title: Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid.
abstract: Ralstonia eutropha JMP134(pJP4) is able to grow on minimal media containing the pollutants 3-chlorobenzoate (3-CB) or 2,4-dichlorophenoxyacetate (2,4-D). tfd genes from the 88 kb plasmid pJP4 encode enzymes involved in the degradation of these compounds. During growth of strain JMP134 in liquid medium containing 3-CB, a derivative strain harbouring a approximately 95 kb plasmid was isolated. This derivative, designated JMP134(pJP4-F3), had an improved ability to grow on 3-CB, but had lost the ability to grow on 2,4-D. Sequence analysis of pJP4-F3 indicated that the plasmid had undergone a deletion of approximately 16 kb, which included the tfdA-tfdS intergenic region, spanning the tfdA gene to a previously unreported IS1071 element. The loss of the tfdA gene explains the failure of the derivative to grow on 2,4-D. A approximately 23 kb duplication of the region spanning tfdR-tfdD(II)C(II)E(II)F(II)-tfdB(II)-tfdK-ISJP4-tfdT-tfdC(I)D(I)E(I)F(I)-tfdB(I), giving rise to a 51-kb-long inverted repeat, was also observed. The increase in gene copy number for the tfdCD(DC)EF gene cluster may provide an explanation for the derivative strain's improved growth on 3-CB. These observations are additional examples of the metabolic plasticity of R. eutropha JMP134, one of the more versatile pollutant-degrading bacteria.
authors.affiliation: Laboratorio de Microbiologı́a, Departamento de Genética Molecular y Microbiologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Casilla 114-D, Santiago, Chile1.
authors.forename: Pascale
authors.initials: P
authors.lastname: Clément
authors.affiliation: Division of Microbiology, National Research Centre for Biotechnology - GBF, Braunschweig, Germany2.
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.affiliation: Laboratorio de Microbiologı́a, Departamento de Genética Molecular y Microbiologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Casilla 114-D, Santiago, Chile1.
authors.forename: Bernardo
authors.initials: B
authors.lastname: González
mesh_terms: D015084:2,4-Dichlorophenoxyacetic Acid / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D002723:Chlorobenzoates / Q000378:metabolism*; D020118:Cupriavidus necator / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA; D014157:Transcription Factors
chemical_list: D001426:Bacterial Proteins; D002723:Chlorobenzoates; D004268:DNA-Binding Proteins; C086733:TfdR protein, Alcaligenes eutrophus; D014157:Transcription Factors; C036427:3-chlorobenzoic acid; D015084:2,4-Dichlorophenoxyacetic Acid