Complete Nucleotide Sequence of TOL Plasmid pDK1 Provides Evidence for Evolutionary History of IncP-7 Catabolic Plasmids

Abstract

To understand the mechanisms for structural diversification of Pseudomonas-derived toluene-catabolic (TOL) plasmids, the complete sequence of a self-transmissible plasmid pDK1 with a size of 128,921 bp from Pseudomonas putida HS1 was determined. Comparative analysis revealed that (i) pDK1 consisted of a 75.6-kb IncP-7 plasmid backbone and 53.2-kb accessory gene segments that were bounded by transposon-associated regions, (ii) the genes for conjugative transfer of pDK1 were highly similar to those of MOB H group of mobilizable plasmids, and (iii) the toluene-catabolic (xyl) gene clusters of pDK1 were derived through homologous recombination, transposition, and site-specific recombination from the xyl gene clusters homologous to another TOL plasmid, pWW53. The minireplicons of pDK1 and its related IncP-7 plasmids, pWW53 and pCAR1, that contain replication and partition genes were maintained in all of six Pseudomonas strains tested, but not in alpha-or betaproteobacterial strains. The recipient host range of conjugative transfer of pDK1 was, however, limited to two Pseudomonas strains. These results indicate that IncP-7 plasmids are essentially narrow-host-range and self-transmissible plasmids that encode MOB H group-related transfer functions and that the host range of IncP-7-specified conjugative transfer was, unlike the situation in other well-known plasmids, narrower than that of its replication.Bacterial genes for the utilization of recalcitrant environmental pollutants such as herbicides, pesticides, and petroleum and other industrial waste compounds are often found on plasmids and chromosomally specified integrative and conjugative elements (ICEs) (57). Although the origins of such catabolic genes still remain unknown, it seems most likely that, once established, the catabolic gene modules spread between plasmids and chromosomes through intracellular movements of insertion sequence (IS)-flanked composite transposons (68) and class II (Tn3-related) transposons (61, 63) and intercellular conjugative transfers of plasmids and ICEs (36, 65). The genes associated with the degradation of man-made xenobiotic compounds (e.g., atrazine, 2,4-dichlorophenoxyacetate, and haloacetates) have predominantly been found on broad-hostrange and incompatibility group P-1 (IncP-1) plasmids, whereas the genes responsible for the degradation of natural aromatic hydrocarbons (e.g., phenol, naphthalene, and toluene/xylenes) via the meta-cleavage catabolic pathways are mainly located on IncP-2, IncP-7, and IncP-9 plasmids, which have been found exclusively in Pseudomonas species (38).Studies of the archetypal 119-kb and IncP-9 toluene/xylenecatabolic (TOL) plasmid pWW0 from Pseudomonas putida mt-2 have greatly contributed to the detailed clarification of genetic and biochemical mechanisms for the aerobic degradation of toluene/xylenes (72). The pWW0-specified xyl genes are organized as four transcriptional units within the class II transposons, Tn4651 and Tn4653 (62): (i) the upper pathway operon (xylXYZLTEGFJQKIH) for the conversion ...

Host range diversification within the IncP-1 plasmid group

“…Such a divergence in the plasmid backbone genes within an Inc group (,80 % amino-acid sequence identity between homologues) has also been reported for the groups IncQ (Loftie-Eaton & Rawlings, 2012), IncP-9 (Sevastsyanovich et al, 2008) and IncX (Johnson et al, 2012), whereas relatively low divergence was observed among the currently available plasmid sequences of groups IncA/C (Fricke et al, 2009), IncI (Takahashi et al, 2011) andIncP-7 (Yano et al, 2010). Reduced similarity was observed, for an as yet unknown reason, specifically in a partitioning gene in IncI and IncP-7 groups despite high similarity in the replication and transfer genes within the Inc groups (Takahashi et al, 2011;Yano et al, 2010). This divergence in plasmid backbone sequence within a group of closely related plasmids may be the consequence of adaptive mutations that allow specialization towards specific bacterial hosts.…”

Structural and Molecular Genetic Analyses of the Bacterial Carbazole Degradation System

“…79) To date, in addition to pCAR1, complete nucleotide sequences have been reported for three other IncP-7 group plasmids: naphthalene degradative plasmid pND6-1, 80) toluene degradative plasmids pWW53, 81) and pDK1. 82) The replication and partition function regions of these plasmids were well conserved with that of pCAR1, and a 53.2-kb IncP-7 plasmid backbone was proposed based on a comparison of the nucleotide sequences. 82) Recently, seven IncP-7 naphthalene and salicylate degradative plasmids were also reported.…”

“…82) The replication and partition function regions of these plasmids were well conserved with that of pCAR1, and a 53.2-kb IncP-7 plasmid backbone was proposed based on a comparison of the nucleotide sequences. 82) Recently, seven IncP-7 naphthalene and salicylate degradative plasmids were also reported. 83) Thus IncP-7 plasmids are gaining importance as degradative plasmids.…”

“…A limited recipient range of conjugative transfer is also the case for pDK1. 82) Using pDK1, Yano et al 82) reported recently that the host range of IncP-7-specified conjugative transfer was, unlike for other well-known plasmids, narrower than that of its replication, suggesting that the host range of self-transmissible IncP-7 plasmids is in general restricted by the conjugation system rather than the replication system.…”

“…52,54,55) The corresponding region was proposed to be a part of the IncP-7 plasmid backbone. 82) According to a classification scheme based on the homology of the conjugative relaxase, 84) pCAR1 belongs to the MOB H group of mobilizable plasmids. Transfers of pCAR1 to P. resinovorans CA10dm4 and P. putida KT2440 were detected experimentally at frequencies of 3 Â 10 À1 and 3 Â 10 À3 per donor cell, 57) suggesting that pCAR1 is in fact a self-transmissible plasmid.…”