title: Location and sequence analysis of a 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase-encoding gene (bpdF) of the biphenyl/polychlorinated biphenyl degradation pathway in Rhodococcus sp. M5.
abstract: The 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPD) hydrolase-encoding gene (bpdF) in the biphenyl (BP)/polychlorinated biphenyl (PCB)-degrading bacterium, Rhodococcus sp. M5 (M5), was found to be located within a 4.5-kb HindIII-BamHI genomic DNA that was 5.4 kb downstream from the bpdC1C2BADE gene cluster. The deduced amino acid (aa) sequence of bpdF revealed that the hydrolase contains 297 aa (32679 Da) that was verified by expression in the Escherichia coli T7 RNA polymerase/promoter system. Unlike previously known HOPD hydrolases, the aa sequence of BpdF appears unique. Interestingly, all HOPD hydrolases and related proteins from the phenol and toluene/xylene degradation pathways, were found to have a bias in the codon usage in the catalytic Ser within the conserved VGNS(M/F)GG motif.
authors.affiliation: Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec, Canada. LAU@biotech.lan.nrc.ca
authors.forename: P C
authors.initials: PC
authors.lastname: Lau
authors.forename: J
authors.initials: J
authors.lastname: Garnon
authors.forename: D
authors.initials: D
authors.lastname: Labbé
authors.forename: Y
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001673:Biodegradation, Environmental; D003001:Cloning, Molecular; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence; D005231:Fatty Acids, Unsaturated / Q000378:metabolism*; D005798:Genes, Bacterial / Q000235:genetics*; D006867:Hydrolases / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D011078:Polychlorinated Biphenyls / Q000378:metabolism; D015183:Restriction Mapping; D012240:Rhodococcus / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012694:Serine / Q000235:genetics; D013379:Substrate Specificity
chemical_list: D003062:Codon; D005231:Fatty Acids, Unsaturated; D012694:Serine; C018971:2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoic acid; D011078:Polychlorinated Biphenyls; D006867:Hydrolases; C062907:2,6-dioxo-6-phenylhexa-3-enoate hydrolase