title: Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676.
abstract: The car and ant operons originally isolated from Pseudomonas resinovorans strain CA10 contain the genes encoding the carbazole/dioxin-degrading enzymes and anthranilate 1,2-dioxygenase, respectively, and are located on the plasmid pCAR1. The entire nucleotide sequence of pCAR1 was determined to elucidate the mechanism by which the car operon may have been assembled and distributed in nature. pCAR1 is a 199,035-bp circular plasmid, and carries 190 open reading frames. Although the incompatibility group of pCAR1 is unclear, its potential origin for replication, OriP, and Rep and Par proteins appeared to be closely related to those of plasmid pL6.5 isolated from Pseudomonas fluorescens. The potential tellurite-resistance klaABC genes identified in the neighboring region of repA gene were also related to those in IncP plasmid originally identified from pseudomonads. On the other hand, we found genes encoding proteins that showed low but significant homology (20-45% identity) with Trh and Tra proteins from Enterobacteriaceae, which are potentially involved in conjugative transfer of plasmids or genomic island, suggesting that pCAR1 is also a conjugative plasmid. In pCAR1, we found tnpAcCST genes that encoded the proteins showing >70% length-wise identities with those are encoded by the toluene/xylene-degrading transposon Tn4651 of TOL plasmid pWW0. Both car and ant degradative operons were found within a 72.8-kb Tn4676 sequence defined by flanking tnpAcC and tnpST genes and bordered by a 46-bp inverted repeat (IR). Within Tn4676 and its flanking region, we found the remnants of numerous mobile genetic elements, such as the duplicated transposase genes that are highly homologous to tnpR of Tn4653 and the multiple candidates of IRs for Tn4676 and Tn4653-like element. We also found distinct regions with high and low G+C contents within Tn4676, which contain an ant operon and car operon, respectively. These results suggested that multiple step assembly could have taken place before the current structure of Tn4676 had been captured.
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, 113-8657, Tokyo, Japan.
authors.forename: Kana
authors.initials: K
authors.lastname: Maeda
authors.forename: Hideaki
authors.initials: H
authors.lastname: Nojiri
authors.forename: Masaki
authors.initials: M
authors.lastname: Shintani
authors.forename: Takako
authors.initials: T
authors.lastname: Yoshida
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Habe
authors.forename: Toshio
authors.initials: T
authors.lastname: Omori
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002227:Carbazoles / Q000378:metabolism*; D003227:Conjugation, Genetic / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D004147:Dioxins / Q000378:metabolism*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009030:Mosaicism / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D011549:Pseudomonas / Q000145:classification / Q000235:genetics* / Q000378:metabolism*
chemical_list: D002227:Carbazoles; D004251:DNA Transposable Elements; D004147:Dioxins; C041514:carbazole