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

> **NIH NIH R35** · ROCKEFELLER UNIVERSITY · 2021 · $53,560

## 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. Advances in this understanding are stuck on the difficulty of
visualizing transient intermediates that underlie the key transitions between stable states of the
transcription cycle, and the difficulty of visualizing complex macromolecular assemblies involved in
regulation, structural problems where X-ray crystallography has severe limitations.
While the stable RNAP states around the transcription cycle (RNAP catalytic core, RNAP
holoenzyme, RNAP holoenzyme open promoter complex, RNAP elongation complex) are relatively
well characterized and understood, the transitions between the stable states are poorly understood.
Major transitions include:
Holoenzyme + promoter DNA è open promoter complex (initiation)
Open promoter complex è elongation complex (promoter escape, σ dissociation)
Elongation complex è core RNAP + DNA + completed RNA transcript (termination)
Each of these transitions are characterized by unstable, transient intermediates that are extremely
challenging for structural biology.
At every stage of the transcription cycle, RNAP function is modulated by interactions with extrinsic
regulatory factors. Assembling and crystallizing transcription complexes containing extrinsic
regulators also presents challenges for structural biology.
Due to recent advances, cryo-electron microscopy (cryo-EM) now offers a route to structural and
mechanistic characterization of these intermediates and large assemblies. We will use cryo-electron
microscopy, in combination with X-ray crystallography and other approaches, to exploit this
opportunity and provide a complete characterization of the bacterial transcription cycle.

## Key facts

- **NIH application ID:** 10388954
- **Project number:** 3R35GM118130-06S1
- **Recipient organization:** ROCKEFELLER UNIVERSITY
- **Principal Investigator:** Seth A. Darst
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $53,560
- **Award type:** 3
- **Project period:** 2016-05-01 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10388954

## Citation

> US National Institutes of Health, RePORTER application 10388954, Structure, function, and regulation of the bacterial transcription cycle (3R35GM118130-06S1). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10388954. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*