Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype

• Published in: Microbiology (Society for General Microbiology) 2006-09, Vol.152 (9), p.2689-2701
• Main Authors: Haines, Anthony S, Akhtar, Parveen, Stephens, Elton R, Jones, Karen, Thomas, Christopher M, Perkins, Caroline D, Williams, Jacqueline R, Day, Martin J, Fry, John C
• Format: Article
• Language: English
• Subjects: Bacteriology; Base Composition; Base Sequence; Biological and medical sciences; Conjugation, Genetic; DNA Primers; DNA Probes; DNA Restriction Enzymes - metabolism; DNA, Bacterial - genetics; Drug Resistance, Bacterial - genetics; Environment; Fresh Water; Fundamental and applied biological sciences. Psychology; Genetics; Mercury - pharmacology; Microbiology; Models, Genetic; Molecular Sequence Data; Nucleic Acid Amplification Techniques; Nucleic Acid Hybridization; Phylogeny; Plasmids - classification; Plasmids - genetics; Plasmids - isolation & purification; Polymerase Chain Reaction; Replication Origin; Replicon; Restriction Mapping; Retroelements; Sequence Analysis, DNA
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.28941-0

1 School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK 2 Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF1 3TL, UK Correspondence Christopher M. Thomas c.m.thomas{at}bham.ac.uk Nine mercury-resistance plasmids isolated from river epilithon were assessed for their ability to retrotransfer the non-conjugative IncQ plasmid, R300B, derivatives of which have commercial uses that may result in accidental or deliberate release into the environment. Retrotransfer frequencies ranging from 2.1 x 10 –4 to 1.75 x 10 –5 were obtained for five of the nine plasmids – the remaining plasmids showed low or undetectable retrotransfer ability. The majority of the retrotransfer-proficient plasmids could not be classified by the tests used. Classical incompatibility testing with RP4 identified pQKH6, pQKH54 and pQM719 as IncP-1. Hybridization to replicon probes confirmed this for pQKH6 and pQM719 and added pQKH33. PCR with primers designed to amplify trfA and korA regions of IncP-1 plasmids did not identify any other plasmids. Plasmids pQKH6 and pQM719 but not pQKH54 produced similar Sph I restriction profiles to the IncP-1 subgroup. The complete nucleotide sequence of pQKH54 was determined, revealing it to have a complete IncP-1 backbone but belonging to a new distinct subgroup which was designated IncP-1 . The results emphasize the ubiquity and diversity of IncP-1 plasmids in the environment but demonstrate that plasmids of as yet unknown groups are also able to retrotransfer IncQ plasmids efficiently. The GenBank/EMBL/DDBJ accession number for the nucleotide sequence of pQKH54 is AM157767. A supplementary table of biologically relevant reading frames identified in the pQKH54 sequence is available with the online version of this paper.