title: Sphingobium sp. HV3 degrades both herbicides and polyaromatic hydrocarbons using ortho- and meta-pathways with differential expression shown by RT-PCR.
abstract: Sphingobium sp. HV3 described as an herbicide degrader harbours the pSKY4 plasmid, encoding an aromatic meta-pathway. The function of the plasmid was studied by Tn5 transposon mutagenesis and plasmid isolation and the degradation capacities of the HV3 strain were re-evaluated. Transcription of the tfdC from ortho-pathway was contrasted to the xylE and bphC of meta-pathway using real-time PCR. Cloning of the Tn5-insertion sites from the megaplasmid revealed genes for both aromatic and polyaromatic degradation. In the mutant Km24 strain the transposon was inserted to an ORF similar to the large subunit of ring hydroxylating dioxygenase, in the Km383 to a cis-biphenyl dihydrodiol dehydrogenase and in the Km187 and Km42 to a reductase component of a dioxygenase. A chlorocathecol ortho-pathway (10 kb) was amplified from the HV3 strain. The transcription of the tfdC was induced by 2,4-dichlorophenoxyacetic acid herbicide and m-xylene caused highest induction of both upper and lower aromatic meta-pathway genes. The detected novel degradation capacities (m-xylene, toluene, biphenyl, fluorene and phenanthrene) can be explained by the presence of functional meta-pathway genes in the pSKY4 megaplasmid. The characterization of the Sphingobium sp. HV3 improves our understanding of versatile catabolic bacteria unveiling roles of degradation pathways and plasmids in biodegradation.
authors.affiliation: Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, Helsinki, Finland.
authors.forename: Timo P
authors.initials: TP
authors.lastname: Sipilä
authors.forename: Pave
authors.initials: P
authors.lastname: Väisänen
authors.forename: Lars
authors.initials: L
authors.lastname: Paulin
authors.forename: Kim
authors.initials: K
authors.lastname: Yrjälä
mesh_terms: D001673:Biodegradation, Environmental; D002396:Catechols / Q000378:metabolism; D003001:Cloning, Molecular; D004251:DNA Transposable Elements / Q000235:genetics; D049308:Dioxygenases / Q000235:genetics / Q000378:metabolism; D004587:Electrophoresis, Agar Gel; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D006540:Herbicides / Q000378:metabolism*; D006841:Hydrocarbons, Aromatic / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D016296:Mutagenesis / Q000235:genetics; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D015183:Restriction Mapping; D020133:Reverse Transcriptase Polymerase Chain Reaction; D042301:Sphingomonadaceae / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D013997:Time Factors
chemical_list: D002396:Catechols; D004251:DNA Transposable Elements; D006540:Herbicides; D006841:Hydrocarbons, Aromatic; D049308:Dioxygenases