# Applying Ribo-Seq and RNA-Seq to identify quorum sensing pheromones and their regulons

> **NIH NIH R21** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2020 · $199,875

## Abstract

Project Summary / Abstract
Intercellular chemical signaling, also known as quorum sensing, is widely used by bacteria to control gene
expression, protein activity, and behaviors in a coordinated manner between individual cells within a community.
Gram-positive bacteria, including the important human pathogen Streptococcus pneumoniae, utilize secreted
peptides as intercellular signals, referred to here as ‘pheromones’. The Rap/Rgg/Npr/PlcR/ PrgX (RRNPP) family
of quorum sensing systems are widespread among Gram-positive bacteria, and within individual genomes,
multiple paralogs of pheromone receptors are typically found. The clear majority of these systems are unstudied
(9 systems are predicted in S. pneumoniae strain D39), largely due to the current limitations on the ability to
identify pheromone genes and their regulatory targets. RRNPP peptide pheromones are encoded by small open
reading frames (sORFs), which, due to their small size and lack of unique characteristics, are generally
unrecognizable in genome sequences. This proposal outlines the development of systematic genome-wide
analyses that will identify sORFs encoding RRNPP pheromones (as well as all other unannotated sORFs that
may have important physiological activities) and the regulons of RRNPP quorum sensing systems. To
accomplish these goals, RNA-seq analysis, combined with the cutting-edge approach of antibiotic-assisted
ribosome profiling (Ribo-seq), will be performed to directly identify and enumerate all transcription and translation
events in bacterial cultures. Development of these methodologies will allow for a rapid increase in the ability to
study communication systems in bacteria and will likely accelerate efforts to manipulate signaling pathways as
a means to alter microbial behaviors, especially virulence attributes of pathogens.

## Key facts

- **NIH application ID:** 9876913
- **Project number:** 5R21AI144500-02
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** MICHAEL J FEDERLE
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $199,875
- **Award type:** 5
- **Project period:** 2019-02-19 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9876913

## Citation

> US National Institutes of Health, RePORTER application 9876913, Applying Ribo-Seq and RNA-Seq to identify quorum sensing pheromones and their regulons (5R21AI144500-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9876913. Licensed CC0.

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