Two different modes of transcription repression of the Escherichia coli acetate operon by IcIR

IcIR is a repressor for the Escherichia coli aceBAK operon, which encodes isocitrate lyase (aceB), malate synthase (aceA) and isocitrate dehydrogenase kinase/phosphorylase (aceK) in the glyoxylate bypass. IcIR also represses the expression of icIR in an autogenous manner. DNase I footprinting and in vitro transcription assays indicated that IcIR binds to an IcIR box (-21 to +14), which overlaps the icIR promoter and thus competes with the RNA polymerase for DNA binding, leading to transcription repression. In the case of the aceBAK operon, IcIR binds to IcIR box 11 between -52 and -19 of the aceB promoter and interferes with binding of the RNA polymerase to this promoter. A secondary IcIR binding site (IcIR box 1) was identified between -125 and -99 of the aceB promoter. IcIR binds to this IcIR box I even after formation of the aceB promoter open complex and, moreover, induces disassembly of the open complex, leading to repression of aceB transcription. In parallel, the location of the C-terminal domain of the RNA polymerase a subunit (alphaCTD) on DNA is shifted close to the IcIR box 1, indicating that direct interaction between the aCTD and the IcIR box I-associated IcIR caused the repression.