Plasmid-encoded γ-hexachlorocyclohexane degradation genes and insertion sequences inSphingobium francense(ex-Sphingomonas paucimobilisSp+)

Abstract

The lin genes encode the gamma-hexachlorocyclohexane (gamma-HCH or lindane) catabolic pathway in lindane-degrading strains. The location and stability of these genes have been explored in the lindane-degrading Sphingobium francense strain Sp+, and in two non-lindane-degrading mutants (Sp1- and Sp2-). The lin genes, linA, linB, linE and linX were localized by hybridization on three of the six plasmids of the S. francense strain Sp+ showing dispersal within the genome. The linC gene was detected by PCR, but was not detected by hybridization on any of the plasmids. The hybridization of the linA and linX genes was negative with the two non-lindane-degrading mutants S. francense strains, Sp1- and Sp2-. The dynamic of this genome associated with gene loss and acquisition, and plasmid rearrangement was explored by a search for associated insertion sequences. A new insertion sequence, ISSppa4, belonging to the IS21 family was detected and compared with IS6100 and ISsp1. Insertion sequence localization was explored on different hybridization patterns (plasmid, total genome) with the lindane-degrading Sp+ strain and the two non-degrading derivatives (Sp1-, Sp2-). Insertion sequence movement and plasmid rearrangement could explain the emergence of the non-lindane-degrading mutants.

Localization of HCH catabolic genes (lin genes) in Sphingobium indicum B90A

“…Furthermore, S. indicum B90A was reported to contain several copies of an insertion sequence, IS6100 (originally isolated from a Gram-positive bacterium, Mycobacterium fortuitum FCI) 16 , which were found to be associated with most of the lin genes in this strain 15 . Recently, several HCH-degrading sphingomonads have been isolated from the HCH contaminated soils from different geographical locations [17][18][19][20][21][22] . These strains were found to contain lin genes highly similar to UT26 and B90A 14,[17][18][19] .…”

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

“…On the contrary in S. japonicum UT26, lin genes were found to be dispersed on three circular replicons (linA, linB and linC) on chromosome I and linDER on the conjugative plasmid pCHQ1 [58]. However, in S. francense Sp+, genes linA, linB, linC and linX were shown to be located on three different plasmids [41]. All these studies point out that lin genes are still evolving and are perhaps passed on to sphingomonads through plasmids.…”

“…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]. Additionally, polyphasic approach based taxonomical characterization revealed that these three strains are infact three different species of the genus Sphingobium [38].…”

“…Later, both these strains were named as Sphingobium francense UT26 and Sphingobium indicum B90A [38]. Additionally bacterial strains, Rhodanobacter lindaniclasticus [39,40] and Sphingomonas paucimobilis Sp+ [41] were isolated from HCH contaminated soil in France. The three Sphingomonas strains were later reclassifi ed as distinct species of genus Sphingobium namely Sphingobium indicum B90A, Sphingobium japonicum UT26 and Sphingobium francense Sp + by using polyphasic taxonomical approach [38].…”

“…A closer investigation revealed that this difference might be due to isolation of B90A from sugarcane fi elds treated with technical HCH [7] whereas Sp+ [41] and UT26 [36] were isolated from soils that were treated with γ-HCH alone.…”