bims-protra 2025-07-06 papers

Issue of 2025–07–06
three papers selected by
Marius d’Hervé, McGill University

Elife. 2025 Jul 02. pii: RP105311. [Epub ahead of print]14

Human eIF2A has a minimal role in translation initiation and in uORF-mediated translational control in HeLa cells.

Mykola Roiuk, Marilena Neff, Aurelio A Teleman.

Translation initiation in eukaryotes requires a 40 S ribosome loaded with initiator tRNA which scans for an initiation codon. The initiator tRNA is usually recruited to the ribosome as part of a ternary complex composed of initiator tRNA, eIF2, and GTP. Although initiator tRNA recruitment was originally ascribed to another factor, eIF2A, it was later disproven and shown to occur via eIF2. Nonetheless, eIF2A is still considered a translation initiation factor because it binds the ribosome and shows genetic interactions with other initiation factors such as eIF4E. The exact function of eIF2A during translation initiation, however, remains unclear. Here, we use ribosome profiling and luciferase reporter assays to systematically test in HeLa cells the role of eIF2A in translation initiation, including translation of upstream ORFs. Since eIF2A is thought to take over the function of eIF2 when eIF2 is inhibited, we also test conditions where the integrated stress response is activated. In none of our assays, however, could we detect a role of eIF2A in translation initiation. It is possible that eIF2A plays a role in translation regulation in specific conditions that we have not tested here, or that it plays a role in a different aspect of RNA biology.

Keywords: biochemistry; chemical biology; developmental biology; eIF2; eIF2A; human; translation

DOI: https://doi.org/10.7554/eLife.105311

Biochemistry (Mosc). 2025 Jun;90(6): 725-753

Selection of UTRs in mRNA-Based Gene Therapy and Vaccines.

Ilya A Volkhin, Anastasia Iu Paremskaia, Maria A Dashian, Darya S Smeshnova, Roman E Pavlov, Olga N Mityaeva, Pavel Yu Volchkov, Andrei A Deviatkin.

The untranslated regions (UTRs) of messenger RNAs (mRNAs) play a crucial role in regulating translational efficiency, stability, and tissue-specific expression. The review describes various applications and challenges of UTR design in the development of gene therapy and mRNA-based therapeutics. UTRs affect critical biological functions, such as mRNA stability, modulation of protein synthesis, and attenuation of immune response. Incorporating tissue-specific microRNA (miRNA)-binding sites into 3' UTRs might improve precise targeting of transgene expression and minimize off-target effects. Nucleotide modifications (pseudouridine, N1-methyladenosine, and N4-acetylcytidine) in mRNA and UTRs in particular, improve mRNA stability and translational efficiency. At the same time, several challenges remain, such as lack of consensus on UTRs best suited for certain biomedical applications. Current efforts are focused on integrating high-throughput screening, computational modeling, and experimental validation to refine UTR-based therapeutic strategies. The review presents current information on the design of UTRs and their role in therapeutic applications, with special focus on the possibilities and limitations of existing approaches.

Keywords: RNA secondary structure; UTR; gene therapy; mRNA vaccine; optimization; rational design

DOI: https://doi.org/10.1134/S0006297924604659

Nat Commun. 2025 Jul 01. 16(1): 5496

Mammalian tRNA acetylation determines translation efficiency and tRNA quality control.

Na Liu, Bingxue Liu, Chun-Rui Ma, Zixin Cai, Jin-Tao Wang, Zi-Qing Chai, Nanlin Zhu, Ting Shao, Yue-Lei Chen, Yu Lin, Yirong Wang, Hong Xu, Xiao-Long Zhou.

Acetylation is a conserved and pivotal RNA modification. Acetylation of tRNA occurs at C12 (ac4C12) in eukaryotic tRNAs. Yeast ac4C12 prevents tRNASer from rapid tRNA decay (RTD) at higher temperatures. However, the biological function of ac4C12 in higher eukaryotes remains unexplored. Moreover, whether mammalian cells contain an RTD pathway is unclear. Here, we deleted Thumpd1, the indispensable factor for ac4C12 biogenesis, in NIH/3T3 cells. Loss of ac4C12 significantly reduced tRNA aminoacylation and translational efficiency physiologically, in particular, of those enriched with Ser/Leu codons with two U/A nucleotides. Remarkably, ac4C12 hypomodification selectively generated rapid tRNALeu(CAG) turnover under heat stress. We demonstrated that tRNALeu(CAG) was degraded by a mammalian RTD (mRTD) mechanism, consisting of Xrn1/Xrn2-mediated 5'-3' exonuclease digestion and intracellular pAp level control by Bpnt1/Bpnt2. Our results reveal both the pivotal roles of ac4C12 in translation and a mRTD pathway for tRNA quality control under heat stress in mammalian cells.

DOI: https://doi.org/10.1038/s41467-025-60723-3