title: The novel bacterial N-demethylase PdmAB is responsible for the initial step of N,N-dimethyl-substituted phenylurea herbicide degradation.
abstract: The environmental fate of phenylurea herbicides has received considerable attention in recent decades. The microbial metabolism of N,N-dimethyl-substituted phenylurea herbicides can generally be initiated by mono-N-demethylation. In this study, the molecular basis for this process was revealed. The pdmAB genes in Sphingobium sp. strain YBL2 were shown to be responsible for the initial mono-N-demethylation of commonly used N,N-dimethyl-substituted phenylurea herbicides. PdmAB is the oxygenase component of a bacterial Rieske non-heme iron oxygenase (RO) system. The genes pdmAB, encoding the α subunit PdmA and the β subunit PdmB, are organized in a transposable element flanked by two direct repeats of an insertion element resembling ISRh1. Furthermore, this transposable element is highly conserved among phenylurea herbicide-degrading sphingomonads originating from different areas of the world. However, there was no evidence of a gene for an electron carrier (a ferredoxin or a reductase) located in the immediate vicinity of pdmAB. Without its cognate electron transport components, expression of PdmAB in Escherichia coli, Pseudomonas putida, and other sphingomonads resulted in a functional enzyme. Moreover, coexpression of a putative [3Fe-4S]-type ferredoxin from Sphingomonas sp. strain RW1 greatly enhanced the catalytic activity of PdmAB in E. coli. These data suggested that PdmAB has a low specificity for electron transport components and that its optimal ferredoxin may be the [3Fe-4S] type. PdmA exhibited low homology to the α subunits of previously characterized ROs (less than 37% identity) and did not cluster with the RO group involved in O- or N-demethylation reactions, indicating that PdmAB is a distinct bacterial RO N-demethylase.
authors.affiliation: Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Gu
authors.forename: Chaoyang
authors.initials: C
authors.lastname: Zhou
authors.forename: Sebastian R
authors.initials: SR
authors.lastname: Sørensen
authors.forename: Ji
authors.initials: J
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: He
authors.forename: Peiwen
authors.initials: P
authors.lastname: Yu
authors.forename: Xin
authors.initials: X
authors.lastname: Yan
authors.forename: Shunpeng
authors.initials: S
authors.lastname: Li
mesh_terms: D001711:Biotransformation; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004579:Electron Transport; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006540:Herbicides / Q000378:metabolism*; D008969:Molecular Sequence Data; D010089:Oxidoreductases, N-Demethylating / Q000235:genetics / Q000378:metabolism*; D010671:Phenylurea Compounds / Q000378:metabolism*; D010802:Phylogeny; D016958:Pseudomonas putida / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D042301:Sphingomonadaceae / Q000201:enzymology* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D006540:Herbicides; D010671:Phenylurea Compounds; D010089:Oxidoreductases, N-Demethylating