A 90-Kilobase Conjugative Chromosomal Element Coding for Biphenyl and Salicylate Catabolism in Pseudomonas putida KF715

Abstract

The biphenyl and salicylate metabolic pathways in Pseudomonas putida KF715 are chromosomally encoded. The bph gene cluster coding for the conversion of biphenyl to benzoic acid and the sal gene cluster coding for the salicylate meta-pathway were obtained from the KF715 genomic cosmid libraries. These two gene clusters were separated by 10-kb DNA and were highly prone to deletion when KF715 was grown in nutrient medium. Two types of deletions took place at the region including only the bph genes (ca. 40 kb) or at the region including both the bph and sal genes (ca. 70 kb). A 90-kb DNA region, including both the bph and sal genes (termed the bph-sal element), was transferred by conjugation from KF715 to P. putida AC30. Such transconjugants gained the ability to grow on biphenyl and salicylate as the sole sources of carbon. The bph and sal element was located on the chromosome of the recipient. The bph-sal element in strain AC30 was also highly prone to deletion; however, it could be mobilized to the chromosome of P. putida KT2440 and the two deletion mutants of KF715.A number of biphenyl-utilizing bacteria have been isolated to date. They include gram-negative species of Pseudomonas, Achromobacter, Sphingomonas, Comamonas, Burkholderia, Ralstonia, and Alcaligenes and gram-positive Rhodococcus spp. (1,3,11,37). Because these biphenyl-utilizing strains cometabolize polychlorinated biphenyls (PCB), the biochemistry of PCB degradation has been extensively studied (12). A gene cluster coding for biphenyl-PCB degradation (termed bph) was first cloned from Pseudomonas pseudoalcaligenes KF707 (14). Since then, a number of bph genes have been cloned and sequenced. Southern and sequence analyses of the bph genes revealed that some biphenyl-utilizing strains possess bph genes that are very similar, if not identical, to one another, but some share various degrees of homology (13).The bph genes are present on bacterial chromosomes (8, 14, 16, 35), plasmids (18, 39), and transposons (22, 28, 34). The presence of similar genes in different strains implies that even chromosomal bph genes have or used to have a mechanism for mobilization to other strains. The bph genes of Pseudomonas sp. strain CB406 were mobilized following the construction in vivo of a cointegrate plasmid inserted into the broad-hostrange plasmid RP4 (22). Springael and coworkers (23, 34) identified a transposon, Tn4371, carrying the bph genes encoding conversion of biphenyl to benzoic acid from Ralstonia eutrophus A5 (formerly Alcaligenes eutrophus A5) in which Tn4371 first transposed from the chromosome to indigenous IncP1 plasmid, and the plasmid carrying Tn4371 can be transferred to other strains by conjugation. A recent study shows that Tn4371 is a kind of conjugative transposon of 55 kb (24, 29). Interestingly, another smaller conjugative transposon Tnbph coding for biphenyl catabolism resides within Tn4371. This can be transferred to the recipient strain by conjugation independently. Divergence of the bph genes among various biphenyl-utilizing strains in...

Versatile Transcription of Biphenyl Catabolic bphOperon in Pseudomonas pseudoalcaligenes KF707

“…It was reported that the bph gene cluster involved in the metabolism of biphenyl/4-chlorobiphenyl is located in the 55-kb transposon Tn4371 (17,18,33,34). Our recent study also revealed that the 90-kb bph-sal element coding for biphenyl and salicylate metabolism behaves like a conjugative transposon in Pseudomonas putida KF715 whose bph gene cluster is nearly identical to that of KF707 except that the bphX0X1X2X3 genes were deleted (35). If this is the case in KF707, the bph genes could be foreign genes derived from other strains.…”

Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response

“…They can excise and transfer to recipients through conjugation (mating) and integrate into the chromosome of the recipient (5,6). ICEs encode proteins required for conjugal transfer and can also encode proteins involved in resistance to antibiotics (5,6), metabolism of alternative carbon sources (4,8), symbiosis (9), and other processes (10). ICEs and putative ICEs have been found in many bacteria (10) and are important agents of horizontal gene transfer because they are capable of moving themselves and other DNA to recipients (6,(11)(12)(13).…”

Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls(PCBs).

“…A 90-kb DNA region including both the bph and sal genes (termed bph-sal element) was transferred by conjugation from KF715 to P. putida AC30 (Nishi et al, 2000). These transconjugants gained the ability to grow on biphenyl and salicylate as sole sources of carbon.…”

“…KKS102 are shuffled, and the bphA4 gene is downstream of bphD (Kikuchi et al, 1994a, b). The bph cluster in Pseudomonas putida KF715 is lacking the 3.5 kb bphX region (Hayase et al, 1990;Nishi et al, 2000). In the Rhodococcus sp.…”

“…In total, seven bphClike genes were found in RHA1, of which four were on plasmids and three were on chromosome. KF707-bph: P. pseudoalcaligenes KF707 bph gene cluster (Taira et al, 1992); LB400-bph: B. cepacia LB400 (Erickson and Mondello, 1992;Hofer et al, 1996); KF715-bph: P. putida KF715 (Hayase et al, 1990;Nishi et al, 2000); KKS102-bph: Pseudomonas sp. strain KKS102 (Kikuchi et al, 1994a, b;Kimbara et al, 1989); RHA1-bph: Rhodococcus sp.…”