Down-Regulation of Yeast Helicase Ded1 by Glucose Starvation or Heat-Shock Differentially Impairs Translation of Ded1-Dependent mRNAs.

Neelam Dabas Sen,Hongen Zhang,Alan G Hinnebusch

doi:10.3390/microorganisms9122413

Abstract

Ded1 is an essential DEAD-box helicase in yeast that broadly stimulates translation initiation and is critical for mRNAs with structured 5′UTRs. Recent evidence suggests that the condensation of Ded1 in mRNA granules down-regulates Ded1 function during heat-shock and glucose starvation. We examined this hypothesis by determining the overlap between mRNAs whose relative translational efficiencies (TEs), as determined by ribosomal profiling, were diminished in either stressed WT cells or in ded1 mutants examined in non-stress conditions. Only subsets of the Ded1-hyperdependent mRNAs identified in ded1 mutant cells exhibited strong TE reductions in glucose-starved or heat-shocked WT cells, and those down-regulated by glucose starvation also exhibited hyper-dependence on initiation factor eIF4B, and to a lesser extent eIF4A, for efficient translation in non-stressed cells. These findings are consistent with recent proposals that the dissociation of Ded1 from mRNA 5′UTRs and the condensation of Ded1 contribute to reduced Ded1 function during stress, and they further suggest that the down-regulation of eIF4B and eIF4A functions also contributes to the translational impairment of a select group of Ded1 mRNA targets with heightened dependence on all three factors during glucose starvation.

Highlights

Most eukaryotic mRNAs are translated by the scanning mechanism, which begins with the assembly of a 43S preinitiation complex containing the small (40S) ribosomal subunit loaded with the Met-tRNAi Met initiator and several initiation factors
To assess the possible impact of the different strain backgrounds and culture conditions represented among the various analyzed ribosome-profiling datasets, we examined the correlations between the relative translation levels (ribosome-protected mRNA fragments (RPFs) summed over the coding sequences) for each of the 1566 Ded1 hyperdependent mRNAs, obtained from the ribosome-profiling results for the nonstressed WT control strains grown on glucose-containing medium at 30 ◦ C for each of the four conditions of glucose starvation at 30 ◦ C, heat-shock at 42 ◦ C vs. 30 ◦ C, rapamycin treatment at 30 ◦ C, or the ded1-ts mutation at 37 ◦ C
It was reported that bulk polysome assembly was rapidly impaired within only 10 min of glucose withdrawal and partial recovery after 3 h, during which a broad reprogramming of translation occurred compared to glucose-replete cells (+Glu), as determined by the ribosome profiling of cells in the two conditions

Summary

Introduction

Most eukaryotic mRNAs are translated by the scanning mechanism, which begins with the assembly of a 43S preinitiation complex containing the small (40S) ribosomal subunit loaded with the Met-tRNAi Met initiator and several initiation factors (eIFs). The. 43S PIC binds to the 50 -end of mRNA, with eIF4F bound to the m7 G cap (comprised of cap-binding protein eIF4E, scaffolding subunit eIF4G, and DEAD-box RNA helicase eIF4A), and scans the 50 -untranslated region (UTR) to identify the start codon. PIC joins with the large (60S) subunit to form an 80S initiation complex ready to begin protein synthesis (reviewed in [1,2]). Both 43S PIC attachment to mRNA and subsequent scanning are inhibited by secondary structures in the mRNA 50 UTR [3] that are thought to be resolved by DEAD/H-box RNA helicases.

Methods

Results

Conclusion