Poster abstracts

Poster number 146 submitted by Zhaokun Liu

Dissecting the role of ops sequence in recruiting transcription factor RfaH

Zhaokun Liu (Department of Microbiology and The Center for RNA Biology, The Ohio State University), Irina Artsimovitch (Department of Microbiology and The Center for RNA Biology, The Ohio State University)

Abstract:
Synthesis of long RNAs by RNA polymerases (RNAP) requires accessory factors that help RNAP to overcome numerous roadblocks along the template. RfaH, the best characterized regulator capable of switching the elongating RNAP into a processive state, belongs to the only universally conserved family of transcription factors. RfaH is recruited to the transcription elongation complex via direct interactions with bases of a 12-nt ops element in the non-template DNA strand exposed on the surface of RNAP. The individual roles of these 12 nucleotides remain unclear: while some nucleotides may directly interact with RfaH, others could exert their effects through interaction with RNAP. Initial molecular modeling suggested that only the upstream 6 ops nucleotides can interact with RfaH, but in vivo lux reporter assays demonstrated that substitutions in the downstream half of the ops element have equally strong effect on gene expression. The latter substitutions may interfere with RNAP pausing at ops T11 position, which was hypothesized to be essential for RfaH recruitment. Recent structural studies suggested that pockets on RNAP may contribute to base-specific recognition of the template and non-template DNA strands during transcription. In this work, we probed the roles of ops nucleotides in RNAP pausing and RfaH recruitment.

Keywords: RfaH recruitment, ops element, base specific recruitment