Not merely a cofactor: eukaryotic Initiation Factor 4B (eIF4B) acts independently of eIF4A and preferentially stimulate translation of long mRNAs with structured 5’UTRs and low potential for closed-loop assembly

Authors

• ND Sen
• F Zhou
• M Harris
• NT Ingolia
• AG Hinnebusch

Abstract

DEAD-box RNA helicases eIF4A and Ded1 promote eukaryotic translation initiation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. eIF4B is a cofactor for eIF4Abut might also promote these reactions independently of eIF4A. We addressed this possibility in vivo by ribosome footprint profiling of a mutant lacking eIF4B (tif3Δ) and comparing the changes in global translational efficiencies (TEs) to those seen in mutants with impaired eIF4A or Ded1 activity. Elimination of eIF4B evoked broader and more extensive changes in TE than did inactivation of eIF4A, despite comparable reductions in bulk translation, and only a few genes displayed unusually strong requirements for both factors. However, the effects of eIF4B and eIF4A mutations on TEs genome-wide are significantly correlated and both mutations preferentially impacts mRNAs with longer, more structured 5’UTRs. These findings reveal an eIF4A-independent role for eIF4B in addition to its function as eIF4A cofactor in promoting PIC attachment or scanning on structured 5’UTRs. An eIF4A-independent function of eIF4B in overcoming an inhibitory 5’-proximal structure was also indicated by reporter analysis. Interestingly, eIF4B, eIF4A, and Ded1 mutations all preferentially impaired translation of longer mRNAs, which have greater than average propensity for 5’UTR structure. These effects were mitigated by a heightened potential to form the closed-loop mRNP via eIF4F-Pab1 interactions, suggesting that closed-loop assembly cooperates with eIF4B, eIF4A and Ded1 to facilitate initiation with structured 5’UTRs. Our study highlights the unique roles of yeast eIF4B and RNA helicases eIF4A and Ded1 in regulating the yeast translatome.

Scientific Focus Area: Molecular Biology and Biochemistry

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