title: Regulatory system of the protocatechuate 4,5-cleavage pathway genes essential for lignin downstream catabolism.
abstract: Sphingobium sp. strain SYK-6 converts various lignin-derived biaryls with guaiacyl (4-hydroxy-3-methoxyphenyl) and syringyl (4-hydroxy-3,5-dimethoxyphenyl) moieties to vanillate and syringate. These compounds are further catabolized through the protocatechuate (PCA) 4,5-cleavage (PCA45) pathway. In this article, the regulatory system of the PCA45 pathway is described. A LysR-type transcriptional regulator (LTTR), LigR, activated the transcription of the ligK-orf1-ligI-lsdA and ligJABC operons in the presence of PCA or gallate (GA), which is an intermediate metabolite of vanillate or syringate, respectively, and repressed transcription of its own gene. LigR bound to the positions -77 to -51 and -80 to -48 of the ligK and ligJ promoters, respectively, and induced DNA bending. In the presence of PCA or GA, DNA bending on both promoters was enhanced. The LigR-binding regions of the ligK and ligJ promoters in the presence of inducer molecules were extended and shortened, respectively. The LTTR consensus sequences (Box-K and Box-J) in the ligK and ligJ promoters were essential for the binding of LigR and transcriptional activation of both operons. In addition, the regions between the LigR binding boxes and the -35 regions were required for the enhancement of DNA bending, although the binding of LigR to the -35 region of the ligJ promoter was not observed in DNase I footprinting experiments. This study shows the binding features of LigR on the ligK and ligJ promoters and explains how the PCA45 pathway genes are expressed during degradation of lignin-derived biaryls by this bacterium.
authors.affiliation: Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
authors.forename: Naofumi
authors.initials: N
authors.lastname: Kamimura
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Takamura
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Hara
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kasai
authors.forename: Ryo
authors.initials: R
authors.lastname: Natsume
authors.forename: Toshiya
authors.initials: T
authors.lastname: Senda
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Katayama
authors.forename: Masao
authors.initials: M
authors.lastname: Fukuda
authors.forename: Eiji
authors.initials: E
authors.lastname: Masai
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D018983:DNA Footprinting; D003850:Deoxyribonuclease I; D024202:Electrophoretic Mobility Shift Assay; D005707:Gallic Acid / Q000031:analogs & derivatives / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D062385:Hydroxybenzoates / Q000378:metabolism*; D008031:Lignin / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D042301:Sphingomonadaceae / Q000235:genetics / Q000378:metabolism*; D014641:Vanillic Acid / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D062385:Hydroxybenzoates; C009091:protocatechuic acid; D005707:Gallic Acid; D008031:Lignin; C001945:syringic acid; D003850:Deoxyribonuclease I; D014641:Vanillic Acid