Fig. 7

prc controls the VgrR regulon and VgrR promoter-binding landscapes. a Venn diagram showing the number of genes with promoters that potentially bound to VgrR. ChIP-seq was used to identify the VgrR-binding DNAs. Genes identified from the WT strain and the prc mutant are shown. b Predicted consensus VgrR-binding DNA motif based on ChIP-seq data. Weblogo was used to show the nucleotide composition. c Functional classification of the VgrR-regulated genes identified by ChIP-seq. Gene details are listed in Supplementary Table 4. d An electrophoretic mobility shift assay revealed that VgrR directly bound the promoter region of prc. PCR products of the promoter region were labelled with [γ-³²P]ATP and used as DNA probes. Unlabelled DNA and unspecific DNA were used as competitors. The sequence of the DNA probe is shown below, with the VgrR-binding motif in magenta. Numbers indicate the location relative to the translation initiation site. Each experiment was repeated two times. Triangle indicates VgrR–DNA complexes. e vgrR positively controls the transcription of prc. qRT-PCR was used to quantify prc mRNA in different bacterial strains before and after osmostress stimulation (1.0 M sorbitol, 5 min). Amplification of the cDNA of tmRNA was used as an internal control. A representative of three independent experiments is shown. f Deletion of prc decreases VgrR-promoter binding in bacterial cells. ChIP-qPCR was employed to quantify the enrichment of VgrR at the promoter region of prc under osmostress growth conditions (NYG medium plus 1.0 M sorbitol for 5 min) or no stimulation. The experiment was repeated three times. In e and f, error bars indicate the standard deviations. Asterisks indicate significant differences relative to the WT strain (Student’s t-test, P < 0.05)