# Mechanism of transcript elongation control by RfaH

> **NIH NIH R01** · OHIO STATE UNIVERSITY · 2021 · $374,091

## Abstract

NusG/Spt5 proteins are the only known universally conserved transcriptional regulators that
coevolved with RNA polymerase since the last universal common ancestor. The best studied
members of this family are Escherichia coli NusG, an essential housekeeping protein that acts
together with the transcription termination factor Rho to silence foreign DNA and antisense
transcription, and its paralog RfaH, a non-essential protein required for expression of a few
horizontally-acquired operons that contain an ops sequence in their leader regions. In our
previous work, we established RfaH as a model to elucidate the mechanism of transcription
processivity conferred by NusG proteins. However, recent structural studies by us and others
propose paradigm-shifting models for how NusG proteins function. The new structures revealed
unexpected interactions and suggested that NusG proteins may promote elongation by
facilitating translocation, inhibiting backtracking and swiveling, chaperoning the nascent RNA,
and constraining the flexible nontemplate DNA strand. These hypotheses require extensive
validation that we propose to carry out with RfaH in Aim 1. RfaH activates gene expression in
part by silencing Rho, which imposes strong polarity in RfaH-controlled operons, yet these
operons lack canonical Ro recognition sequences. Using a genetic selection for suppressors of
ΔrfaH, we identified alterations in a flexible connector region of Rho that we propose disrupt an
allosteric signal required for termination. In Aim 2, we will study the role of the connector region
and NusG in potentiating Rho action at suboptimal RNAs. Activation of gene expression by RfaH
is thought to be mediated by recruitment of ribosome to RfaH-target RNAs that are missing
Shine-Dalgarno motifs. In Aim 3, we will determine where the ribosome is recruited to the
transcribing RNA polymerase and whether it scans after loading on mRNA. We will also test if
RfaH couples transcription and translation and will look for new factors affecting translation of
RfaH-dependent operons.

## Key facts

- **NIH application ID:** 10152602
- **Project number:** 5R01GM067153-17
- **Recipient organization:** OHIO STATE UNIVERSITY
- **Principal Investigator:** IRINA ARTSIMOVITCH
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $374,091
- **Award type:** 5
- **Project period:** 2003-02-01 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10152602

## Citation

> US National Institutes of Health, RePORTER application 10152602, Mechanism of transcript elongation control by RfaH (5R01GM067153-17). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10152602. Licensed CC0.

---

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