Organization of lin Genes and IS 6100 among Different Strains of Hexachlorocyclohexane-Degrading Sphingomonas paucimobilis : Evidence for Horizontal Gene Transfer

Abstract

The organization of lin genes and IS6100 was studied in three strains of Sphingomonas paucimobilis (B90A, Sp؉, and UT26) which degraded hexachlorocyclohexane (HCH) isomers but which had been isolated at different geographical locations. DNA-DNA hybridization data revealed that most of the lin genes in these strains were associated with IS6100, an insertion sequence classified in the IS6 family and initially found in Mycobacterium fortuitum. Eleven, six, and five copies of IS6100 were detected in B90A, Sp؉, and UT26, respectively. IS6100 elements in B90A were sequenced from five, one, and one regions of the genomes of B90A, Sp؉, and UT26, respectively, and were found to be identical. DNA-DNA hybridization and DNA sequencing of cosmid clones also revealed that S. paucimobilis B90A contains three and two copies of linX and linA, respectively, compared to only one copy of these genes in strains Sp؉ and UT26. Although the copy number and the sequence of the remaining genes of the HCH degradative pathway (linB, linC, linD, and linE) were nearly the same in all strains, there were striking differences in the organization of the linA genes as a result of replacement of portions of DNA sequences by IS6100, which gave them a strange mosaic configuration. Spontaneous deletion of linD and linE from B90A and of linA from Sp؉ occurred and was associated either with deletion of a copy of IS6100 or changes in IS6100 profiles. The evidence gathered in this study, coupled with the observation that the G؉C contents of the linA genes are lower than that of the remaining DNA sequence of S. paucimobilis, strongly suggests that all these strains acquired the linA gene through horizontal gene transfer mediated by IS6100. The association of IS6100 with the rest of the lin genes further suggests that IS6100 played a role in shaping the current lin gene organization.Hexachlorocyclohexane (HCH) was introduced for the control of agricultural pests and of vector-borne diseases in early 1940s. While this compound was used extensively all over the world, several reports on the persistence of HCH isomers (␣, ␤, ␥, and ␦) and their toxic effects on nontarget organisms appeared in the 1980s (11). These reports finally resulted in a ban on or restricted use of HCH in most countries. Neither the ban nor the restricted use has, however, reduced the levels of HCH residues in the environment (6, 25, 33), especially in soils that had a previous history of HCH application (2). One serious problem is the uptake of HCH residues from soil by crops, which then enter food products (1, 31). In addition to no further use of HCH, a decontamination program for HCHpolluted soils would diminish the risk posed by HCH residues to human, plant, and animal health. One possibility for decontamination is spontaneous or induced microbial degradation. Unfortunately, spontaneous microbial degradation of HCH isomers proceeds rather slowly (10, 15), although a number of bacteria which can degrade one or more isomers of HCH have been isolated. Thus, addition of naturally occu...

Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane

“…This study provided evidence that genetic organization of lin genes and their stability is strongly associated with IS6100 [8]. IS6100 was initially isolated from Mycobacterium fortuitum and copies of IS6100 that were sequenced from B90A, Sp+ and UT26 were found to be 100% identical to that of Mycobacterium fortuitum [8].…”

“…A thorough analysis of two copies of linA revealed 88% amino acids similarity between them. The C-terminal region of one of the linA gene in B90A was found to be replaced by 22 nucleotides of adjoining IS6100 element [8]. The two copies were named as linA1 and linA2 and while linA1 was found only in S. paucimobilis B90A, linA2 was 100% identical to that of S. paucimobilis UT26 and S. paucimobilis Sp+ [46].…”

“…The association of lin genes with IS6100 further prompted us to investigate the organization of lin genes in B90A. DNA-DNA hybridization data revealed that lin genes were nearly identical in B90A, Sp+ and UT26 and were found to be associated with IS6100 [8].…”

“…Studies on the organization of lin genes in these three strains [8] made it clear that lin genes have entered in sphingomonads from outside sources and do not originally belong to sphingomonads. All these lin genes were subsequently reported to be either present on plasmids or chromosomes [41,58,59].…”

“…This was the fi rst report on microbial degradation of the most recalcitrant β isomer of HCH. Gradually, the strain was extensively studied and has formed the basis of several novel discoveries such as the association of mobile genetic element (IS6100) with the catabolic lin genes [8]; the elucidation of HCH degradation pathway intermediates [9] as well as application-based bioremediation studies [10]. In this article we describe the alarming situation of environmental contamination by HCH, the function and genetic organization of lin genes in S. indicum B90A and the possibilities of decontamination of HCH through bioremediation by bioaugmentation.…”