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

PLoS One. 2016 May 18;11(5):e0155485. doi: 10.1371/journal.pone.0155485. eCollection 2016.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodegradation, Environmental
  • Biotransformation
  • Environmental Pollutants / metabolism*
  • Gene Deletion
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Glucose / metabolism
  • High-Throughput Nucleotide Sequencing
  • Metabolic Networks and Pathways
  • Nitrophenols / metabolism*
  • Operon
  • Pseudomonas putida / genetics*
  • Pseudomonas putida / metabolism*
  • RNA, Untranslated / genetics
  • Transcription, Genetic

Substances

  • Environmental Pollutants
  • Nitrophenols
  • RNA, Untranslated
  • Glucose

Grants and funding

Support was provided by: National Natural Science Foundation of China. No. 31400098 [http://www.nsfc.gov.cn/] to ZLC (This funder had a role in data collection and analysis and decision to publish); National Natural Science Foundation of China. No. 31270095 [http://www.nsfc.gov.cn/] to ZLC (This funder had a role in data collection and analysis, decision to publish); Natural Science Foundation of Jiangsu Province. No. BK2012029 [http://www.jskjjh.gov.cn] to ZLC (This funder had a role in data collection and analysis, decision to publish).