title: The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the beta-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria.
abstract: Terrabacter sp. strain DBF63 is capable of degrading fluorene (FN) to tricarboxylic acid cycle intermediates via phthalate and protocatechuate. Genes were identified for the protocatechuate branch of the beta-ketoadipate pathway (pcaR, pcaHGBDCFIJ) by sequence analysis of a 70 kb DNA region of the FN-catabolic linear plasmid pDBF1. RT-PCR analysis of RNA from DBF63 cells grown with FN, dibenzofuran, and protocatechuate indicated that the pcaHGBDCFIJ operon was expressed during both FN and protocatechuate degradation in strain DBF63. The gene encoding beta-ketoadipate enol-lactone hydrolase (pcaD) was not fused to the next gene, which encodes gamma-carboxymuconolactone decarboxylase (pcaC), in strain DBF63, even though the presence of the pcaL gene (the fusion of pcaD and pcaC) within a pca gene cluster has been thought to be a Gram-positive trait. Quantitative RT-PCR analysis revealed that pcaD mRNA levels increased sharply in response to protocatechuate, and a biotransformation experiment with cis,cis-muconate using Escherichia coli carrying both catBC and pcaD indicated that PcaD exhibited beta-ketoadipate enol-lactone hydrolase activity. The location of the pca gene cluster on the linear plasmid, and the insertion sequences around the pca gene cluster suggest that the ecologically important beta-ketoadipate pathway genes, usually located chromosomally, may be spread widely among bacterial species via horizontal transfer or transposition events.
authors.affiliation: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Habe
authors.affiliation: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Jin-Sung
authors.initials: JS
authors.lastname: Chung
authors.affiliation: Department of Chemistry, Faculty of Sciences, Science University of Tokyo, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Ishida
authors.affiliation: Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, 241-7 Kaidobata-nishi, Shimoshinjo-nakano, Akita 010-0195, Japan.
authors.forename: Kano
authors.initials: K
authors.lastname: Kasuga
authors.affiliation: Geo and Water Environmental Engineering Department, Obayashi Corporation, 4-640 Shimokiyoto, Kiyose-shi, Tokyo 204-0011, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Ide
authors.affiliation: Department of Chemistry, Faculty of Sciences, Science University of Tokyo, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Takemura
authors.affiliation: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Nojiri
authors.affiliation: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Yamane
authors.affiliation: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Toshio
authors.initials: T
authors.lastname: Omori
mesh_terms: D000192:Actinomycetales / Q000235:genetics* / Q000378:metabolism; D000272:Adipates / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002265:Carboxylic Ester Hydrolases / Q000235:genetics / Q000378:metabolism; D005449:Fluorenes / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D062385:Hydroxybenzoates / Q000378:metabolism*; D008969:Molecular Sequence Data; D005810:Multigene Family; D010957:Plasmids / Q000235:genetics*; D020560:Proteobacteria / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D000272:Adipates; D001426:Bacterial Proteins; D005449:Fluorenes; D062385:Hydroxybenzoates; C027316:3-oxoadipic acid; C009091:protocatechuic acid; C041509:fluorene; D002265:Carboxylic Ester Hydrolases; C021927:3-oxoadipate enol-lactonase