DOI: 10.1101/453969Oct 26, 2018Paper

RNA polymerase clamp movement aids dissociation from DNA but is not required for RNA release at intrinsic terminators

BioRxiv : the Preprint Server for Biology
Michael J BellecourtRobert Landick

Abstract

In bacteria, viability requires efficient disassembly of elongating transcription complexes (ECs) in a 2-3 nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminator signals trigger pausing over weak RNA-DNA base pairs followed by formation of a strong, GC-rich stem-loop structure in the RNA exit channel of RNA polymerase (RNAP) to inactivate nucleotide addition and induce dissociation of RNA and RNAP from DNA. Although study of RNA and DNA movements during termination has produced multiple models, the roles of RNAP conformational changes remain poorly defined. RNAP contains a clamp domain that closes around the nucleic-acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp displacement is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine-crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that these perturbations were due primarily to changes in elongation rate, not the competing rate at which the EC commits to termination. After commitment, however, in...Continue Reading

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