Genomic organization and genomic dynamism of versatile sphingomonads

γ-六氯环己烷（γ-HCH）是一种完全人造的氯化农药，由于其毒性和在高地土壤中的长期持久性，已造成严重的环境问题。在我们以前的研究中，确定了一个典型的γ-HCH降解菌株，日本鞘氨醇菌UT 26的完整基因组序列。将γ-HCH转化为马来酰乙酸的“特异性”lin基因（linA至linE）分布在UT 26基因组中的1号染色体（linA、linB和linC）和质粒pCHQ 1（linD和linE）上。IS 6100通常不仅在UT 26中，而且在其他γ-六氯环己烷降解菌株中，都与“特定”lin基因非常接近。为了更深入地了解γ-HCH降解细菌的出现和进化，确定了其他三个此类菌株的基因组序列草图，它们是鞘氨醇单胞菌属MM-1、鞘氨醇囊菌属TKS和鞘氨醇囊菌属MI 1205（5），它们是在不同的地理区域分离的，并与完整的基因组序列进行了比较。 ...更多信息 UT 26和其他密切相关但不降解γ-六氯环己烷的鞘氨醇单胞菌菌株的基因组序列。前三株γ-HCH降解菌株也都具有“特异性”lin基因，但这些基因在其基因组中的位置与UT 26上的位置不同，例如MM-1在三个质粒上携带这些基因。此外，四种γ-HCH降解物的基因组含量和组织结构也各不相同。这些结果表明，这些降解剂已被创建独立的横向基因转移的“特定”林基因。对UT 26中13个拷贝的IS 6100侧翼区的分析表明，染色体和质粒之间的DNA交换是通过IS 6100转座进行的。我们使用基于sacB的IS包埋技术确实揭示了内源性IS 6100在UT 26中的转座性。这些结果有力地表明，IS 6100在γ-HCH降解细菌中“特定”lin基因的传播及其基因组重排中发挥着重要作用。

gamma-Hexachlorocyclohexane (gamma-HCH)is a completely man-made chlorinated pesticide that has caused serious environmental problems due to its toxicity and long persistence in upland soils. In our previous study, the complete genome sequence of an archetypal gamma-HCH-degrading strain, Sphingobium japonicum UT26, was determined. The ‘specific' lin genes (linA to linE)for the conversion of gamma-HCH to maleylacetate are dispersed on chromosome 1 (linA, linB, and linC)and a plasmid pCHQ1 (linD and linE)in the UT26 genome. IS6100 is often found in close proximity to the ‘specific' lin genes not only in UT26 but also in other gamma-HCH-degrading strains. To get more insights into the appearance and evolution of gamma-HCH-degrading bacteria, the draft genome sequences of three other such strains, Sphingomonas sp. MM-1, Sphingobium sp. TKS, and Sphingobium sp. MI1205 (5), which were isolated at geographically different area with one another, were determined and compared with the complete ge … More nome sequences of UT26 and other closely related but non-gamma-HCH-degrading sphingomonad strains. All the former three gamma-HCH-degrading strains also have the ‘specific' lin genes, but the location of such genes on their genomes are different from that on UT26, and for example, MM-1 carries such genes on three plasmids. Furthermore, genome contents and organizations of the four gamma-HCH-degraders are different with one another. These results suggested that these degraders had been created independently by lateral gene transfer of the ‘specific' lin genes. Analysis of flanking regions of 13 copies of IS6100 in UT26 suggested the DNA exchanges between chromosome and plasmids via the IS6100 transposition. Our use of sacB-based IS entrapment technique indeed revealed the transposability of endogenous IS6100 in UT26. These results strongly suggested that IS6100 plays important roles in the dissemination of the ‘specific' lin genes among gamma-HCH-degrading bacteria as well as in their genome rearrangements Less