Kinetic mechanism for the binding of eIF4F and tobacco etch virus internal ribosome entry site RNA: Effects of eIF4B and poly(A)-binding protein

Abstract

The wheat germ eukaryotic translation initiation factor (eIF) 4F binds tightly to the mRNA internal ribosome entry site (IRES) of tobacco etch virus (TEV) to promote translation initiation. When eIF4F is limiting, TEV is preferentially translated compared with host cell mRNA. To gain insight into the dynamic process of protein synthesis initiation and the mechanism of binding, the kinetics of eIF4F binding to TEV IRES were examined. The association rate constant (kon) and dissociation rate constant (koff) for eIF4F binding to IRES were 59 ± 2.1 μm-1 s-1 and 12.9 ± 0.3 s-1, respectively, comparable with the rates for capped RNA. Binding of eIF4E or eIF4F to the cap of mRNA is the rate-limiting step for initiation of cap-dependent protein synthesis. The concentration dependence of the reactions suggested a simple onestep association mechanism. However, the association rate was reduced more than 10-fold when KCl concentration was increased from 50 to 300mM, whereas the dissociation rate constant was increased 2-fold. The addition of eIF4B and poly(A)- binding protein enhanced the association rate of eIF4F ∼3-fold. These results suggest a mechanism where eIF4F initially binds electrostatically, followed by a conformational change to further stabilize binding. Poly(A)-binding protein and eIF4B mainly affect the eIF4F/TEV association rate. These results demonstrate the first direct kinetic measurements of translation initiation factor binding to an IRES. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.