The helicase Ded1p controls use of near-cognate translation initiation codons in 5′UTRs

The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian ortholog DDX3 are critical for translation initiation(1). Mutations in DDX3 are linked to tumorigenesis(2–4) and intellectual disability(5), and the enzyme is targeted by diverse viruses(6). How Ded1p and its orthologs engage RNAs in translation initiation has been a longstanding, unresolved question. Here we integrate transcriptome-wide analyses of RNA translation, structure, and Ded1p-RNA binding and show that the impact of Ded1p on translation initiation is connected to near-cognate initiation codons in 5′UTRs. Ded1p associates with the scanning translation pre-initiation complex at the mRNA entry channel. Repression of Ded1p activity leads to accumulation of RNA structure in 5′UTRs, translation initiation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main ORFs. The data reveal a program for translation regulation that links Ded1p, activation of near-cognate start codons and mRNA structure. We show that this program plays a role in meiosis where a marked decrease in Ded1p levels is accompanied by activation of alternative translation initiation sites seen with repressed Ded1p activity. Our observations indicate that Ded1p impacts translation initiation by controlling the use of near-cognate initiation codons that are proximal to mRNA structure in 5′UTRs.