bacteriophage T4 AsiA protein contacts the β-flap domain of RNA polymerase

• Published in: Proceedings of the National Academy of Sciences - PNAS 2009, Vol.106 (16), p.6597-6602
• Main Authors: Yuan, Andy H, Nickels, Bryce E, Hochschild, Ann
• Format: Article
• Language: English
• Subjects: bacteria; bacteriophages; DNA; DNA-directed RNA polymerase; Escherichia coli; regulatory proteins; sigma factors
• ISSN: 0027-8424; 1091-6490

To initiate transcription from specific promoters, the bacterial RNA polymerase (RNAP) core enzyme must associate with the initiation factor σ, which contains determinants that allow sequence-specific interactions with promoter DNA. Most bacteria contain several σ factors, each of which directs recognition of a distinct set of promoters. A large and diverse family of proteins known as "anti-σ factors" regulates promoter utilization by targeting specific σ factors. The founding member of this family is the AsiA protein of bacteriophage T4. AsiA specifically targets the primary σ factor in Escherichia coli, σ⁷⁰, and inhibits transcription from the major class of σ⁷⁰-dependent promoters. AsiA-dependent transcription inhibition has been attributed to a well-documented interaction between AsiA and conserved region 4 of σ⁷⁰. Here, we establish that efficient AsiA-dependent transcription inhibition also requires direct protein-protein contact between AsiA and the RNAP core. In particular, we demonstrate that AsiA contacts the flap domain of the RNAP β-subunit (the β-flap). Our findings support the emerging view that the β-flap is a target site for regulatory proteins that affect RNAP function during all stages of the transcription cycle.