Fig. 3.

Bind-n-seq reveals binding sites of YipR in the Xanthomonas campestris. a Representative results generated by generated by MERMADE under barcode AAA. b Manual filtering from MERMADE shows enriched motifs (Cut-off 3.0 fold) identified under different binding conditions. c The automatic filtering analysis report from MERMADE using Extractmotif package (Cut-off 3.0 fold) shows (d) qRT-PCR analysis reveals that mutation of yipR in leads to the elevation in expression of XC_2633 validating previous observations seen using RNA-seq analysis. e Binding of YipR to the XC_2633 promoter is modulated by the presence and absence of “CCCTCTC” motif. The impact presence and absence of “CCCTCTC” motif on the binding of YipR to the XC_2633 promoter was assessed by the use of electromobility shift assay (EMSA). The DIG-labelled promoter fragment was incubated with purified YipR and XC_2633 promoter with or without binding motif. His-MBP tag alone and DNA fragment alone were used as negative control in the assay