Structure/Function of the Bacterial TRCF

Rockefeller University, New York NY

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Abstract

DESCRIPTION (provided by applicant): TRCF (Transcription Repair Coupling Factor) is a widely conserved bacterial protein that couples DNA repair with transcription. TRCF recognizes RNAP stalled at a non-coding template site of DNA damage, disrupts the transcription complex to release the transcript and RNAP, and recruits the DNA excision repair machinery to the site. The mechanism of RNA release has been illuminated by the discovery that TRCF causes forward translocation of RNAP, using an ATP-dependent motor that is highly homologous to that of the Holliday branch migration protein RecG. TRCF is a large (130 kDa), multi-functional protein with a complex structure/function relationship that is currently understood only from sequence analysis and genetic manipulation. In this grant, we propose detailed structural studies to elucidate the structure/function relationship of TRCF, to reveal conformational changes involved in the ATP-hydrolysis cycle and its coupling to the DNA translocase activity, and to reveal the interactions of TRCF with the RNAP ternary elongation complex. Specifically, we propose to: 1. Determine the X-ray crystal structure of TRCF. 2. Determine the structural basis for TRCF DNA translocase activity through X-ray crystal structures with nucleotides and/or nucleotide analogs. 3. Determine the structural basis for the specific transcription termination activity of TRCF through structural studies of an RNAP ternary elongation complex (RNAP/DNA/RNA) with TRCF.