Repression of transcription initiation by Escherichia coli FNR protein: repression by FNR can be simple

Naturally occurring promoters that are repressed by the Escherichia coli FNR protein are complex. In this work, we have constructed a simple semi-synthetic promoter that is repressed by FNR binding to a single site that overlaps the promoter -35 element. Our results show that a single site for FNR is sufficient for effective repression. This semi-synthetic promoter provides a simple tool for monitoring FNR binding to target sites in the absence of its activation function. We have exploited this to study FNR mutants that are defective in repressing the ndh promoter, a complex naturally occurring promoter that is repressed by FNR.