Conformational Heterogeneity and Bubble Dynamics in Single Bacterial Transcription Initiation Complexes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Nov 28

PMID 29177430

Citations 12

Authors

Diego Duchi

Kristofer Gryte

Nicole C Robb

Zakia Morichaud

Carol Sheppard

Konstantin Brodolin

Sivaramesh Wigneshweraraj

Achillefs N Kapanidis

Affiliations

Soon will be listed here.

Abstract

Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP-DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.

Citing Articles

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Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway.

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The dynamic landscape of transcription initiation in yeast mitochondria.

Sohn B, Basu U, Lee S, Cho H, Shen J, Deshpande A Nat Commun. 2020; 11(1):4281.

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