The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere.
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.
Tauch
Andreas
A
Zentrum für Genomforschung, Universität Bielefeld, D-33615 Bielefeld, Germany1.
Schneiker
Susanne
S
Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
Selbitschka
Werner
W
Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
Pühler
Alfred
A
Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2.
van Overbeek
Leo S
LS
Plant Research International, 6700AA Wageningen, The Netherlands3.
Smalla
Kornelia
K
Biologische Bundesanstalt für Land-und Forstwirtschaft, D-38104 Braunschweig, Germany4.
Thomas
Christopher M
CM
School for Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK5.
Bailey
Mark J
MJ
NERC Institute of Virology and Environmental Microbiology, Oxford OX1 3SR, UK6.
Forney
Larry J
LJ
Department of Biology, University of Idaho, Moscow, ID 83844, USA7.
Weightman
Andrew
A
Cardiff School of Biosciences, University of Wales, Cardiff CF10 3TL, UK8.
Ceglowski
Piotr
P
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland9.
Pembroke
Tony
T
Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland10.
Tietze
Erhard
E
Robert Koch-Institut, Bereich Wernigerode, D-38855 Wernigerode, Germany11.
Schröder
Gunnar
G
Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12.
Lanka
Erich
E
Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12.
van Elsas
Jan Dirk
JD
Plant Research International, 6700AA Wageningen, The Netherlands3.
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*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D021382:Protein Sorting Signals