# Structure, function, and regulation of the bacterial transcription cycle

> **NIH NIH R35** · ROCKEFELLER UNIVERSITY · 2021 · $893,989

## Abstract

Project Summary
Transcription is the major control point of gene expression and RNA polymerase (RNAP), conserved
from bacteria to man, is the central enzyme of transcription. Our long term goal is to understand the
mechanism of transcription and its regulation. Determining three-dimensional structures of RNAP and
its complexes with DNA, RNA, and regulatory factors, is an essential step. We focus on highly
characterized prokaryotic RNAPs.
The basic elements of the transcription cycle, initiation, elongation, and termination, were elucidated
through study of prokaryotes. A detailed structural and functional understanding of the entire
transcription cycle is essential to explain the fundamental control of gene expression and to target
RNAP with small-molecule antibiotics. Moreover, a complete understanding of how a complex,
molecular machine uses binding and chemical energy to effect conformational changes that drive the
cycle, and how regulators modulate the cycle, is of fundamental interest.
The transcription cycle is marked by a series of stable complexes (core è holo è RPo è EC) that
interconvert through transient intermediates. The transitions between stable states are points of
heavy regulation that are poorly understood due to the lack of structural information. Major transitions
include:
Holoenzyme + promoter DNA è open promoter complex (initiation)
Open promoter complex è elongation complex (promoter escape, s dissociation)
Elongation complex è core RNAP + DNA + completed RNA transcript (termination)
Each of these transitions is characterized by unstable, transient intermediates that are extremely
challenging for structural biology. Cryo-electron microscopy (cryo-EM) has emerged as a powerful
method to visualize these transient states. We are combining cryo-EM with other approaches to
mechanistically and structurally characterize transient intermediates that govern transitions in the
bacterial transcription cycle, including promoter melting, the initiation to elongation transition, and
transcription termination. These findings will provide insight into the behavior of macromolecular
machines throughout biology.

## Key facts

- **NIH application ID:** 10167429
- **Project number:** 2R35GM118130-06
- **Recipient organization:** ROCKEFELLER UNIVERSITY
- **Principal Investigator:** Seth A. Darst
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $893,989
- **Award type:** 2
- **Project period:** 2016-05-01 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10167429

## Citation

> US National Institutes of Health, RePORTER application 10167429, Structure, function, and regulation of the bacterial transcription cycle (2R35GM118130-06). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10167429. Licensed CC0.

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