title: The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere.
abstract: Plasmid pIPO2 is a cryptic, conjugative, broad-host-range plasmid isolated from the wheat rhizosphere. It efficiently self-transfers between alpha, beta and gamma 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 39815 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.
authors.affiliation: Zentrum für Genomforschung, Universität Bielefeld, D-33615 Bielefeld, Germany1.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.affiliation: Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
authors.forename: Susanne
authors.initials: S
authors.lastname: Schneiker
authors.affiliation: Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
authors.forename: Werner
authors.initials: W
authors.lastname: Selbitschka
authors.affiliation: Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Plant Research International, 6700AA Wageningen, The Netherlands3.
authors.forename: Leo S
authors.initials: LS
authors.lastname: van Overbeek
authors.affiliation: Biologische Bundesanstalt für Land-und Forstwirtschaft, D-38104 Braunschweig, Germany4.
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
authors.affiliation: School for Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK5.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Thomas
authors.affiliation: NERC Institute of Virology and Environmental Microbiology, Oxford OX1 3SR, UK6.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Bailey
authors.affiliation: Department of Biology, University of Idaho, Moscow, ID 83844, USA7.
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Forney
authors.affiliation: Cardiff School of Biosciences, University of Wales, Cardiff CF10 3TL, UK8.
authors.forename: Andrew
authors.initials: A
authors.lastname: Weightman
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland9.
authors.forename: Piotr
authors.initials: P
authors.lastname: Ceglowski
authors.affiliation: Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland10.
authors.forename: Tony
authors.initials: T
authors.lastname: Pembroke
authors.affiliation: Robert Koch-Institut, Bereich Wernigerode, D-38855 Wernigerode, Germany11.
authors.forename: Erhard
authors.initials: E
authors.lastname: Tietze
authors.affiliation: Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Schröder
authors.affiliation: Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12.
authors.forename: Erich
authors.initials: E
authors.lastname: Lanka
authors.affiliation: Plant Research International, 6700AA Wageningen, The Netherlands3.
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D020090:Chromosome Segregation; D003227:Conjugation, Genetic / Q000235:genetics*; D004261:DNA Replication; D004269:DNA, Bacterial / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D008969:Molecular Sequence Data; D018517:Plant Roots / Q000382:microbiology*; D010957:Plasmids / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D021382:Protein Sorting Signals; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013045:Species Specificity; D014908:Triticum / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D021382:Protein Sorting Signals