The hepatitis C virus (HCV) is a single stranded RNA virus which contains an internal ribosome entry site (IRES) which is essential for viral translation initiation.  This occurs in a cap-independent method requiring fewer host co-factors than typical eukaryotic cap driven translation.  Previously, we have shown that the highly conserved HCV IRES subdomain IIa undergoes a conformational switch upon binding a benzimidazole ligand.  We have obtained x-ray crystal structures of IRES subdomain IIa in the absence and presence of a ligand.  Subdomain IIa adopts a bent conformation in the absence of a binding ligand but a straightened conformation in the presence of a binding ligand which reveals a deep solvent excluded binding pocket. This conformational switching mechanism is essential for placing domain II in the correct orientation on the ribosome.  Recently, we have identified this binding pocket and conformational switching mechanism to be triggered by a guanine residue which docks at the Hoogsteen edge of G in a Watson-Crick G-C pair.  This geometry is very similar to a common base triple found in other RNA structures.  We propose that a guanosine residue in the viral mRNA emerging from the ribosome acts as a cognate ligand triggering this conformational switching mechanism and releasing the IRES from the ribosome complex.  Additionally, we have found that the structure of this IRES subdomain IIa is conserved amongst a number of IRES containing viruses.  While these structures do not have sequence homology, they undergo a similar conformational switching mechanism.  A recent x-ray crystal structure of a related viral IRES subdomain IIa, which contains a completely different sequence, reveals a functionally similar way of forming a conformational switching mechanism and placing domain II in the correct orientation on the ribosome.

Conserved conformational switching mechanism in hepatitis C and related viruses internal ribosome entry sites

248th National Meeting (2014)

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