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. 2021 Nov 4;12:6382. doi: 10.1038/s41467-021-26636-7

Fig. 5. PT modification activates phage SW1 by influencing the repressor FpsR.

Fig. 5

a RTLs of SW1 genes in the WP3NR/Dnd and WP3NR/DndΔE strains with point mutations in PT modification sites. b RTLs of SW1 genes in the WP3NR/Dnd and WP3NR/DndΔE strains with fpsR gene deletion. c RF DNA and ssDNA copy numbers of pSW2Dnd-IG and pSW2DndΔE-IG. d RF DNA and ssDNA copy numbers of pSW2DndΔR and pSW2DndΔEΔR. Data are represented as mean ± s.d. and based on three biologically independent samples. The significances were analyzed by two-sided unpaired Student’s t test. Specifically, P = 0.6671 (ns) for fpsA and P = 0.9976 (ns) for fpsB of pSW2Dnd-IG vs pSW2DndΔE-IG; P = 0.5763 (ns) for RF DNA and P = 0.4729 (ns) for pSW2Dnd-IG vs pSW2DndΔE-IG; P = 0.5352 (ns) for fpsA and P = 0.8514 (ns) for fpsB of pSW2DndΔR vs pSW2DndΔEΔR; P = 0.0927 (ns) for RF DNA and P = 0.0486 (∗) for ssDNA of pSW2DndΔR vs pSW2DndΔEΔR. e Chemically synthesized PT-modified DNA probe for SPR assays. The transcription start sites of fpsA are marked with angled arrows. The −35/−10 consensus elements of the fpsA promoter are underlined with solid lines. The PT modification sites and FpsR operator site (O4) are highlighted in yellow and blue, respectively. f. SPR sensorgrams of the binding of FpsR to normal and PT-modified DNA. The FpsR protein was injected over the sensor chip at concentrations ranging from 0.449 to 57.54 nM, and the DNA-binding activity is given in response units (RU). The KD of FpsR binding was subsequently determined. g RTLs of the fpsR gene in different WP3NR strains. Data are represented as mean ± s.d. and based on three biologically independent samples. The significances were analyzed by two-sided unpaired Student’s t test. Specifically, P = 0.0013 (∗∗) and P = 0.8737 (ns) for fpsR in WP3NR/Dnd vs WP3NR/DndΔE and WP3NR/Dnd-IG vs WP3NR/DndΔE-IG, respectively. h Proposed underlying mechanism responsible for the derepression of phage SW1 gene transcription by PT modification. In the WP3NR/Dnd strain, the significantly reduced amount of FpsR preferentially binds to PT-modified DNA instead of normal DNA due to a higher binding affinity, thereby releasing a proportion of the phage promoter to be derepressed. Moreover, as the PT motifs are dynamically and partially modified, a “lagged effect” due to the different time requirements for the change in PT modification status and the reestablishment of prophage repression, may also contribute to the derepression of phage gene transcription. Source data are provided as a Source Data file.