Pcr belong to the dimethyl sulfoxide reductase family of molybdenum-containing proteins, they belong to distinct clades. ClrA is polyphyletic (29), whereas to the best of our knowledge, PcrA is monophyletic (unpublished results). Given the high 16S rRNA gene sequence similarity between these strains, it is somewhat surprising that they have distinct approaches to chlorate metabolism.…”

“…5A), and as such, its architecture resembled those of the recently published PRB Arcobacter sp. strain CAB (18) and other chlorate reducers (29). No genes encoding a separate chlorate reductase were found.…”

“…1) that shared 98% 16S rRNA gene sequence identity with both S. selenatireducens AK4OH1 and S. selenatireducens CUZ. In previous publications, this isolate was unofficially designated Dechloromarinus chlorophilus strain NSS (11,19,29), but in light of its phylogenetic relatedness to the Sedimenticola species subsequently described formally, we consider NSS to be a strain of the genus Sedimenticola. In addition to their relatedness to S. selenatireducens AK4OH1, strains CUZ and NSS were both closely related to the thiotaurinedegrading autotroph Thiotaurens thiomutagens (30) (97% and 98% 16S rRNA gene sequence similarity, respectively) ( Fig.…”

“…The genome of strain NSS encoded chlorate reduction genes flanked by insertion sequences, forming composite transposons. Composite chlorate reduction transposons have recently been shown to be a common property of CRB and represent mobile genetic units by which chlorate metabolism may be transferred (29). The genome of strain NSS carried the genes necessary for chlorate reduction: those encoding the chlorate reduc- (Fig.…”