Fig. 6

Changes in DNA binding affinity of WatR upon acetate stress. A Induction of watP and watS1 gene expression by acetate. The JHM16WF strain expressing watR-Flag from the P_EFTu promoter was grown in NMS medium with 20% (v/v) methane and treated with 3.0 g/L of acetate for 10 min. The mRNA expression levels were detected by qRT-PCR and indicated as values relative to those of untreated control. Each value represents the average ± SD of the relative fold enrichment of three independent experiments, normalized to glgA. Significant difference from untreated sample is shown as **p < 0.05. B Changes in WatR DNA binding upon acetate stress. The JHM16WF strain was grown in NMS medium with 20% (v/v) methane and treated with 3.0 g/L of acetate for 10 min. ChIP analysis was performed with anti-Flag antibody and WatR binding to the promoters was detected by qPCR. Each value represents the average ± SD of the relative fold enrichment of two independent experiments, normalized to a negative control (glgA ORF). Significant difference from untreated sample is shown as *p < 0.1; **p < 0.05. C Model for the WatR-dependent transcriptional regulation of watPAB and watO genes. The WatR-binding sites does not overlap with the RNA binding sites, enabling basal transcription. Upon acetate stress, WatR activates transcription, which involves increasing DNA binding affinity. D Model for the WatR-dependent transcriptional regulation of smORFs. The WatR-binding sites overlap with the RNA binding sites, repressing basal transcription. Upon acetate stress, WatR activates transcription possibly by shifting the binding site to expose the RNA polymerase binding site