Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria

Abstract

Dichloromethane (DCM) dehalogenases enable facultative methylotrophic bacteria t o utilize DCM as sole carbon and energy source. DCM-degrading aerobic methylotrophic bacteria expressing a type A DCM dehalogenase were previously shown to share a Conserved 4.2 kb BamHl DNA fragment containing the dehalogenase structural gene, dcmA, and dcmR, the gene encoding a putative regulatory protein. Sequence analysis of a 10 kb DNA fragment including this region led to the identification of three types of insertion sequences identified as 157354, IS7355 and 157357, and also two ORFs, orf353and orf792, of unknown function. Two identical copies of element 157354 flank the conserved 4.2 kb fragment as a direct repeat. The occurrence of these newly identified 15 elements was shown to be limited to DCM-utilizing methylotrophs containing a type A DCM dehalogenase. The organization of the corresponding dcm regions in 12 DCM-utilizing strains was examined by hybridization analysis using IS-specif ic probes. Six different groups could be defined on the basis of the occurrence, position and copy number of IS sequences. All groups shared a conserved 5.6 kb core region with dcmA, dcmR, orf353 and orf192 as well as 157357. One group of strains including Pseudomonss sp. DM1 contained two copies of this conserved core region. The high degree of sequence conservation observed within the genomic region responsible for DCM utilization and the occurrence of clusters of insertion sequences in the vicinity of the dcm genes suggest that a transposon is involved in the horizontal transfer of the DCM-utilization character among methylotrophic bacteria.

Phylogeny Poorly Predicts the Utility of a Challenging Horizontally Transferred Gene in Methylobacterium Strains

“…Within this genomic island, the dcm cluster contains three other genes, including the transcriptional regulator dcmR and two proteins of unknown function dcmB and dcmC and is flanked on both sides by IS1354 elements. This four-gene dcm islet is conserved within most DCM-degrading strains (18). However, a strain of M. extorquens DM4 with a deletion of the genomic island, known as DM4-2cr (20), requires only the dcmA gene to recover growth on DCM (21).…”

“…Among several strains isolated for their ability to grow on DCM as the sole carbon and energy source (15,16), a strain of Methylobacterium extorquens known as DM4 has been investigated in the most detail. Through HGT, this strain has acquired a gene, dcmA, encoding a cytoplasmic glutathione S-transferase that converts DCM to formaldehyde, with the concomitant release of two molecules of hydrochloric acid (17,18). In M. extorquens DM4, the dcmA gene lies within a 126-kb genomic island that shows clear evidence of horizontal transfer, including a lower GC content (19).…”

Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer byDehalococcoides ethenogenesStrain 195

“…Among them, the best characterized are the haloalkane dehalogenase of Rhodococcus rhodochrous (28,46), the haloacetate dehalogenases of Xanthobacter autotrophicus (59) and Delftia acidovorans (53), and the dichloromethane dehalogenase in methylotrophic bacteria (49). More closely related to the numerous putative reductive dehalogenases of Dehalococcoides ethenogenes strain 195, a recent study revealed that the tetrachloroethene reductive dehalogenase genes (pceAB) of Desulfitobacterium hafniense strain TCE1 was embedded in a composite transposon, TnDha1, and that this transposon is probably also present in two other Desulfitobacterium strains.…”

Identification and cloning of a gene encoding dichloromethane dehalogenase from a methylotrophic bacterium, Bacillus circulans WZ-12 CCTCC M 207006

“…DM11 from solvent-contaminated sludge, and methylotrophs DM6 and facultative DM5 isolated from various solvent-polluted soil. Few representatives of glutathione S-transferases are yet known in bacteria [4,5]. Only sequence data are available in most cases, although results with bacterial enzymes for which biochemical investigations have been carried out suggest enzymatic functions not usually observed in eukaryotic GST [6,7].…”

“…Bacteria, capable of growth with DCM as the sole source of carbon and energy under both aerobic and anaerobic conditions, have been isolated over the past two decades [4]. These include Hyphomicrobium sp DM2 and Methylobacterium sp DM4 isolated from groundwater, Methylophilus sp.…”