Structure of Haloacetate-Catabolic IncP-1β Plasmid pUO1 and Genetic Mobility of Its Residing Haloacetate-Catabolic Transposon

Abstract

The self-transmissible plasmid pUO1 from Delftia acidovorans strain B carries two haloacetate-catabolic transposons, TnHad1 and TnHad2, and the mer genes for resistance to mercury. The complete 67,066-bp sequence of pUO1 revealed that the mer genes were also carried by two Tn402/Tn5053-like transposons, Tn4671 and Tn4672, and that the pUO1 backbone regions shared 99% identity to those of the archetype IncP-1␤ plasmid R751. Comparison of pUO1 with three other IncP-1␤ plasmids illustrated the importance of transposon insertion in the diversity and evolution of this group of plasmids. Mutational analysis of the four outermost residues in the inverted repeats (IRs) of TnHad2, a Tn21-related transposon, revealed a crucial role of the second residue of its IRs in transposition.It has been demonstrated that bacterial genes for the degradation of various xenobiotic compounds are often loaded on transposable elements that are mainly classified into two major groups: class I and class II transposons (14). The class I transposon is a mobile element in which a short DNA segment is flanked by two copies of an insertion sequence (IS). The class II transposon usually carries transposase (TnpA), resolvase (TnpR), and a resolution (res) site between short terminal inverted repeats (IRs) and transposes by a two-step processcointegration and resolution (3, 9). Broad-host-range and selftransmissible plasmids are well known to contribute to the wide dissemination of these catabolic transposons (13). The successful conjugal transfer of these plasmids facilitates the spread of the catabolic transposons and at times promotes the evolution of novel catabolic pathways by genetic rearrangements (15). A 67-kb self-transmissible and broad-host-range but not-well characterized plasmid, pUO1, from Delftia acidovorans strain B carries, in addition to the mer genes for resistance to mercury, two haloacetate dehalogenase genes (dehH1 and dehH2) on the two transposons, TnHad1 and TnHad2 (Fig. 1A) (10). TnHad1, with a size of 8.9 kb, is a class I transposon that carries dehH2 between two directly repeated copies of IS1071 (8), and dehH1 and TnHad1 are loaded on a 15.6-kb class II transposon, TnHad2, that lacks the tnpA and tnpR genes (Fig. 1A) (10). TnHad2 has the 38-bp terminal IRs, IR1 and IR3, and the res site (Fig. 1A and 2A), each of which shares extensive homology to the corresponding sequence of Tn21, and the supply in trans of the Tn21 transposition genes enables the complete transposition of TnHad2 (10). The sequence of IR2, which is highly homologous to IR1, is also located very close to the res site, although the 5Ј end of IR2 on pUO1 is occupied by the C residue (Fig. 1A and 2A). In our previous study (10), we replaced this C residue with the T residue, and the mini-TnHad2 derivative flanked by this IR2 derivative (5Ј-TGGG end) and IR1 (5Ј-GGGG end) (Fig. 2B) was found to transpose at a high frequency in the presence of the Tn21 tnpA gene. This finding was unexpected, since (i) the outermost four G residues of the IRs are conserved in ...

Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1β plasmids without accessory mobile elements

“…Most of these accessory genes are inserted in one or both of two specific regions of the backbone, e.g. the IncP-1b plasmid pUO1 contains two haloacetate-catabolic transposons in the oriV-trfA region and two mercury-resistance transposons in the trb-tra region (Sota et al, 2003). In general, IncP-1 plasmids have at least one accessory gene (encoding degradation of xenobiotic compounds or resistance to antibiotics or heavy metals) that has been postulated to be acquired during adaptive evolution of this group of 3Present address: Tamai Pediatric Clinic, Oita, Japan.…”

Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment

“…Consistent with this observation, IncP1-␤ plasmids are broad host range; that is, they have the ability to replicate, and thus be stably maintained, in a broad range of bacterial genera (56). The resistance and biodegradation genes were always found inserted into two regions of the IncP1-␤ plasmid backbone near inverted repeat elements that probably serve as recognition sites for transposons (54). Thus, these plasmids may vary widely in size and the types of genes they carry according to the selective pressure imposed in given environmental pockets.…”

“…Plasmid pADP-1 consists of 108,845 base pairs and was identified as belonging to a plasmid class known as the IncP-1␤ group (52). The plasmid backbone of pADP-1 shows 99% sequence identity to comparable regions of the following sequenced plasmids: (a) pR751 from Enterobacter aerogenes encoding trimethoprin resistance (53), (b) pUO1 from Delftia acidovorans encoding for the biodegradation of haloacetate (54), and (c) pB4 that was isolated from an environmental community of microorganisms and encoding resistance to chromate and various antibiotics (55).…”

“…work to determine their complete DNA sequences (54,(57)(58)(59). The DNA sequences obtained to date suggest that the catabolic plasmid genes have been assisted in their dissemination by insertion sequence (IS) elements.…”

IncP-1β plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet

“…CP000443). Thus, the plasmids pKV11, pKV29 and pKV36 clearly belong to the IncP-1b incompatibility group and their trfA nucleotide sequences cluster within the subgroup of plasmids represented by the catabolic plasmids pGNB1, pJP4 (Trefault et al, 2004), pUO1 (Sota et al, 2003) and pADP-1 (Martinez et al, 2001), the antibiotic-resistance plasmids pB8 (Schlüter et al, 2005) and pB10 (Schlüter et al, 2003), and the mercury-resistance plasmid pTP6 (Smalla et al, 2006).…”