The Regulation of para-Nitrophenol Degradation in Pseudomonas putida DLL-E4
Fig 1
(A) Number of differentially expressed genes under different conditions. Genes downregulated or upregulated in P. putida DLL-E4 and DLL-ΔpnpR grown on glucose plus PNP compared to glucose. Venn diagrams show the overlap between downregulated genes and between upregulated genes for each pairwise comparison. (B) Functional classification of differentially expressed genes under different conditions. Each plot indicates the type of physiological role and the total number of genes with increased or decreased expression within that category in cells grown on the relevant conditions (also see S3 and S4 Tables in the Supporting Information). R-GP refers to P. putida DLL-ΔpnpR grown on 0.25% glucose plus 0.5 mM PNP, R-G refers to strain 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 (figure not drawn to scale). The large open arrows indicate the approximate size of each gene and its direction of transcription. Genes within the same operon are indicated by the same color. Two forward slashes stand for a gap in the genome. The circle and hexagons stand for the products of pnpR and pnpR1, respectively. The thick arrow stands for the transcription of pnpR and pnpR1. The thin solid arrow stands for PnpR’s positive action on the two operons pnpA and pnpC1C2DECX1X2. The thin solid question-marked arrow stands for the unclear regulation of operons pnpAb and pnpC1bC2bDbEbCbX1bX2b by PnpR. The folded arrow stands for PnpR1’s positive action on pnpA operon. The dotted question-marked arrow stands for the unambiguous regulation of the pnpC1bC2bDbEbCbX1bX2b operon by PnpR1. The dotted x-marked arrow indicates that PnpR1 does not regulate the pnpC1C2DECX1X2 operon. The curved solid arrow stands for PNP’s positive action on pnpA. The curved folded arrow stands for HQ’s positive action on operons pnpC1C2DECX1X2 and pnpC1bC2bDbEbCbX1bX2b. (D) Proposed pathway for PNP catabolism in P. putida DLL-E4 with the catabolic reactions catalyzed by PNP degradation gene products.