Characterization of the Interactions between the Bacteriophage T4 AsiA Protein and RNA Polymerase

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Abstract
The anti-σ factor AsiA effects a change in promoter specificity of the Escherichia coli RNA polymerase via interactions with two conserved regions of the σ70 subunit, denoted 4.1 and 4.2. Free AsiA is a symmetrical homodimer. Here, we show that AsiA is monomeric when bound to σ70 and that a subset of the residues that contribute to the homodimer interface also contributes to the interface with σ70. AsiA interacts primarily with C-terminal sections of regions 4.1 and 4.2, which show remarkable sequence similarity. An AsiA monomer can simultaneously, and apparently cooperatively, bind both isolated regions 4.1 and 4.2 at preferred, distinct subsites, whereas region 4.1 alone or region 4.2 alone can interact with either subsite. These results suggest structural and functional plasticity in the interaction of AsiA with σ70 and support the notion of discrete roles for regions 4.1 and 4.2 in transcription regulation by AsiA. Furthermore, we show that AsiA inhibits recognition of the −35 consensus promoter element by region 4 of σ70 indirectly, as the residues on region 4 responsible for AsiA binding are distinct from those involved in DNA binding. Finally, we show that AsiA must directly disrupt the interaction of region 4 with the RNA polymerase β subunit flap domain, resulting in a distance change between region 2 and region 4 of σ70. Thus, a new paradigm for transcription regulation by AsiA is emerging, whereby the distance between the DNA binding domains in σ70 is regulated, and promoter recognition specificity is modulated, by mediating the interactions of the σ region 4 with the β subunit flap domain.

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