How viruses know what’s theirs

Researchers at San Diego State University and Michigan State University are shedding new light on how viruses meticulously pack their genetic material — a breakthrough that could help researchers engineer antivirals and gene therapies. 

The team’s findings, which are published in the Proceedings of the National Academy of Science, reveal how a combination of molecular properties allow viruses to selectively gather their own RNA into protein shells called capsids while ignoring a host cell’s own competing genome. Like molecular armor, capsids shield a virus’s genetic material from damage and help it sneak into host cells.

Knowing how viruses package their RNA with high selectivity — a feat achieved with more than 99% accuracy by some viruses — could help scientists engineer their own versions of capsids in the lab and leverage them as powerful scientific tools. 

“From a health perspective, synthetic capsids can be used to create antivirals that target RNA packaging, which can impact humans, plant and animal agriculture, as well as veterinary medicine,” Kristin Parent said, director of MSU’s Cryo-EM Facility and an author of the latest paper. 

The latest breakthrough was the result of a collaboration between Spartan researchers and those in the Garmann lab at San Diego State University, which examines the complex molecular choreography behind viral replication, infection and evolution.  

“Some RNA viruses are built from fewer than 200 molecules,” said Rees Garmann, an assistant professor in SDSU’s Department of Chemistry and Biochemistry and senior author of the new study.

“And yet they are able to accomplish remarkable feats, like replicating in astronomical numbers and building precise nanoscale structures.” 

The host with the most 

To illustrate the staggering quantities of viruses found on our planet, Parent offers her students this eye-popping illustration: If you scoop up two handfuls of water from Lake Michigan, you’d be holding more viruses than there are humans on Earth. 

Among these viruses, the most abundant types are bacteriophages, or phages — viruses that infect and replicate within bacteria. In their new study, the researchers examined a phage called MS2, which preys on E. coli. 

Viruses rely on the molecular machinery of other cells to replicate. When MS2 attaches to a bacterium, it injects its own genetic material, forcing the host cell to assemble viral copies. 

During this process, viral coat proteins assemble around viral RNA to form a capsid, which protects the genetic cargo. With 180 identical coat proteins arranged to make 20 different sides, the resulting virus looks a bit like a soccer ball or a game die. 

Eventually, when the host cell bursts open, a new generation of these phage copies is released. 

For researchers like Garmann and Parent, the question was how the phage can recognize its own genome and package it so efficiently, especially when the RNA is mingling with the host’s competing genetic material inside the cell. 

“Around 99% of the particles we’re seeing at the end are perfectly formed viral copies, so it’s a high-fidelity process,” said Parent, who’s also a professor in MSU’s Department of Biochemistry and Molecular Biology. 

RNA origami  

Compared to DNA’s iconic double-helix, RNA is single-stranded. This means it can form complex secondary structures like bulges, loops and hairpins.  

Previously, researchers thought a particular structure called a TR stem-loop acted as a packaging signal for MS2. You might think of this as a molecular signpost indicating where viral RNA packaging should begin. 

To see what other factors might influence packaging, the researchers systematically scrambled the MS2 genome, producing RNA constructs with unique properties. These included molecules of varying shape, length and sequence.

Like watching finished products roll off an assembly line after major changes on the factory floor, the team then analyzed capsid packaging outcomes to determine the impact of these RNA tweaks. 

Specifically, they were able to see unique and often surprising capsid packaging results — viral particles that were too small, and even those with inefficient shapes.

What the researchers ultimately discovered was that MS2 coat proteins on their own are highly capable of selectively packaging viral RNA, and that a diverse group of RNA properties, not just the well-known TR stem-loop, had an outsized impact on the process. This included RNA length, sequence and various stem-and-loop structures making a collective difference. 

Through their findings, the team is helping rewrite our understanding of how some viruses achieve their impressive RNA-packaging feats. With synthetic capsids and new genetic cargo, these same molecular mechanisms can be leveraged for the greater good — from gene editing and vaccines to the next generation of RNA-based therapeutics.