Structural Basis for Bacterial Transcription-Coupled DNA Repair

Abstract

Coupling of transcription and DNA repair in bacteria is mediated by transcription-repair coupling factor (TRCF, the product of the mfd gene), which removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair machinery to the site. Here we describe the 3.2 A-resolution X-ray crystal structure of Escherichia coli TRCF. The structure consists of a compact arrangement of eight domains, including a translocation module similar to the SF2 ATPase RecG, and a region of structural similarity to UvrB. Biochemical and genetic experiments establish that another domain with structural similarity to the Tudor-like domain of the transcription elongation factor NusG plays a critical role in TRCF/RNA polymerase interactions. Comparison with the translocation module of RecG as well as other structural features indicate that TRCF function involves large-scale conformational changes. These data, along with a structural model for the interaction of TRCF with the transcription elongation complex, provide mechanistic insights into TRCF function.

A Tandem of SH3-like Domains Participates in RNA Binding in KIN17, a Human Protein Activated in Response to Genotoxics

“…14,15 Furthermore, a Tudor-like domain structurally similar to domain III of NusG and to the subdomains of the hKIN17 C-terminal domain was found recently in the bacterial transcription-repair coupling factor (TRCF), where it mediates interaction with the β subunit of RNA polymerase. 49 Consistently, the C-terminal domain of hKIN17 as the whole protein co-immunoprecipitate with the RNA polymerase II in HeLa nuclear extracts (G.P.-L., unpublished results). Further investigation will be required to identify which cellular RNA interacts with hKIN17 and to understand how hKIN17 functions in RNA metabolism.…”

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

“…3A). UvrB and TRCF are critical components of nucleotide excision repair (NER) system in DNA damage repairs (15,16). The corresponding homologous domains in UvrB and TRCF specifically bind to a domain in UvrA in a competitive manner to coordinate the functionality of bacterial NER system.…”

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

“…Another RNAPassociated transcription factor that promotes forward hypertranslocation of RNAP is the Mfd, an ATPase-dependent DNA translocase (45,46). It binds to the upstream DNA and promotes the forward hypertranslocation of stalled RNAP, leading to the removal of RNAP from the DNA template (47).…”