The Regulation of para-Nitrophenol Degradation in Pseudomonas putida DLL-E4

• Published in: PloS one 2016-05, Vol.11 (5), p.e0155485-e0155485
• Main Authors: Chen, Qiongzhen, Tu, Hui, Luo, Xue, Zhang, Biying, Huang, Fei, Li, Zhoukun, Wang, Jue, Shen, Wenjing, Wu, Jiale, Cui, Zhongli
• Format: Article
• Language: English
• Subjects: Agriculture; Biodegradation; Biodegradation, Environmental; Biology and Life Sciences; Biotransformation; Carbon; Catabolite repression; Degradation; Environmental Pollutants - metabolism; Environmental protection; Gene Deletion; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene regulation; Genes; Genetic aspects; Genomes; Genomics; Glucose; Glucose - metabolism; Glucose dehydrogenase; High-Throughput Nucleotide Sequencing; Hydroquinone; Laboratories; Metabolic Networks and Pathways; Metabolism; Metabolites; Microbial metabolism; Microorganisms; Nitrophenol; Nitrophenols - metabolism; Operon; Physical Sciences; Physiological aspects; Pollutants; Pseudomonas; Pseudomonas putida; Pseudomonas putida - genetics; Pseudomonas putida - metabolism; Regulations; Research and analysis methods; RNA, Untranslated - genetics; Supplementation; Supplements; Transcription; Transcription, Genetic; Transfer RNA; Tricarboxylic acid cycle
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0155485

Pseudomonas putida DLL-E4 can efficiently degrade para-nitrophenol and its intermediate metabolite hydroquinone. The regulation of para-nitrophenol degradation was studied, and PNP induced a global change in the transcriptome of P. putida DLL-E4. When grown on PNP, the wild-type strain exhibited significant downregulation of 2912 genes and upregulation of 845 genes, whereas 2927 genes were downregulated and 891 genes upregulated in a pnpR-deleted strain. Genes related to two non-coding RNAs (ins1 and ins2), para-nitrophenol metabolism, the tricarboxylic acid cycle, the outer membrane porin OprB, glucose dehydrogenase Gcd, and carbon catabolite repression were significantly upregulated when cells were grown on para-nitrophenol plus glucose. pnpA, pnpR, pnpC1C2DECX1X2, and pnpR1 are key genes in para-nitrophenol degradation, whereas pnpAb and pnpC1bC2bDbEbCbX1bX2b have lost the ability to degrade para-nitrophenol. Multiple components including transcriptional regulators and other unknown factors regulate para-nitrophenol degradation, and the transcriptional regulation of para-nitrophenol degradation is complex. Glucose utilization was enhanced at early stages of para-nitrophenol supplementation. However, it was inhibited after the total consumption of para-nitrophenol. The addition of glucose led to a significant enhancement in para-nitrophenol degradation and up-regulation in the expression of genes involved in para-nitrophenol degradation and carbon catabolite repression (CCR). It seemed that para-nitrophenol degradation can be regulated by CCR, and relief of CCR might contribute to enhanced para-nitrophenol degradation. In brief, the regulation of para-nitrophenol degradation seems to be controlled by multiple factors and requires further study.