The control of mRNA translation into proteins is critical for the adaptation of eukaryotic cells to environmental changes and stress conditions.Glucose starvation in yeast is one of the prototypical eukaryotic stresses. The early translation-based responses to glucose starvation are critically important to trigger the subsequent events leading to transcriptional reprogramming, but the involved mRNAs and the mechanisms of their selective regulation remain obscure.
We analysed glucose-specific translational control by Translation Complex Profile sequencing (TCP-seq). TCP-seq measures the footprints of ribosomal complexes along mRNA using a combination of in vivo fixation, complex purification and high-throughput sequencing. Here, to dissect different aspects of translation regulation, we separately recorded footprints of single ribosomes and disomes. We furthermore sequenced footprints of three distinct complexes involving small ribosomal subunits (SSU), those derived from polysomes or ‘singular’ subunits in solution, as well as those that selectively contained the scanning translation initiation factor eIF4A. Under starvation and globally suppressed protein biosynthesis, we observe an increased level of translation of many glucosynthetic mRNAs, such as encoding glucokinase, hexokinase, 3-phosphoglycerate kinase. Increased disome frequencies confirm alteration of the translation rate of these mRNAs. Comparing SSU footprint densities in the translated and singular SSU-bound mRNA fractions, we detect influence of rapid mRNA degradation early into the stress. We further observe many eIF4A-containing complexes in the 5'UTRs (as expected), while others are scattered across the coding sequences or 3'UTRs. A subset of mRNAs active under glucose starvation exhibits scarcer eIF4A binding, possibly leading to a different scanning mode.
Overall, our data uncovers a complex picture of rapid translational changes and presents a collection of transcripts involved in the acute response to stress. It suggests, early in the response major pathways are involved in the translational control, mRNAs are degraded or preserved and their translation, selectively shut down, unperturbed or upregulated.