title: Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas.
abstract: The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.
authors.affiliation: Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark ; Section for Microbiology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Tue Kjærgaard
authors.initials: TK
authors.lastname: Nielsen
authors.affiliation: Section for Microbiology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Zhuofei
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
authors.forename: Erkin
authors.initials: E
authors.lastname: Gözdereliler
authors.affiliation: Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
authors.forename: Jens
authors.initials: J
authors.lastname: Aamand
authors.affiliation: Section for Microbiology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Lars Hestbjerg
authors.initials: LH
authors.lastname: Hansen
authors.affiliation: Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
authors.forename: Sebastian R
authors.initials: SR
authors.lastname: Sørensen
mesh_terms: D015084:2,4-Dichlorophenoxyacetic Acid / Q000378:metabolism; D008456:2-Methyl-4-chlorophenoxyacetic Acid / Q000378:metabolism*; D001673:Biodegradation, Environmental; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D006540:Herbicides / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D012988:Soil Microbiology; D020578:Sphingomonas / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D006540:Herbicides; D015084:2,4-Dichlorophenoxyacetic Acid; D008456:2-Methyl-4-chlorophenoxyacetic Acid