Researchers studied the extensive network of protein-protein interactions that forms in cells infected with the influenza A virus. Credit: Daniela Velasco/EMBL
Every year, seasonal influenza kills up to 650,000 people worldwide and sickens millions more. Now, researchers have gotten a much clearer picture of how the virus takes over its host from the inside.
Scientists at EMBL Hamburg and the Leibniz Research Institute for Molecular Pharmacology (FMP) have mapped, in unprecedented detail, how the influenza A virus hijacks the molecular machinery of infected human cells.
When influenza A invades a cell, it releases RNA carrying instructions for a small set of viral proteins. Those proteins spread through the cell and commandeer its internal machinery to churn out more virus. Understanding exactly how viral and host proteins grab onto each other could point the way to new drugs and vaccines—but that interaction has been notoriously hard to observe without breaking the cell apart first, which risks destroying the very contacts scientists want to study.
To get around that problem, the team turned to a specialized version of cross-linking mass spectrometry developed at FMP Berlin and tailored specifically for virus-infected cells. The method chemically “freezes” proteins in place while they're still touching inside an intact, infected cell, letting researchers capture short-lived or location-specific interactions that would otherwise be lost once the cell is broken open.
The researchers then paired that data with a modified version of AlphaFold, the protein-structure-prediction algorithm that won its creators a Nobel Prize.
“The key advantage of the modified AlphaFold approach is that it allowed us to feed our experimental cross-linking data directly into the structural modeling,” said Jan Kosinski, Group Leader at EMBL Hamburg and Centre for Structural Systems Biology. “This tells the model which parts of the viral and host proteins are close to each other inside infected cells. This was especially useful for virus-host complexes, which are often difficult to predict reliably.”
The study, published in Nature Microbiology, revealed two distinct strategies the virus uses to seize control of its host. The first centers on haemagglutinin, the surface protein influenza uses to latch onto and enter cells. Tracing haemagglutinin's path through the cell's internal transport network revealed a set of host proteins—some with previously unknown functions—that help fold and modify the viral protein during infection.
The second finding involved paraspeckles, small droplet-like structures inside the cell nucleus. Infection caused these organelles to dissolve, releasing RNA-binding proteins that the virus could then repurpose for its own replication. The pattern held consistently across every cell line and flu strain the team tested.
“What surprised us most was the paraspeckles,” said first author Iuliia Kotova, former predoctoral fellow at EMBL Hamburg, now at ETH Zurich. “Watching these tiny organelles in the nucleus dissolve, consistently across every cell line and every flu strain we tested, told us this isn't a side effect of infection—it might be a strategy.”
The researchers note that disrupting paraspeckles may serve the virus in a second way, since some evidence suggests the structures also help regulate the cell's antiviral defenses.
While this study focused on a lab-adapted flu strain, the researchers say the work lays the groundwork for applying the same methodology to viruses of pandemic concern, such as H5N1, to uncover how they multiply inside human cells.