Functional organization of the ends of IS1: specific binding site for an IS1-encoded protein

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Abstract
The IS1-encoded protein InsA binds specifically to both ends of IS1, and acts as a repressor of IS1 gene expression and may be a direct inhibitor of the transposition process. We show here, using DNase I ''footprinting'' and gel retardation, that the InsA binding sites are located within the 24/25 bp minimal active ends of IS1 and that INsA induces DNA bending upon binding. Conformational modification of the ends of IS1 as a result of binding of the host protein integration host factor (IHF) to its site within the minimal ends has been previously observed. Using a collection of synthetic mutant ends we have mapped some of the nucleotide sequence requirements for InsA binding and for transposition activity. We show that sequences necessary for InsA binding are also essential for transposition activity. We demonstrate that InsA and IHF binding sites overlap since some sequence determinants are shared by both InsA and IHF. The data suggest that these ends contain two functional domains: one for binding of InsA and IHF, and the other for transposition activity. A third region, when present, may enhance transposition activity with an intact right end. This ''architecture'' of the ends of IS1 is remarkably similar to that of IS elements IS10, IS50 and IS903.