SNAP output for PDB entry 8ad1 [SNAP web server]

PDB-id

8ad1; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription

Method

cryo-EM (4.1 Å)

Summary

RNA polymerase at u-rich pause bound to RNA putl triple mutant - pause prone, closed clamp state

Reference

Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022): "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020.

Abstract

RNA can regulate its own synthesis without auxiliary proteins. For example, U-rich RNA sequences signal RNA polymerase (RNAP) to pause transcription and are required for transcript release at intrinsic terminators in all kingdoms of life. In contrast, the regulatory RNA putL suppresses pausing and termination in cis. However, how nascent RNA modulates its own synthesis remains largely unknown. We present cryo-EM reconstructions of RNAP captured during transcription of putL variants or an unrelated sequence at a U-rich pause site. Our results suggest how putL suppresses pausing and promotes its synthesis. We demonstrate that transcribing a U-rich sequence, a ubiquitous trigger of intrinsic termination, promotes widening of the RNAP nucleic-acid-binding channel. Widening destabilizes RNAP interactions with DNA and RNA to facilitate transcript dissociation reminiscent of intrinsic transcription termination. Surprisingly, RNAP remains bound to DNA after transcript release. Our results provide the structural framework to understand RNA-mediated intrinsic transcription termination.