The combined contribution of both RhlI and PqsE to RhlR binding.

The combined contribution of RhlI and PqsE to RhlR binding was calculated using ChIP-seq enrichment values from Table 1 at each ChIP-seq peak center using the following equation: (WTenrichment—ΔrhlIΔpqsE_enrichment)/(WTenrichment—ΔrhlR_enrichment)*100. We note that values were greater than 100% for ten sites (indicated by #), likely due to experimental noise (eight values were <140%). There were also three values <0, and those were set to 0 (indicated by ^). These were cases where RhlR binding increased in the ΔrhlIΔpqsE strain, but binding in the WT strain was also very low, and we were unable to identify a match to the RhlR consensus motif associated with these sites. Characterized QS genes of interest are highlighted: lecB (magenta), lasB (dark green), hcnA (light green), rhlA (cyan), phzA1 (olive), and phzA2 (brown).

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