Cryo-EM Reveals 3D Structure of Nipah Virus RNA Polymerase

For the first time, researchers from the Max Planck Institute (MPI) for Multidisciplinary Sciences and the University Medical Center Göttingen (UMG) have demonstrated how the Nipah virus replicates its genetic material in infected cells. In humans, this virus can cause fatal encephalitis.

Led by Hauke Hillen, the team used cryo-electron microscopy to create a three-dimensional image of the viral "copying machine." Their findings, published in Nature Communications, could pave the way for future antiviral treatments against Nipah virus infections.

Understanding the Threat

Disease outbreaks caused by viruses that jump from animals to humans remain a global challenge. Many pandemics originate through this transmission route, underscoring the need for early research to develop effective treatments and vaccines before an epidemic or pandemic emerges.

The World Health Organization considers the Nipah virus a significant health threat. It has triggered multiple outbreaks in Asia in recent years, with bats serving as the primary carriers. The virus spreads rapidly among humans and can be fatal in up to 70% of cases. Currently, there are no approved medications or vaccines specifically targeting Nipah virus infections.

A New Approach to Drug Development

For the first time, researchers have visualized the three-dimensional structure of the Nipah virus's RNA polymerase—the enzyme responsible for copying the virus's genetic material—at molecular resolution. This breakthrough was achieved by the team led by Hauke Hillen, who heads the Structure and Function of Molecular Machines research group at UMG and the MPI for Multidisciplinary Sciences.

RNA polymerase is crucial for viral replication because it both activates viral genes and duplicates the virus’s genetic material. This makes it a promising target for antiviral drug development. Using cryo-electron microscopy, the researchers captured high-resolution images of the RNA polymerase in two distinct states: free-floating and attached to viral RNA.

Capturing the Viral Copy Machine

The team used advanced electron microscopy to capture thousands of individual images of the RNA polymerase after shock-freezing it in these two states. With the help of high-performance computing, they reconstructed a 3D model with near-atomic resolution.

"This is an important milestone because, until now, we didn’t know exactly what the Nipah virus RNA polymerase looked like or how it interacted with viral RNA. Our data show that it shares similarities with polymerases from related viruses, such as Ebola, but also has unique features," explained Hauke Hillen.

The study revealed how the RNA polymerase binds to newly synthesized RNA and nucleotide building blocks while using the viral genome as a template for replication.

"These results are particularly exciting because no one has previously captured a molecular snapshot of the RNA polymerase in its active state, even for related viruses like Ebola. By comparing the free and RNA-bound states, we not only determined its structure but also gained new insights into its dynamics. Such data could guide the development of drugs that inhibit the RNA polymerase," added Fernanda Sala, postdoctoral researcher and first author of the study.

How the Study Advances Research

The RNA polymerase acts as the virus’s molecular copying machine, reading the viral genome and creating new genetic material. Many antiviral drugs work by inhibiting viral RNA polymerase—examples include remdesivir for COVID-19 and acyclovir for herpes. However, without a clear understanding of the Nipah virus polymerase’s structure, designing effective inhibitors has been a challenge.

Deciphering the Polymerase Structure

The Nipah virus RNA polymerase consists of two subunits: the L protein and the P protein. To analyze its structure, researchers isolated these proteins and examined them using cryo-electron microscopy.

After freezing the RNA polymerase molecules in solution at -196°C, they captured thousands of images under an electron microscope. These images were then processed using advanced computational techniques to reconstruct a three-dimensional model with near-atomic accuracy.

The high-resolution images provided an unprecedented view of how the L and P proteins work together to form the functional polymerase complex.

Observing RNA Polymerase in Action

To understand how the RNA polymerase interacts with the viral genome during replication, the researchers recreated the process in a test tube. They provided the polymerase with an RNA template and nucleotide building blocks and then analyzed its activity using biochemical methods.

Their experiments confirmed that the purified RNA polymerase was active, successfully generating new RNA from nucleotides. Finally, using cryo-electron microscopy, they captured the 3D structure of the RNA polymerase in its active, RNA-bound state at molecular resolution.

Implications for Future Treatments

This research marks a major step toward understanding the Nipah virus at the molecular level. By revealing how the RNA polymerase functions and interacts with viral RNA, the study provides crucial insights that could inform the development of targeted antiviral drugs.

As Nipah virus outbreaks continue to pose a global health risk, these findings contribute to the foundation for potential therapeutic interventions—offering hope for future treatments and preparedness against emerging viral threats.