Multiple Mechanisms Contribute to Lateral Transfer of an Organophosphate Degradation (opd) Island in Sphingobium fuliginis ATCC 27551

Abstract

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.

Degradative plasmids from sphingomonads

“…The first example of a sequenced and carefully analysed degradative plasmid from a sphingomonad was plasmid pNL1 from Sphingomonas (now Novosphingobium) aromaticivorans F199, which carries all genes required for the degradation of biphenyl, naphthalene, m-xylene and p-cresol . Subsequently, the sequence analysis of plasmids pCAR3 (carrying all the genes for the mineralization of carbazole), pCHQ1 (coding for the linRED genes participating in the degradation of c-hexachlorocyclohexane) and pPDL2 (coding for a parathion hydrolase involved in organophosphate degradation) has been published (Shintani et al, 2007;Nagata et al, 2011;Pandeeti et al, 2012; Table 1).…”

Metabolic remodeling in Escherichia coli MG1655. A prophage e14‐encoded small RNA, co293, post‐transcriptionally regulates transcription factors HcaR and FadR

“…Both the opd and mpd genes are carried on a mobile genetic element. Identical opd and mpd genes are found among taxonomically unrelated soil bacteria [4][5][6], and even dissimilar indigenous plasmids found in bacteria isolated from diverse geographical regions contain identical opd gene clusters [7]. There are four indigenous plasmids in OP-degrading Sphingobium fuliginis ATCC 27551 [8], one of which, the opd-containing pPDL2, has been shown to be a mobilizable plasmid within which the opd region has unique organizational features [4,9].…”

“…to protocatechuate degradation, the opd gene forms part of an active transposon [6]. The mobilizable plasmid also contains an integrase and an attachment (attB) site that facilitate site-specific integration, and recent studies have shown its ability to integrate at an artificially created attB site.…”

A comparison of organophosphate degradation genes and bioremediation applications

“…Further study of the purported opd transposon on pPDL2 of S. fuliginis ATCC 27551 has confirmed that the gene lies on a catabolic transposon along with genes that encode for aromatic transporter proteins and protocatechuate dioxygenase. The authors have also identified an integrase that allows for lateral integration into a new host chromosome should the organism be unable to replicate the pPDL2 plasmid providing a likely explanation for the gene's sudden emergence in many new genera of soil bacteria (Pandeeti et al ., ). Furthermore, the closest homologues of the insertion operon and transposase found within the opd gene clusters on these plasmids are also found in strains of A. tumefaciens , and with the discovery of the aforementioned opdA gene reported from a strain of A. radiobacter , this could indicate an evolutionary origin in Agrobacterium (Horne et al ., 2002a; Siddavattam et al ., ).…”