Analysis of Regions within the Bacteriophage T4 AsiA Protein Involved in its Binding to the σ70 Subunit of E. coli RNA Polymerase and its Role as a Transcriptional Inhibitor and Co-activator

Abstract Bacteriophage T4 AsiA, a protein of 90 amino acid residues, binds to the σ 70 subunit of Escherichia coli RNA polymerase and inhibits host or T4 early transcription or, together with the T4 MotA protein, activates T4 middle transcription. To investigate which regions within AsiA are involved in forming a complex with σ 70 and in providing transcriptional functions we generated random mutations throughout AsiA and targeted mutations within the C-terminal region. We tested mutant proteins for their ability to complement the growth of T4 asiA am phage under non-suppressing conditions, to inhibit E. coli growth, to interact with σ 70 region 4 in a two-hybrid assay, to bind to σ 70 in a native protein gel, and to inhibit or activate transcription in vitro using a T4 middle promoter that is active with RNA polymerase alone, is inhibited by AsiA, and is activated by MotA/AsiA. We find that substitutions within the N-terminal half of AsiA, at amino acid residues V14, L18, and I40, rendered the protein defective for binding to σ 70 . These residues reside at the monomer–monomer interface in recent NMR structures of the AsiA dimer. In contrast, AsiA missing the C-terminal 44 amino acid residues interacted well with σ 70 region 4 in the two-hybrid assay, and AsiA missing the C-terminal 17 amino acid residues (Δ74–90) bound to σ 70 and was fully competent in standard in vitro transcription assays. However, the presence of the C-terminal region delayed formation of transcriptionally competent species when the AsiA/polymerase complex was pre-incubated with the promoter in the absence of MotA. Our results suggest that amino acid residues within the N-terminal half of AsiA are involved in forming or maintaining the AsiA/σ 70 complex. The C-terminal region of AsiA, while not absolutely required for inhibition or co-activation, aids inhibition by slowing the formation of transcription complexes between a promoter and the AsiA/polymerase complex.