Research in Brief: The What, Why, and How

Comparison of protein structure in SARS-CoV2 and PEDV

In this edition:

Research from the Kirchdoerfer Lab in the Department of Biochemistry and the Institute for Molecular Virology, in collaboration with the Coon Lab, identifies that multiple coronaviruses share protein features in critical viral machinery. Here’s the run down on their latest research, which is published in Nucleic Acids Research, and its implications for treating diverse coronavirus infections.

  • Coronaviruses are a large and varied family of viruses that infect humans and other animals.
  • Researchers are working to gain a deeper understanding of coronaviruses and identify targets for antivirals that treat these rapidly-evolving viruses.
  • Findings indicate that mechanisms of RNA replication may be conserved across the coronavirus family, suggesting the possibility of antivirals that treat multiple coronaviruses.

What background information do you need to know?

While the term “coronavirus” is now often used colloquially to mean COVID-19 illness or SARS-CoV-2 (the virus that causes COVID-19), there are several coronaviruses, including the common cold, which infect and cause illness in humans. Coronaviruses are, in fact, a large and varied family of viruses that infect a wide array of animals, including domesticated cats and dogs and agriculturally important livestock. Porcine epidemic diarrhea virus (PEDV), for example, is a coronavirus first documented in the U.S. in 2013 which causes a diarrheal disease in pigs and is especially deadly in piglets. An outbreak of PEDV can have devastating economic consequences for impacted farms.

As ubiquitous as coronaviruses are, they remain difficult to treat with antivirals.

Why is it difficult to develop antivirals to treat coronaviruses?

Coronaviruses are RNA viruses, which means that they cause infection by inserting their own RNA into a host’s cells and hijacking the host’s molecular machinery to make proteins encoded in viral RNA. Inhibiting the virus’ ability to replicate its RNA could slow down their mode of infection.

But identifying RNA replication as a target for antivirals is relatively simple compared to what comes next: determining when and where in the process to attack.

The complex of protein subunits which viruses use to replicate their RNA is known collectively as an RNA polymerase. Antivirals that target RNA polymerase trick the complex into incorporating the antivirals instead of making more RNA during viral replication. This can cause the viral RNA polymerase to slow, stop, or create a large burden of errors. The result is a halt in viral replication, killing the virus.

In coronaviruses, RNA polymerase machinery is notoriously large and complicated, with at least 12 viral subunits (other RNA viruses are comprised of just a handful of subunits). Developing effective antivirals requires decoding the form, function, and interactions among the many subunits.

How have scientists made progress?

The Kirchdoerfer Lab took pictures of PEDV RNA polymerase using cryo-electron microscopy (cryo-EM), a high-resolution imaging technique that reveals the form of biomolecules in a variety of orientations. These images gave the scientists a more nuanced understanding of PEDV RNA replication by visualizing how subunits in the RNA polymerase assemble, orient, and bind to other molecules.

Assembly of an active PEDV polymerase complex.
Assembly of an active PEDV polymerase complex. Pictured is a coordinate model of the PEDV core polymerase complexes docked into their corresponding electron density maps colored by chain.

The scientists then compared the structure of PEDV RNA polymerase to that of SARS-CoV-2. They observed that the RNA polymerases of these two distinct coronaviruses have similar structures. This result suggests that the orientation and function of RNA polymerase subunits has been conserved as coronaviruses evolved, and that drugs which attack coronavirus RNA polymerase may effectively treat a wide range of coronaviruses.

Their research also lends insight into the function of a subunit thought to keep RNA bound to the polymerase. Although the subunit detached during sample preparation, the RNA and polymerase remained tightly bound to each other, debunking the prevailing theory about the subunit’s function.

The Kirchdoerfer Lab’s findings collectively pave the way for further research into the function of coronavirus RNA polymerase subunits, bringing us one step closer to developing effective antivirals to treat coronaviruses that infect us, our pets, and our livestock.

Written by Renata Solan.

In Research In Brief: The What, Why, and How, we explore new research from the UW–Madison Department of Biochemistry to learn more about the world around us — and inside us.
This edition of Research in Brief: The What, Why, and How is based on the following publication:
Anderson, Hoferle, Kennan, Chojnacki, Lee, Coon, and Kirchdoerfer. An alphacoronavirus polymerase structure reveals conserved replication factor functions, Nucleic Acids Research, 2024 Mar 5, gkae153.
This research was funded in party by the following grants: NIH/NIAID AI123498 and AI158463; USDA WIS03099; NIH R35GM118110.