The ability to distinguish between cellular RNA and viral RNA – a process called self-nonself-discrimination – is fundamental to the innate immune response of all animals. When viruses infect cells, they replicate inside the host cell, and this process generates double stranded viral RNA (which does not naturally occur in the cell) as an intermediate.
In humans and other vertebrates, the presence of these non-self RNA molecules is typically detected by a protein called MDA5, a cytoplasmic RNA sensor. MDA5 initiates the production of antiviral proteins that restrict the infection.
In this study, published in Nature Structural and Molecular Biology, the Crick researchers provide a detailed understanding of the first steps of this crucial defence mechanism. The researchers obtained 3D structures of MDA5 bound to double-stranded RNA, which allowed them to pinpoint exactly how the sensor protein recognises the viral RNA and initiates the cellular antiviral response.
The structures revealed that MDA5 does not distinguish between self and nonself RNA sequences, instead they distinguish based on the shape. While cellular RNA forms a continuous helix, viral RNA has a kink in the middle, exposing a specific binding site for MDA5.
A fundamental immune mechanism
“MDA5 is one of the most important sensors in the innate immune system, and it is essential for antiviral immunity. Therefore, understanding how it works in such intricate detail provides significant insights into how our bodies fight viral infections,” explains lead author Dr. Carlos R. Ortiz-Caravaca, Group Leader in RNA Biology at the Crick.
To obtain the 3D structures of MDA5 with RNA, the researchers used a technique called cryo-electron microscopy combined with biochemical assays to pinpoint how MDA5 discriminates against self and nonself RNAs.
In the cryo-electron microscopy, the structures were determined at a resolution of 3.4 Å (Ångströms), which allowed the researchers to visualise the individual atoms of the RNA helices and the protein folds.
By understanding exactly how MDA5 recognises double stranded viral RNA and triggers antiviral defences, the researchers can now seek to develop new treatments for viral infections, including emerging viruses like SARS-CoV-2 and MERS-CoV.
“For some viral infections, such as influenza, the body is very good at generating an effective antiviral response against the infection. By gaining a detailed understanding of how this process happens, we can use that knowledge to improve the body’s immune response to viral infections for which we don’t have effective defences,” says Dr. Ortiz-Caravaca.
Unveiling the details
The team observed that MDA5 contains two RNA-binding domains: one domain is in charge of ‘sensing’ the RNA, while the other is responsible for signalling to activate the antiviral response.
Upon viral infection, the sensor domain finds and binds to the viral double-stranded RNA. This binding event causes a conformational change that exposes the signalling domain, allowing the protein to transmit the signal and activate the antiviral response.
MDA5 is part of a wider group of RNA sensor proteins that are all involved in the defence against viruses. The researchers hope to apply the same techniques to understand how other sensors work, and in this way build a comprehensive picture of the different ways cells discriminate viruses and protect themselves from infection.
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The Francis Crick Institute is a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease. Its researchers are tackling the biggest questions in biology through experimental science and interdisciplinary collaborations, and its scientific breakthroughs are helping to translate research into treatments for patients.
The Crick was established in 2015 and is based in London, UK. The Crick is a partnership between six organisations: the Medical Research Council Laboratory of Molecular Biology, Cancer Research UK, the Wellcome Sanger Institute, University College London, Imperial College London and King’s College London.
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Contact
Laura Marr, Communications Officer
laura.marr@crick.ac.uk
07919 923366
Scientific contact
Dr Carlos R. Ortiz-Caravaca
Group Leader in RNA Biology, The Francis Crick Institute
carlos.ortiz-caravaca@crick.ac.uk
