Illustration of a ribosome interacting with viral RNA.

Decoding Viral RNA: How Ribosomes Remodel Genetic Messages

Kai Mendoza in Science & Nature August 2025 • 4 min read.

"Unlocking the Secrets of RNA Structure to Understand Viral Gene Regulation"

Gene expression, the process by which our cells read and use the instructions encoded in our DNA, is a tightly controlled affair. At the heart of this process lies RNA, a versatile molecule that acts as an intermediary between DNA and protein synthesis. RNA isn't just a passive carrier of information; it's an active player, capable of folding into intricate three-dimensional structures that dictate its function.

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Viruses, masters of efficiency, often exploit these structural intricacies to hijack the host cell's machinery for their own replication.

Now, a team of scientists has delved into the complex world of viral RNA, uncovering a fascinating mechanism by which ribosomes, the protein-synthesizing workhorses of the cell, can physically reshape viral RNA structure. This discovery, focused on the turnip yellow mosaic virus (TYMV), sheds light on how viruses fine-tune gene expression and opens up new avenues for antiviral drug development.

How Do Ribosomes Change RNA Structure?

Illustration of a ribosome interacting with viral RNA.

The study focuses on the 3'-untranslated region (UTR) of TYMV RNA, a region that doesn't code for proteins but plays a crucial role in regulating translation, the process of protein synthesis. The researchers discovered that the 3'-UTR acts as a sensor, responding to the presence of ribosomes by undergoing conformational changes.

Think of the 3'-UTR as a sophisticated switchboard, comprised of two key domains: the pseudoknot domain (UPD) and the tRNA-like structure (TLS). The UPD acts as a sensor, detecting the proximity of ribosomes, while the TLS influences translation efficiency. The researchers found that when a ribosome gets close to the UPD, it triggers a structural change that affects the TLS, ultimately altering the rate at which proteins are produced.

Ribosome-Induced Changes: The arrival of a ribosome near the UPD causes it to unfold.
Communication Conduit: This unfolding propagates through a "spine" of continuously stacked bases to the TLS.
Translation Adjustment: The TLS, in turn, adjusts translation efficiency based on the status of the UPD.

To visualize these structural gymnastics, the team used X-ray crystallography, a powerful technique that allows scientists to determine the three-dimensional structure of molecules at the atomic level. The resulting structure revealed that the UPD and TLS are connected by a flexible linker, allowing for communication between the two domains. The study also pinpointed specific mutations within the UPD that disrupt its ability to sense ribosomes, leading to altered translation levels.

Why Is This Important?

This research provides a crucial understanding of how viruses manipulate RNA structure to control gene expression. By uncovering the interplay between ribosomes and viral RNA, scientists can now explore new strategies for disrupting viral replication. Imagine developing antiviral drugs that target the flexible linker between the UPD and TLS, preventing the ribosome from triggering the necessary structural changes. Or perhaps, designing molecules that stabilize the UPD, keeping the TLS in an 'off' state, effectively silencing viral protein production. The possibilities are vast, and this study serves as a critical stepping stone towards innovative antiviral therapies.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1038/s41467-018-07542-x, Alternate LINK

Title: Ribosome-Induced Rna Conformational Changes In A Viral 3′-Utr Sense And Regulate Translation Levels

Subject: General Physics and Astronomy

Journal: Nature Communications

Publisher: Springer Science and Business Media LLC

Authors: Erik W. Hartwick, David A. Costantino, Andrea Macfadden, Jay C. Nix, Siqi Tian, Rhiju Das, Jeffrey S. Kieft

Published: 2018-11-29

Everything You Need To Know

What is the role of ribosomes in viral RNA structure, and how does this impact viral gene expression?

Ribosomes, the protein-making machinery within cells, play a crucial role in altering the structure of viral RNA. Specifically, they can physically reshape the RNA structure, influencing how viruses control their genes. This happens through the interaction of ribosomes with the 3'-untranslated region (UTR) of the viral RNA, particularly in the turnip yellow mosaic virus (TYMV). When a ribosome approaches the pseudoknot domain (UPD) of the 3'-UTR, it triggers a conformational change that affects the tRNA-like structure (TLS), ultimately altering the rate of protein production. This interplay between ribosomes and viral RNA is essential for viral gene expression and replication, making ribosomes a key player in this process.

Can you explain the specific components of the 3'-UTR of TYMV RNA and how they interact with ribosomes?

The 3'-UTR of the turnip yellow mosaic virus (TYMV) RNA acts as a sensor that responds to the presence of ribosomes. It is composed of two key domains: the pseudoknot domain (UPD) and the tRNA-like structure (TLS). The UPD serves as a sensor, detecting the proximity of ribosomes, while the TLS influences the efficiency of translation, the process of protein synthesis. When a ribosome gets close to the UPD, it triggers a structural change, causing the UPD to unfold. This unfolding propagates through a 'spine' of stacked bases to the TLS, which then adjusts translation efficiency based on the status of the UPD. These interactions are critical for the regulation of viral gene expression.

How does the structural change in viral RNA, specifically in the UPD and TLS, affect the process of protein synthesis?

The structural change in the viral RNA, particularly within the pseudoknot domain (UPD) and tRNA-like structure (TLS), directly affects protein synthesis. When a ribosome interacts with the UPD, it causes the UPD to unfold. This unfolding transmits through a connection to the TLS. The TLS then adjusts the efficiency of translation, influencing how proteins are produced from the viral RNA. By modulating translation efficiency, viruses can finely control the amount of proteins produced, thereby regulating their replication cycle and ensuring effective hijacking of the host cell's machinery.

What are the potential implications of this research for developing new antiviral therapies?

This research provides a crucial understanding of how viruses manipulate RNA structure to control gene expression, opening up exciting possibilities for novel antiviral strategies. Understanding the interplay between ribosomes and viral RNA allows scientists to explore new ways of disrupting viral replication. For instance, researchers could develop antiviral drugs that target the flexible linker connecting the UPD and TLS, preventing the structural changes needed for viral protein production. Another approach could involve designing molecules that stabilize the UPD, effectively silencing viral protein production. These innovative approaches could lead to more effective treatments for viral infections.

How was X-ray crystallography used to study the interaction between ribosomes and viral RNA, and what did it reveal?

X-ray crystallography was used to determine the three-dimensional structure of the viral RNA at the atomic level, providing detailed insights into the interaction between ribosomes and viral RNA. This powerful technique revealed that the pseudoknot domain (UPD) and the tRNA-like structure (TLS) are connected by a flexible linker, facilitating communication between the two domains. The study identified specific mutations within the UPD that disrupted its ability to sense ribosomes, leading to altered translation levels. This structural information is crucial for understanding how the ribosome triggers conformational changes in the viral RNA and how these changes affect gene expression, paving the way for targeted antiviral drug development.