Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A

Identification of 5′ UTRs sufficient to confer Ded1 dependence of LUC reporter expression. (A) Schematic of reporters containing promoter, 5′ UTR, and first 20 codons of candidate genes, fused to firefly luciferase coding sequences (FLUC) and a modified RPL41A 3′ UTR. (B) Changes in ribosome density of the 22 candidate genes (from ribosome footprints) in ded1-cs versus WT cells plotted against the ratio of LUC expression in ded1-cs versus WT for corresponding reporters. Strains were grown in SC−Leu−Ura at 30°C, diluted to OD₆₀₀∼0.1, and grown for ∼three doublings at 23°C (∼18 h for ded1-cs and ∼10 h for WT). Luciferase activities were assayed in whole cell extracts (WCE), normalized to total protein, and reported in relative light units (RLUs) per mg of protein, as means (±SEM) determined from six transformants.