# Bacterial Transcription Complexes

> **NIH NIH R37** · RUTGERS, THE STATE UNIV OF N.J. · 2020 · $91,141

## Abstract

Project Summary
This proposal addresses transcription initiation, elongation, and termination by bacterial RNA polymerase
(RNAP).
In transcription initiation, RNAP: (i) binds to promoter DNA, yielding an RNAP-promoter closed complex; (ii)
unwinds promoter DNA, yielding an RNAP-promoter open complex; (iii) synthesizes the first ~11 nucleotides of
RNA as an RNAP-promoter initial transcribing complex, using a "scrunching" mechanism in which RNAP
remains stationary on promoter DNA and pulls in adjacent DNA in each nucleotide-addition cycle; and (iv)
escapes from the promoter. In transcription elongation, RNAP synthesizes the remaining nucleotides of RNA
as an RNAP-DNA elongation complex, using a "stepping" mechanism in which RNAP moves forward on DNA
in each nucleotide-addition cycle. In transcription termination, RNAP stops synthesizing RNA, releases RNA,
and dissociates from DNA. Each of these reactions is a target for regulators. Understanding transcription
initiation, elongation, termination, and regulation will require defining the structural transitions in protein and
DNA in each reaction, the kinetics of structural transitions, and the mechanisms by which regulators affect
structural transitions.
In the current period, we defined the structural basis of transcription start-site selection, de novo transcription
initiation, non-canonical-initiating-nucleotide-dependent transcription initiation, initial transcription, and Class II
transcription activation; we developed high-throughput-sequencing approaches that enable comprehensive
analysis of DNA-sequence determinants for transcription; we developed multiplexed crosslinking approaches
that enable comprehensive analysis of protein-DNA interactions in transcription; we developed ensemble and
single-molecule fluorescence assays that enable monitoring of RNAP clamp and RNAP trigger-loop
conformation in solution; and we defined binding sites and mechanisms for small-molecule inhibitors of
transcription.
The proposed work will build on the findings of the current period. The proposed work will use x-ray
crystallography, single-molecule biophysics, biochemistry, and genetics to address five specific aims:
Specific Aim 1: Determination of the structural basis of RNAP slippage
Specific Aim 2: Determination of the structural basis of RNAP translocation
Specific Aim 3: Analysis of RNAP translocation in elongation, pausing, and termination
Specific Aim 4: Analysis of RNAP clamp conformation in elongation, pausing, and termination
Specific Aim 5: Analysis of RNAP trigger-loop conformation in elongation, pausing, and termination

## Key facts

- **NIH application ID:** 10133797
- **Project number:** 3R37GM041376-32S1
- **Recipient organization:** RUTGERS, THE STATE UNIV OF N.J.
- **Principal Investigator:** RICHARD H. EBRIGHT
- **Activity code:** R37 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $91,141
- **Award type:** 3
- **Project period:** 2020-05-01 → 2021-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10133797

## Citation

> US National Institutes of Health, RePORTER application 10133797, Bacterial Transcription Complexes (3R37GM041376-32S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10133797. Licensed CC0.

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