# Mechanism of CsrA-Mediated Global Control

> **NIH NIH R01** · UNIVERSITY OF FLORIDA · 2020 · $425,851

## Abstract

Insight into posttranscriptional regulation and global regulatory circuitry will be sought through the study
of the Csr system of Escherichia coli. Csr includes: CsrA, an RNA binding protein that regulates translation
and/or mRNA stability of numerous target mRNAs; CsrB and CsrC, sRNAs that sequester and antagonize CsrA;
BarA-UvrY, a two-component signal transduction system that activates csrB and csrC transcription; and CsrD,
a protein that forms a complex with EIIAGlc, activating it to target CsrB/C RNAs for degradation by RNase E. CsrA
regulates metabolism, motility and multicellular behavior on a multi-systems scale, as well as virulence circuits
of numerous pathogens. Our transcriptomics studies identified hundreds of RNAs that bind to CsrA in vivo. Csr
is reciprocally linked to a number of other global regulatory circuits. This complex circuitry allows Csr to reinforce
the regulatory effects of multiple stress response systems at a posttranscriptional level.
 The specific aims are: 1) Footprinting of the CsrA-RNA transcriptome. We are developing next-gen
sequencing methods to derive in vivo protein binding and secondary structure information for the transcriptome.
We will apply this innovative approach to identify CsrA-RNA footprints and RNA structural changes caused by
CsrA binding throughout the transcriptome. The results will suggest new regulatory mechanisms and roles for
CsrA and will have a broad and powerful impact on the field of RNA biology. 2) Regulation of sRNA-mRNA
basepairing by CsrA. Transcriptomics and gel shift studies show direct CsrA binding to several basepairing
sRNAs and suggest that CsrA-sRNA binding influences sRNA-mRNA pairing and regulation. Genetic and
biochemical studies will be used to investigate CsrA interaction with a model sRNA and its effects on sRNA
structure, Hfq-sRNA binding, and other features of sRNA-mRNA regulation. 3) The critical role(s) of CsrA in
bacterial growth. A csrA deletion (csrA) causes severe growth defects, however the way in which CsrA
supports bacterial growth is poorly understood. Using an “evolve and resequence” approach, we monitored the
rapid adaptive evolution of several independent csrA populations. Potential csrA suppressors were sequenced
in genes with known regulatory connections to CsrA and with no known relationship. Single and multiple mutant
combinations will be reconstructed using CRISPR-Cas9 and tested for effects on csrA growth to authenticate
suppressors. Pathways for suppression and the inferred roles of CsrA in supporting growth will be confirmed
using transcriptomics and other analyses, thereby uncovering crucial functions of CsrA for growth.
 Our long-range objectives are to fully understand the components, molecular mechanisms, genetic
circuitry and biological functions of Csr, thereby defining the principles that underpin a regulatory super-network.
Csr (Rsm) controls the expression of virulence factors, transmission traits and/or persistence of numerous
pathog...

## Key facts

- **NIH application ID:** 9933052
- **Project number:** 5R01GM059969-21
- **Recipient organization:** UNIVERSITY OF FLORIDA
- **Principal Investigator:** PAUL L BABITZKE
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $425,851
- **Award type:** 5
- **Project period:** 1999-08-01 → 2022-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9933052

## Citation

> US National Institutes of Health, RePORTER application 9933052, Mechanism of CsrA-Mediated Global Control (5R01GM059969-21). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9933052. Licensed CC0.

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