Conformational changes of the upstream DNA mediated by H-NS and FIS regulate E. coli RrnB P1 promoter activity.

The two proteins FIS and H-NS had previously been shown to regulate ribosomal RNA (rRNA) transcription by interacting with the promoter upstream DNA. FIS is known as an activator whereas H-NS had been demonstrated to function as a repressor. Details of the antagonistic control mechanisms are not yet solved. Here, we have addressed the question how the two proteins cooperate to exert both, positive and negative control of rRNA transcription. By mobility shift experiments and footprinting studies we show that FIS and H-NS binding sites partially overlap but appear to interact with different sites of a curved DNA helix. Although not mutually exclusive, the two proteins compete each other for binding. Both proteins, by changing the DNA curvature, effect circularization reactions of DNA fragments in different ways. Our results imply that binding of the proteins induces alternate DNA conformations with favourable or unfavourable topology for the formation of active transcription complexes. Together the findings presented here help to answer some of the open questions about the concerted molecular mechanism of transcription factors for the regulation of stable RNA synthesis.