eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G.
DEAD-box RNA helicases eukaryotic translation initiation factor 4A (eIF4A) and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. Eukaryotic translation initiation factor 4B (eIF4B) is a cofactor for eIF4A but also might function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. However, either eliminating eIF4B or inactivating eIF4A preferentially impacts mRNAs with longer, more structured 5' untranslated regions (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 mRNAs. eIF4B, eIF4A, and Ded1 mutations also preferentially impair translation of longer mRNAs in a fashion mitigated by the ability to form closed-loop messenger ribonucleoprotein particles (mRNPs) via eIF4F-poly(A)-binding protein 1 (Pab1) association, suggesting cooperation between closed-loop assembly and eIF4B/helicase functions. Remarkably, depleting eukaryotic translation initiation factor 4G (eIF4G), the scaffold subunit of eukaryotic translation initiation factor 4F (eIF4F), preferentially impacts short mRNAs with strong closed-loop potential and unstructured 5' UTRs, exactly the opposite features associated with hyperdependence on the eIF4B/helicases. We propose that short, highly efficient mRNAs preferentially depend on the stimulatory effects of eIF4G-dependent closed-loop assembly.
Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
Neelam Dabas
ND
Sen
Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
Fujun
F
Zhou
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; Department of Biology, Johns Hopkins University, Baltimore, MD 21218.
Michael S
MS
Harris
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; Department of Biology, Johns Hopkins University, Baltimore, MD 21218.
Nicholas T
NT
Ingolia
Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; ahinnebusch@nih.gov.
Alan G
0000-0002-1627-8395
AG
Hinnebusch
D020121:5' Untranslated Regions; D053487:DEAD-box RNA Helicases / Q000235:genetics*; D039601:Eukaryotic Initiation Factor-4A / Q000235:genetics; D039562:Eukaryotic Initiation Factor-4F / Q000235:genetics; D039603:Eukaryotic Initiation Factor-4G / Q000235:genetics*; D039642:Eukaryotic Initiation Factors / Q000235:genetics*; D009690:Nucleic Acid Conformation; D039102:Poly(A)-Binding Proteins / Q000235:genetics; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics; D012270:Ribosomes / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
D020121:5' Untranslated Regions; D039562:Eukaryotic Initiation Factor-4F; D039603:Eukaryotic Initiation Factor-4G; D039642:Eukaryotic Initiation Factors; D039102:Poly(A)-Binding Proteins; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; C031799:eIF-4B; C450100:pab1 protein, S cerevisiae; D039601:Eukaryotic Initiation Factor-4A; C492152:DED1 protein, S cerevisiae; D053487:DEAD-box RNA Helicases
Ded1; eIF4A; eIF4B; eIF4G; translation