Fig. 6: CdbA binds DNA in a moderately sequence-specific manner.
a CdbA binds DNA with sequence specificity. Upper panels, zoom in on ChIP-seq results for selected DNA fragments from different peaks sorted by peak rank and shown as log2 enrichment over input for one replicate. ORFs are shown as black arrows. Horizontal red line indicates 250 bp fragments used for EMSA analysis with position of peak summit indicated with a vertical red line. Lower panels, EMSA analysis of CdbA binding to DNA fragments shown in upper panels. Concentration of CdbA added is indicated. c-di-GMP was added to a final concentration of 100 µM in the last lane, 10 min prior addition of DNA probe. Kd was calculated based on two replicates. Source data are provided as a Source Data file. b MEME-ChIP results for CdbA binding motif search. Left panels, motif identified based on top 100 peaks and the probability distribution of the identified motif occurrence across the input sequences in which position 0 corresponds to peak summits; right panels, as in the left panels except that the top 500 peaks were analyzed. For both analysis 100 bp (peak summit ±50 bp) were used as input sequences for the MEME-ChIP analysis. c EMSA analysis of CdbA binding to WT and mutant DNA fragments of MXAN_4058 promoter. Below each image, the sequence of the WT binding motif and the two mutant variants are indicated with substituted bp indicated in red. Experiments were done as in (a) and Kd calculated based on two replicates. Source data are provided as a Source Data file. d RT-qPCR analysis of gene expression in WT and a strain depleted for CdbA-mCh for 24 h. Peak rank is indicated. Transcript levels are shown as mean ± SD from three biological replicates with each three technical replicates relatively to WT. *p < 0.05 in two-sided Student’s t-test, between WT and CdbA-mCh depletion. Individual data points are in green–gray. Exact p-values and source data are provided in the Source data file.
