Related Experiment Video

Updated: Sep 7, 2025

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues
07:10

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

9.1K

RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for

Daniel G Mediati1, Julia L Wong1, Wei Gao2

  • 1School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.

Nature Communications
|June 22, 2022
PubMed

Insights

Methicillin-resistant Staphylococcus aureus (MRSA) with vancomycin intermediate resistance (VISA) can be resensitized to antibiotics. This study reveals that mRNA-mRNA interactions, specifically the vigR 3' untranslated region (UTR), regulate bacterial cell wall thickness and antibiotic sensitivity.

Area of Science:

  • Microbiology
  • Molecular Biology
  • Genetics

Background:

  • Treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections relies on last-line antibiotics like vancomycin.
  • Treatment failures are often associated with vancomycin-intermediate Staphylococcus aureus (VISA) isolates, characterized by reduced vancomycin sensitivity due to mutations.
  • While small RNA (sRNA) expression changes under antibiotic stress in VISA are noted, the functions of most RNA regulators remain unclear.

Purpose of the Study:

  • To investigate RNA-RNA interactions in VISA isolates using RNase III-CLASH.
  • To characterize the functions of previously uncharacterized sRNAs and identify novel regulatory mechanisms.
  • To explore the role of mRNA-mRNA interactions in coordinating gene expression and antibiotic resistance.

Main Methods:

  • Utilized CLASH (crosslinking, ligation, and sequencing of hybrids) coupled with RNase III to capture in vivo RNA-RNA interactions.
  • Identified hundreds of novel RNA-RNA interactions, including mRNA-mRNA interactions.
  • Investigated the regulatory function of the vigR 3' untranslated region (UTR) through gene deletion and phenotypic analysis.

Main Results:

  • RNase III-CLASH successfully identified numerous RNA-RNA interactions, enabling functional characterization of sRNAs.
  • Discovered that a long 3' untranslated region (UTR) of an mRNA, termed vigR 3'UTR, acts as a regulatory hub.
  • Demonstrated that vigR 3'UTR directly base-pairs with mRNAs to promote expression of folD and isaA, impacting cell wall thickness and resensitizing VISA to vancomycin.

Conclusions:

  • RNase III-CLASH is a valuable tool for uncovering RNA-RNA interactions and characterizing RNA regulators.
  • Staphylococcus aureus employs mRNA-mRNA interactions as a significant mechanism for coordinating gene expression.
  • Targeting the vigR 3'UTR and its interactions offers a potential strategy to overcome vancomycin resistance in MRSA infections.

More Related Videos

Nanomechanics of Drug-target Interactions and Antibacterial Resistance Detection11:56

Nanomechanics of Drug-target Interactions and Antibacterial Resistance Detection

Published on: October 25, 2013

14.3K
Biosensor for Detection of Antibiotic Resistant Staphylococcus Bacteria14:04

Biosensor for Detection of Antibiotic Resistant Staphylococcus Bacteria

Published on: May 8, 2013

24.6K

Related Concept Videos

Types of RNA01:23

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
64.7K
Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
88
Development of Antibiotic Resistance01:30

Development of Antibiotic Resistance

Antibiotic resistance is a major public health concern that arises when bacteria evolve mechanisms to withstand the effects of antibiotic treatments. This resistance can be intrinsic, acquired through genetic mutations, or transferred between bacteria via horizontal gene transfer. The development of antibiotic resistance poses significant challenges in treating bacterial infections and necessitates ongoing research to develop new therapeutic strategies.Intrinsic resistance occurs when bacterial...
192
Gene Regulation in Microbial Communities: Quorum Sensing01:28

Gene Regulation in Microbial Communities: Quorum Sensing

Quorum sensing is a mechanism of bacterial communication that enables coordinated gene expression in response to changes in population density. This facilitates collective behaviors that enhance survival, resource acquisition, and ecological adaptation. This process relies on small signaling molecules called autoinducers that accumulate as bacterial populations grow. When a critical threshold concentration of autoinducers is reached, bacterial cells collectively modify gene expression,...
90
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
110