# Mechanism, Activation, and Control of rRNA Transcription

> **NIH NIH R01** · UNIVERSITY OF WISCONSIN-MADISON · 2020 · $584,184

## Abstract

PROJECT SUMMARY / ABSTRACT:
The synthesis of the translation apparatus is central to growth and development of all organisms,
and its regulation has been a central issue in molecular microbioogy for over 50 years. Recently,
it has become clear that an understanding of the mechanisms responsible for rRNA and tRNA
transcription can provide fundamental insights into the mechanism of transcription in general.
We determined in the previous project period that not only does the nucleotide derivative ppGpp
directly regulate rRNA promoters, but it also directly regulates transcription much more widely
than previously expected, with more than 700 transcripts changing either negatively or positively
within 5 minutes of ppGpp induction. In the major aim of the proposal, we will analyze the
regulation of transcription by ppGpp and its cofactor DksA. We found that there are two distinct
binding sites for ppGpp on E. coli RNA polymerase (RNAP). We will determine the binding
affinities of ppGpp for each binding site, determine whether binding is cooperative, develop and
test mechanistic models for ppGpp action at each site including the mechanism of positive control,
determine the regulatory roles of each ppGpp binding site on different promoters in vitro and in
vivo, and address the roles of the two sites in regulation of transcription elongation. Finally, we
will use metabolomic and proteomic approaches to identify ppGpp targets on proteins other than
RNAP and investigate their significance.
In the second aim, we will investigate the mechanisms of transcription factors that, like DksA, bind
directly to RNAP. These include TraR and its homologs, distant DksA-like proteins carried on
widely-distributed extrachromosomal elements; R. sphaeroides DksA-like and CarD-like proteins
that appear to be important for regulation for responses to light; and E. coli Crl, a Sigma S
holoenzyme assembly factor.
We recently discovered that E. coli rRNA operons form a bacterial nucleolus-like structure that is
not dependent on transcription but nevertheless requires the rRNA promoter region. In the third
aim, we will continue to determine the cis- and trans-acting determnants for this structure and its
consequences for cellular physiology.

## Key facts

- **NIH application ID:** 9980419
- **Project number:** 5R01GM037048-34
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** Richard L. Gourse
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $584,184
- **Award type:** 5
- **Project period:** 1988-07-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9980419

## Citation

> US National Institutes of Health, RePORTER application 9980419, Mechanism, Activation, and Control of rRNA Transcription (5R01GM037048-34). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9980419. Licensed CC0.

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