GSE137021
Temperature-dependent regulation of upstream open reading frame translation in s. cerevisiae
Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae. Initiation from NCCs or AUGs in the 5'-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae. Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 °C relative to 30 °C and decreased efficiency at 20 °C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5'-leader relative to the 5'-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. Overall, our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae. Overall design: We examined the effect of changes in culture temperature on usage of alternate start sites upstream of the annotated start codon AUG (translation of upstream open reading frame i.e. uORF). We calculated global translational efficiencies (TEs) by ribosome footprint profiling of BY4741 cells cultured at multiple temperatures. The study includes 12 samples, comprised of 6 mRNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates of cells cultured at 20 °C, 30 °C. and 37 °C. The ribo-seq data generated in this study are previously published (Martin-Marcos et al., 2017, eLife 2017;6:e31250 DOI: 10.7554/eLife.31250). The ribo-seq data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSM2895484, GSM2895485, GSM2895488, GSM2895489, GSM2895490, GSM2895491.