A novel translational control mechanism involving RNA structures within coding sequences

Abstract

The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEADbox helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses, we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site; second, they are directly bound by Dhh1 with a specific binding distribution; and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

“…In addition, the eIF4A cofactor eIF4B has been found to stimulate translation of long mRNAs containing structured 5′ UTRs in budding yeast independently of eIF4A, as demonstrated by ribosome profiling, which also correlates with 5′ UTR structure accessibility assessed in vitro 60 . Finally, following the release of eIF4A upon recognition of the start site, the budding yeast DEAD-box helicase Dhh1 specifically promotes translation of mRNAs that have long and highly structured coding regions 61 . These examples highlight how diverse RNA helicases and initiation factors can target specific mRNAs with structured regions or motifs, which otherwise may serve as roadblocks to scanning and translation initiation.…”

mRNA structure regulates protein expression through changes in functional half-life

“…What is the mechanistic basis for the observed relationship between CDS secondary structure and functional mRNA half-life? Numerous RNA binding proteins (RBPs) interact with secondary structures, with the RNA helicase DDX6 and double-stranded RNA binding protein Staufen both having been reported to positively impact translation (Jungfleisch et al, 2017). It is also possible that more structured RNAs are less prone to cleavage by single strand-specific endonucleases, although endonucleolytic cleavage is thought to only contribute to the degradation in specific cases (Schoenberg, 2011;Wilamowski et al, 2018).…”

Using ribosome profiling to quantify differences in protein expression: a case study in Saccharomyces cerevisiae oxidative stress conditions

“…Numerous recent studies have used ribosome profiling data has been used to study 76 translation regulatory mechanisms (Jungfleisch et al, 2017;Yordanova et al, 2018) Here we perform differential gene expression analysis using RNA-Seq and Ribo-Seq data 81 during oxidative stress in Saccharomyces cerevisiae, a condition that is known to trigger 82 important regulatory changes both at the transcriptional and translational levels (Shenton 83 et al, 2006;Gerashchenko et al, 2012). We compare the results to proteomics data 84 obtained from the same samples.…”