Impact of uORFs in mediating regulation of translation in stress conditions

Abstract

Background A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question. Results By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe. Conclusion We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches.

pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation

“…To date, only a subset of them have been functionally characterized, and they have been shown to play essential functions regulating a plethora of fundamental processes such as DNA repair, RNA splicing, calcium signaling, cell metabolism and tissue regeneration [3][4][5][6][7][8][9][10][11] . Importantly, mounting evidence suggests that microproteins have a role in stress response [12][13][14][15] . In fact, several studies have observed an increased translation of sORFs in response to different cellular stresses such as oxygen and glucose deprivation 16 , viral and bacterial infection 17,18 and even tumor initiation 19 .…”

Newly synthesized mRNA escapes translational repression during the acute phase of the mammalian unfolded protein response

“…The predominant mechanism mediating escape from translational repression is through mRNA uORFs in the 5'-UTRs that serve to enhance translation of downstream coding regions when eIF2α is phosphorylated [4]. However, we and others have found transcripts lacking uORFs associated with ribosomes during the acute UPR [2,8,[61][62][63]. Based on our observation that XBP1 mRNA is induced and harbors long poly(A) tails, we evaluated whether poly(A) tail length influences the association of the XBP1 transcript with polyribosomes by polysome profile analysis.…”

Newly synthesized mRNA escapes translational repression during the acute phase of the mammalian unfolded protein response

“…The predominant mechanism mediating escape from translational repression is through mRNA uORFs in the 5'-UTRs that serve to enhance translation of downstream coding regions when eIF2α is phosphorylated (Wek 2018). However, we and others have found transcripts lacking uORFs associated with ribosomes during the acute UPR (Guan et al 2017;van den Beucken et al 2007;Moro et al 2021;Pavitt and Ron 2012;Jaud et al 2020). Based on our observation that XBP1 mRNA is induced and harbors long poly(A) tails, we evaluated whether poly(A) tail length influences the association of the XBP1 transcript with polyribosomes by polysome profile analysis.…”