Viruses lack their own molecular machinery required for protein synthesis. Instead, they hijack the host’s protein-making machinery, specifically ribosomes and translational factors. This process is essential for viral multiplication and infection. Viruses have RNA genomes or mRNAs containing structured regions called Internal Ribosomal Entry Sites (IRES) that help capture the host ribosome to translate viral genes while translation of host genes is blocked.
In a new study published in eLife, researchers at the Indian Institute of Science (IISc) used cryo-electron microscopy (cryo-EM) to decode how the encephalomyocarditis virus (EMCV) IRES hijacks the host’s protein synthesis machinery. EMCV is a rodent-borne animal virus that causes heart and brain inflammation, reproductive problems, and neurological disorders in many mammals. Targeting the IRES could open up new therapeutic strategies against this virus and similar viruses – like the poliovirus – that employ the same mechanism.
IRES were initially discovered more than a decade ago in EMCV and the poliovirus. But so far, their structure and specific mechanisms by which they act remained elusive. “Nothing was known in terms of the details of how [the virus] captures the host ribosome – other than the translational factors involved – and how exactly it does so biochemically,” says Tanweer Hussain, Associate Professor at the Department of Developmental Biology and Genetics (DBG), IISc and corresponding author.
To address this gap, Deepakash Das, PhD student in Hussain’s lab and first author, devised a pulldown strategy using an EMCV IRES-containing mRNA to isolate the EMCV IRES pre-initiation complex from cell lysate of rabbit reticulocytes (immature red blood cells). This pre-initiation complex is the assembly that the viral RNA forms with the host ribosome to hijack it, marking the first step in making viral proteins.
Using a specially designed bait protein, the team fished out and captured the entire IRES complex intact, including various key components of translation initiation – the 40S ribosomal subunit, the initiator tRNA, and the eIF2 (eukaryotic initiation factor 2) complex – from the cell lysate, and then examined it using cryo-EM. “Early purification attempts went well – something of a beginner’s luck – but many subsequent rounds failed to produce usable results,” says Hussain. “Cryo-EM grids frequently failed to yield enough particles for a reliable structure, but we persisted.”
Eventually, cryo-EM images showed that the EMCV IRES directly interacts with the 40S ribosomal unit and initiator tRNA of the host – a mechanism that hasn’t been used by other viruses before – to hijack the host translational machinery.
“We wanted to have a full picture of the IRES and ribosomal interactions so that we can design inhibitors targeting this region later,” explains Das. “CryoEM is the go-to technique that can actually give us a real-world picture of whatever is happening.”
The team also found that the viral RNA structurally mimics part of the host ribosome’s own RNA and closely resembles a corresponding region in the IRES of poliovirus, suggesting that the two viral families may share the same hijacking strategy.
Since the interface that this IRES uses isn’t employed by the host cells’ own protein machinery, there’s an opportunity to design drugs that specifically block it, the researchers say. “We hope to selectively target only the viral translation pathway, leaving host translation unaffected. This is what we plan to test next, using mimics and candidate drug compounds,” says Hussain.
eLife
Structural insights into the recruitment of viral type 2 IRES to ribosomal preinitiation complex for protein synthesis
25-Jun-2026