Department of Animal Science, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
G3 (Bethesda). 2012 Dec;2(12):1541-54. doi: 10.1534/g3.112.004051. Epub 2012 Dec 1.
The complete sequence of pPDL2 (37,317 bp), an indigenous plasmid of Sphingobium fuliginis ATCC 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attP, typically seen in integrative mobilizable elements (IME). In agreement with this sequence information, site-specific recombination was observed between pPDL2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attB site at the 3' end of the seryl tRNA gene of Sphingobium japonicum. The opd gene cluster on pPDL2 was found to be part of an active catabolic transposon with mobile elements y4qE and Tn3 at its flanking ends. Besides the previously reported opd cluster, this transposon contains genes coding for protocatechuate dioxygenase and for two transport proteins from the major facilitator family that are predicted to be involved in transport and metabolism of aromatic compounds. A pPDL2 derivative, pPDL2-K, was horizontally transferred into Escherichia coli and Acinetobacter strains, suggesting that the oriT identified in pPDL2 is functional. A well-defined replicative origin (oriV), repA was identified along with a plasmid addiction module relB/relE that would support stable maintenance of pPDL2 in Sphingobium fuliginis ATCC 27551. However, if pPDL2 is laterally transferred into hosts that do not support its replication, the opd cluster appears to integrate into the host chromosome, either through transposition or through site-specific integration. The data presented in this study help to explain the existence of identical opd genes among soil bacteria.
PDL2 质粒（37317bp）是一株地衣芽孢杆菌 ATCC 27551 的内源性质粒，它编码有机磷降解基因（opd）。该质粒含有一个整合酶（int）基因和一个附着位点 attP，这通常存在于整合可移动元件（IME）中。根据这一序列信息，在 pPDL2 和一个具有温度敏感复制子和克隆 attB 位点的人工质粒之间观察到了位点特异性重组，该 attB 位点位于日本分枝杆菌丝氨酸 tRNA 基因的 3'末端。在 pPDL2 上，opd 基因簇被发现是一个活跃的代谢转座子的一部分，其侧翼有移动元件 y4qE 和 Tn3。除了之前报道的 opd 基因簇，这个转座子还包含编码原儿茶酸双加氧酶和两个主要易化因子家族转运蛋白的基因，这些基因预测参与芳香族化合物的运输和代谢。pPDL2 的一个衍生物 pPDL2-K 被水平转移到大肠杆菌和不动杆菌菌株中，这表明在 pPDL2 中鉴定的 oriT 是功能性的。一个明确的复制起点（oriV）、repA 以及一个质粒成瘾模块 relB/relE 被鉴定出来，这将支持 pPDL2 在地衣芽孢杆菌 ATCC 27551 中的稳定维持。然而，如果 pPDL2 横向转移到不支持其复制的宿主中，opd 基因簇似乎会通过转座或位点特异性整合到宿主染色体中。本研究提供的资料有助于解释土壤细菌中存在相同的 opd 基因的原因。
