The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere The GenBank accession number for the pIPO2T sequence reported in this paper is AJ297913.

Abstract

Plasmid pIPO2 is a cryptic, conjugative, broad-host-range plasmid isolated from the wheat rhizosphere. It efficiently self-transfers between α, β and γ Proteobacteria and has a mobilizing/retromobilizing capacity for IncQ plasmids. The complete nucleotide sequence of pIPO2 is presented on the basis of its mini-Tn5 ::luxABtet-tagged derivative, pIPO2T. The pIPO2 sequence is 39 815 bp long and contains at least 43 complete ORFs. Apart from a suite of ORFs with unknown function, all of the genes carried on pIPO2 are predicted to be involved in plasmid replication, maintenance and conjugative transfer. The overall organization of these genes is different from previously described plasmids, but is similar to the genetic organization seen in pSB102, a conjugative plasmid recently isolated from the bacterial community of the alfalfa rhizosphere. The putative conjugative transfer region of pIPO2 covers 23 kb and contains the genes required for DNA processing (Dtr) and mating pair formation (Mpf). The organization of these transfer genes in pIPO2 is highly similar to the genetic organization seen in the environmental plasmid pSB102 and in pXF51 from the plant pathogen Xylella fastidiosa. Plasmids pSB102 and pXF51 have recently been proposed to form a new family of environmental broad-host-range plasmids. Here it is suggested that pIPO2 is a new member of this family. The proposed Mpf system of pIPO2 shares high amino acid sequence similarity with equivalent VirB proteins from the type IV secretion system of Brucella spp. Sequence information was used to design primers specific for the detection of pIPO2. Environmental DNA from a range of diverse habitats was screened by PCR with these primers. Consistently positive signals for the presence of pIPO2 were obtained from a range of soil-related habitats, including the rhizospheres of young wheat plants, of field-grown oats and of grass (all gramineous plants), as well as from the rhizosphere of tomato plants. These data add to the growing evidence that plasmids carry advantageous genes with as yet undefined functions in plant-associated communities.

Conjugative plasmids: vessels of the communal gene pool

“…For example, a 45 kb cryptic plasmid belonging to a new family was isolated based only on its ability to mobilize a resistance plasmid, a general property shared by most conjugative plasmids. This plasmid, pIPO2T, is widespread in rhizosphere populations and contains a suite of ORFs with unknown functions in addition to genes predicted to be involved in plasmid replication, maintenance and conjugative transfer (Tauch et al 2002). In other studies, an ingenious transposon capture method was used to isolate nonspecific plasmid DNA from the human gut flora, thereby recovering several small cryptic plasmids (Jones & Marchesi 2007), and a PCR-based method was used to amplify and sequence environmental ORFs related to class 1 integrons (Stokes et al 2001).…”

Comparative genome analysis of the α-proteobacteria: Relationships between plant and animal pathogens and host specificity

“…Together, these findings suggest that parts of chromosome 2 may have been originally acquired from a plasmid. The recent identification of the closest sequenced homologs to date of the Brucella virB genes on conjugative plasmids from microbes of the rhizosphere of wheat and alfalfa lends further support to this idea (31,32).…”

Horizontal gene transfer between bacteria

“…Plasmid pIPO2 was isolated in R. eutropha based on its mobilizing capacity. Replicon typing and sequencing of the complete plasmid (Tauch et al, 2002) revealed that this cryptic plasmid of a size of approx. 45 kbp was not related to any of the known BHR plasmids except to plasmid pSB102 (Schneiker et al, 2001).…”