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Types of RNA

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...

Types of RNA

Types of RNA

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 regulating 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 Performs Diverse...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

RNA Stability

RNA Stability

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Related Experiment Video

Updated: Apr 24, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Newton's cradle-like allosteric mechanism explains regulatory RsmE RNA binding.

Esteban Finol¹, Fred F Damberger¹, Miroslav Krepl²

¹Institute for Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.

Nature Communications

|April 22, 2026

Summary

This summary is machine-generated.

Bacterial non-coding RNAs (ncRNAs) like RsmZ act as protein sponges, sequestering regulatory proteins. This study reveals a Newton's cradle-like mechanism explaining how RsmZ binding affinity changes, facilitating protein handover.

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Last Updated: Apr 24, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

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Published on: February 12, 2022

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An Assay for Quantifying Protein-RNA Binding in Bacteria

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

Area of Science:

Bacterial regulatory networks
RNA-protein interactions
Molecular mechanisms of gene regulation

Background:

The Csr/Rsm system controls bacterial gene expression via non-coding RNAs (ncRNAs) and regulatory proteins.
In Pseudomonas protegens, RsmZ ncRNA sequesters RsmE protein dimers, acting as a 'protein sponge' to regulate translation.
The binding of RsmE to RsmZ exhibits negative cooperativity, where initial binding reduces affinity for subsequent binding events.

Purpose of the Study:

To elucidate the molecular mechanism behind the negative cooperativity observed in RsmE binding to RsmZ.
To understand how this mechanism facilitates the handover of RsmE from mRNA to ncRNA.

Main Methods:

Isothermal Titration Calorimetry (ITC) to measure binding thermodynamics.
Nuclear Magnetic Resonance (NMR) spectroscopy to probe structural and dynamic changes.
Molecular Dynamics (MD) simulations to model the allosteric mechanism.

Main Results:

An allosteric mechanism, analogous to a Newton's cradle, was identified.
Binding at one site on RsmZ induces conformational and dynamic changes at a second site.
This allosteric coupling explains the reduced affinity for the second RsmE dimer binding and facilitates protein handover.

Conclusions:

The Newton's cradle-like allosteric mechanism governs RsmE binding to RsmZ in Pseudomonas protegens.
This mechanism is crucial for the efficient handover of RsmE dimers from target mRNAs to the RsmZ ncRNA.
Understanding this process provides insights into bacterial gene regulation and RNA-protein interactions.