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.
Highlights
Introduction paraNitrophenol (PNP) is listed as a priority environmental pollutant by the United States Environmental Protection Agency [1]
DLL-ΔpnpR grown on 0.25% glucose, E4-GP refers to P. putida DLL-E4 grown on 0.25% glucose plus 0.5 mM PNP, and E4-G refers to strain DLL-E4 grown on 0.25% glucose. (C) Organization and proposed regulatory circuit of the PNP degradation genes of P. putida DLL-E4
A E4-G represents strain DLL-E4 grown on 0.25% glucose. b E4-GP represents strain DLL-E4 grown on 0.25% glucose plus 0.5 mM PNP. c R-G represents strain DLL-ΔpnpR grown on 0.25% glucose. d R-GP represents strain DLL-ΔpnpR grown on 0.25% glucose plus 0.5 mM PNP. doi:10.1371/journal.pone.0155485.t001
Summary
Introduction paraNitrophenol (PNP) is listed as a priority environmental pollutant by the United States Environmental Protection Agency [1]. (ii) Strain DLL-ΔpnpR showed a similar expression profile when grown on PNP plus glucose (represented by R-GP) compared to growth on glucose only (represented by R-G) (Fig 1A). In P. putida DLL-E4 [12], PNP degradation genes are made of two HQ degradation operons (pnpC1C2DECX1X2 and pnpC1bC2bDbEbCbX1bX2b) and the 4 independent genes pnpR, pnpA, pnpB, and pnpAb (S1 Fig, Fig 1C and 1D).
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