title: Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways.
abstract: Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by tfd genes, are located in the 88 kb, self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well-conserved IncP-1 beta backbone and the previously reported tfd genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short-chain fatty acid oxidation. ORFs related to mobile elements, including the Tn501-encoded mercury resistance determinants, an IS1071-based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP-1 alpha plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.
authors.affiliation: Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, and Millennium Institute for Fundamental and Applied Biology, Santiago, Chile.
authors.forename: N
authors.initials: N
authors.lastname: Trefault
authors.forename: R
authors.initials: R
authors.lastname: De la Iglesia
authors.forename: A M
authors.initials: AM
authors.lastname: Molina
authors.forename: M
authors.initials: M
authors.lastname: Manzano
authors.forename: T
authors.initials: T
authors.lastname: Ledger
authors.forename: D
authors.initials: D
authors.lastname: Pérez-Pantoja
authors.forename: M A
authors.initials: MA
authors.lastname: Sánchez
authors.forename: M
authors.initials: M
authors.lastname: Stuardo
authors.forename: B
authors.initials: B
authors.lastname: González
mesh_terms: D000222:Adaptation, Physiological; D001482:Base Composition; D001673:Biodegradation, Environmental; D020118:Cupriavidus necator / Q000235:genetics* / Q000378:metabolism*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004785:Environmental Pollutants / Q000378:metabolism*; D023061:Gene Order; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D006841:Hydrocarbons, Aromatic / Q000378:metabolism*; D017669:Mercury Compounds / Q000633:toxicity; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D009876:Operon; D010957:Plasmids / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004785:Environmental Pollutants; D006841:Hydrocarbons, Aromatic; D017669:Mercury Compounds