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Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

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Related Experiment Video

Updated: Jun 24, 2025

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

Fragment Screening to Identify Inhibitors Targeting Ribosome Binding of Shiga Toxin 2.

Michael J Rudolph¹, Anastasiia M Tsymbal², Arkajyoti Dutta³

¹New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, United States.

ACS Infectious Diseases

|June 14, 2024

Summary

Researchers identified new small molecules targeting Shiga toxin 2 (Stx2A1) by binding its ribosome site. These compounds offer a promising new therapeutic strategy against Shiga toxin-producing E. coli infections.

Keywords:

Shiga toxins X-ray crystal structure depurination inhibition fragment-based drug discovery ribosome binding ribosome-inactivating protein

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Last Updated: Jun 24, 2025

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

Area of Science:

Microbiology
Toxicology
Medicinal Chemistry

Background:

Shiga toxins are key virulence factors in Shiga toxin-producing E. coli (STEC) and S. dysenteriae.
Current therapies for Shiga toxin-induced diseases are limited.
Shiga toxins inhibit protein synthesis by depurinating the sarcin/ricin loop of ribosomes.

Purpose of the Study:

To identify small molecules that inhibit Shiga toxin 2 (Stx2) activity.
To target the previously unexploited ribosome binding site of Stx2.

Main Methods:

Fragment library screening against the Stx2 A1 subunit (Stx2A1).
Identification and synthesis of analogs based on a validated fragment (BTB13086).
Assay of binding affinity and inhibitory activity of synthesized compounds.

Main Results:

A fragment, BTB13086, was identified that binds to the Stx2A1 ribosome binding site.
BTB13086 mimics the binding of ribosomal P-stalk proteins.
Synthesized analogs demonstrated similar binding affinity and inhibitory activity against Stx2A1.

Conclusions:

First compounds identified that bind the Stx2A1 ribosome binding site and inhibit its activity.
These novel compounds represent a promising starting point for developing therapeutics against STEC infections.