title: Impact of pnpR, a LysR-type regulator-encoding gene, on the cellular processes of Pseudomonas putida DLL-E4.
abstract: LysR-type transcriptional regulators (LTTRs) regulate various cellular processes in bacteria. pnpR is an LTTR-encoding gene involved in the regulation of hydroquinone (HQ) degradation, and its effects on the cellular processes of Pseudomonas putida DLL-E4 were investigated at the physiological, biochemical and molecular levels. Reverse transcription polymerase chain reaction revealed that pnpR positively regulated its own expression and that of the pnpC1C2DECX1X2 operon; additionally, pnpR partially regulated the expression of pnpA when P. putida was grown on para-nitrophenol (PNP) or HQ. Strains DLL-E4 and DLL-ΔpnpR exhibited similar cellular morphologies and growth rates. Transcriptome analysis revealed that pnpR regulated the expression of genes in addition to those involved in PNP degradation. A total of 20 genes were upregulated and 19 genes were downregulated by at least 2-fold in strain DLL-ΔpnpR relative to strain DLL-E4. Bioinformatic analysis revealed putative PnpR-binding sites located in the upstream regions of genes involved in PNP degradation, carbon catabolite repression and other cellular processes. The utilization of L-aspartic acid, L-histidine, L-pyroglutamic acid, L-serine, γ-aminobutyric acid, D,L-lactic acid, D-saccharic acid, succinic acid and L-alaninamide was increased at least 1.3-fold in strain DLL-ΔpnpR as shown by BIOLOG assays, indicating that pnpR plays a potential negative regulation role in the utilization of carbon sources.
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Qiongzhen
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Hui
authors.initials: H
authors.lastname: Tu
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Fei
authors.initials: F
authors.lastname: Huang
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Yicheng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 211800, P.R. China.
authors.forename: Weiliang
authors.initials: W
authors.lastname: Dong
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Wenhui
authors.initials: W
authors.lastname: Wang
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Zhoukun
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, P.R. China.
authors.forename: Fei
authors.initials: F
authors.lastname: Wang
authors.affiliation: Key Laboratory of Agricultural Environmental Microbiology, the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China czl@njau.edu.cn.
authors.forename: Zhongli
authors.initials: Z
authors.lastname: Cui
mesh_terms: D001224:Aspartic Acid / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D057465:Catabolite Repression; D019295:Computational Biology; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005809:Genes, Regulator; D006639:Histidine / Q000378:metabolism; D019344:Lactic Acid / Q000378:metabolism; D009596:Nitrophenols / Q000378:metabolism; D009876:Operon; D016958:Pseudomonas putida / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D012694:Serine / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D001426:Bacterial Proteins; D009596:Nitrophenols; D001224:Aspartic Acid; D019344:Lactic Acid; D012694:Serine; D006639:Histidine
keywords: PNP degradation; Pseudomonas putida DLL-E4; carbon source utilization; cellular process; gene regulation; pnpR deletion