Genomic organization and genomic dynamism of versatile sphingomonads

六六六是一种完全人工合成的氯化农药，因其毒性大，在旱地土壤中长期存在而造成严重的环境问题。在我们之前的研究中，我们测定了一株典型的伽玛-六氯环己烷降解菌株Sphingobium Japan onicum UT26的全基因组序列。将γ-六氯环己烷转化为顺丁烯二酸乙酯的LIN基因(LINA到LINE)分散在UT26基因组的1号染色体(LINA、LINB和LINC)和pCHQ1(LIND和LINE)上。IS6100不仅在UT26中发现，而且在其他伽马-六氯环己烷降解菌株中也经常发现与特定的LIN基因非常接近。为了更深入地了解伽马-六氯环己烷降解菌的出现和进化，研究了另外三株这样的菌株--鞘氨醇单胞菌的基因组序列草案。Mm-1，Sphingobium sp.TKS和Sphingobium sp.对分离于不同地区的MI1205(5)进行了鉴定，并与完整的GE…进行了比较更多UT26和其他密切相关但不降解伽马六氯环己烷的鞘氨醇单胞菌的Nome序列。前三株伽马-六氯环己烷降解菌也都有LIN基因，但这些基因在基因组上的位置与UT26上的不同，例如MM-1在三个质粒上携带这样的基因。此外，四种伽马-六氯环己烷降解物的基因组内容和组织结构各不相同。这些结果表明，这些降解物是通过‘特定的’LIN基因的横向基因转移而独立产生的。对UT26中IS6100的13个拷贝的侧翼区分析表明，染色体和质粒之间通过IS6100转座进行了DNA交换。我们使用基于SACB的IS包埋技术确实揭示了内源IS6100在UT26中的转座能力。这些结果有力地表明，IS6100在伽马-六氯环己烷降解菌中特异性LIN基因的传播中起重要作用，而在它们的基因组重排中发挥的作用较少

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