bims-micpro 2023-10-01 papers

Issue of 2023‒10‒01
two papers selected by
Thomas Farid Martínez, University of California, Irvine

Proc Natl Acad Sci U S A. 2023 Oct 03. 120(40): e2214636120

Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep.

Arthur Millius, Rikuhiro G Yamada, Hiroshi Fujishima, Kazuhiko Maeda, Daron M Standley, Kenta Sumiyama, Dimitri Perrin, Hiroki R Ueda.

Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.

Keywords: RNA; circadian rhythms; mass spectrometry; ribosome profiling; uORF

DOI: https://doi.org/10.1073/pnas.2214636120

Biochimie. 2023 Sep 21. pii: S0300-9084(23)00244-4. [Epub ahead of print]

The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes.

Antonin Tidu, Franck Martin.

Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.

Keywords: 5′UTR; IRES; Ribosome; Translation; uORF

DOI: https://doi.org/10.1016/j.biochi.2023.09.017