bims-protra 2025-11-02 papers

Issue of 2025–11–02
four papers selected by
Marius d’Hervé, McGill University

Cell Rep. 2025 Oct 28. pii: S2211-1247(25)01264-1. [Epub ahead of print]44(11): 116493

DDX3X acts as a selective dual switch regulator of mRNA translation in acute ER stress.

Abd-El Monsif A Shawky, Allison V Eckhardt, Josef B Mick, Mahmoud F Dondeti, Kenneth Avanzino, Constantine A Simintiras, Maria Hatzoglou, Anastasios Vourekas.

Regulation of eukaryotic mRNA translation initiation greatly impacts gene expression and is critical for cellular stress response. DDX3X is a ubiquitous DEAD-box RNA helicase whose precise role in scanning and translation regulation in non-stressed and stressed cells remains incompletely understood. Here, we show that DDX3X associates with thousands of mRNAs as part of the eIF4F-mediated 48S scanning complex and exerts dual regulatory effects, promoting or repressing translation of select mRNAs under basal conditions and reversing this regulation during acute endoplasmic reticulum stress. Initiation profiling reveals mechanistically distinct modes of DDX3X action linked to its binding patterns across the 5' UTR and coding sequence. We further uncover that mRNAs selectively regulated by DDX3X exhibit specific patterns of cytidine N4-acetylation near start codons, with shared de-repression observed upon NAT10 knockdown. Together, our findings reveal DDX3X as a context-sensitive regulator that has a possible functional connection with epitranscriptomic features in translation control.

Keywords: CP: Molecular biology; DDX3X; RNA helicase; ac4C; eIF3; endoplasmic reticulum stress; post-transcriptional modifications; post-transcriptional regulation of gene expression; translation initiation

DOI: https://doi.org/10.1016/j.celrep.2025.116493

Biology (Basel). 2025 Oct 17. pii: 1430. [Epub ahead of print]14(10):

Remodeling of Germ Cell mRNPs for Translational Control.

Brett D Keiper, Hayden P Huggins.

The localization and remodeling of mRNPs is inextricably linked to translational control. In recent years there has been great progress in the field of mRNA translational control due to the characterization of the proteins and small RNAs that compose mRNPs. But our initial assumptions about the physical nature and participation of germ cell granules/condensates in mRNA regulation may have been misguided. These "granules" were found to be non-membrane-bound liquid-liquid phase-separated (LLPS) condensates that form around proteins with intrinsically disordered regions (IDRs) and RNA. Their macrostructures are dynamic as germ cells differentiate into gametes and subsequently join to form embryos. In addition, they segregate translation-repressing RNA-binding proteins (RBPs), selected eIF4 initiation factors, Vasa/GLH-1 and other helicases, several Argonautes and their associated small RNAs, and frequently components of P bodies and stress granules (SGs). Condensate movement, separation, fusion, and dissolution were long conjectured to mediate the translational control of mRNAs residing in contained mRNPs. New high-resolution microscopy and tagging techniques identified order in their organization, showing the segregation of similar mRNAs and the stratification of proteins into distinct mRNPs. Functional transitions from repression to activation seem to corelate with the overt granule dynamics. Yet increasing evidence suggests that the resident mRNPs, and not the macroscopic condensates, exert the bulk of the regulation.

Keywords: biomolecular condensates; eIF4E-interacting proteins (4EIPs); eukaryotic translation initiation factor 4E (eIF4E); germ cell granules; liquid–liquid phase separation (LLPS); mRNA translational control; macrostructures; messenger ribonucleoproteins (mRNPs); ribosomes; substructures

DOI: https://doi.org/10.3390/biology14101430

Cell Rep. 2025 Oct 28. pii: S2211-1247(25)01263-X. [Epub ahead of print]44(11): 116492

Real-time tracking of mRNP complex assembly reveals various mechanisms that synergistically enhance translation repression.

Marco Payr, Julia Meyer, Eva-Maria Geissen, Janosch Hennig, Olivier Duss.

Protein biosynthesis must be highly regulated to ensure proper spatiotemporal gene expression and thus cellular viability. Translation is often modulated at the initiation stage by RNA-binding proteins through either promotion or repression of ribosome recruitment to the mRNA. However, it largely remains unknown how the kinetics of mRNA ribonucleoprotein (mRNP) assembly on untranslated regions (UTRs) relate to its translation regulation activity. Using Sex-lethal (Sxl)-mediated translation repression of msl-2 in female fly dosage compensation as a model system, we show that different mechanisms in mRNP assembly synergistically achieve tight translation repression. Using multicolor single-molecule fluorescence microscopy, we show that Sxl targets its binding sites via facilitated diffusion and multivalent binding, Unr recruitment is accelerated over 500-fold by RNA-bound Sxl, and Hrp48 further stabilizes RNA-bound Sxl indirectly via ATP-independent RNA remodeling. Overall, we provide a framework to study how multiple RBPs dynamically cooperate with RNA to achieve function.

Keywords: CP: Molecular biology; NMR; RNA chaperone; RNP dynamics; dosage compensation; mRNP complex formation; protein-RNA interactions; single-molecule FRET; translation regulation

DOI: https://doi.org/10.1016/j.celrep.2025.116492

Vavilovskii Zhurnal Genet Selektsii. 2025 Oct;29(6): 737-743

A new combination of 5'- and 3'-untranslated regions increases the expression of mRNAs in vitro and in vivo.

D N Antropov, O V Markov, A S Dome, P A Puchkov, E V Shmendel, D V Gladkikh, V M Golyshev, A M Matveeva, M A Maslov, G A Stepanov.

mRNA vaccine technologies have been actively developing since the beginning of the 21st century and have received a major boost from new findings about the functioning of the immune system and the development of efficient vehicles for nucleic acid delivery. The mRNA vaccine demonstrates superior properties compared to the DNA vaccine, primarily due to accelerated mRNA vaccine development, enhanced flexibility, and the absence of integration into the genome. Artificial mRNAs have biotechnological and medical applications, including the development of antiviral and anticancer mRNA therapeutics. The effective expression of therapeutic mRNA depends upon the appropriate selection of structural elements. Along with the addition of the 5'-cap, appropriate polyadenylation, and sequence codon optimization, 5'- and 3'-untranslated regions (UTRs) play an important role in the translation efficiency of therapeutic mRNAs. In this study, new plasmids containing a novel combination of UTR pairs, namely 5'-UTR-4 and 3'-UTR AES-mtRNR1, were constructed to obtain artificial mRNAs encoding green fluorescent protein (GFP) and firefly luciferase (FLuc) with new structural elements and properties. The novel combination of the UTRs, which is described in this article for the first time, in addition to sufficient polyadenylation and pseudouridinilation of mRNA, was demonstrated to strongly increase the translation of codon-optimized sequences of reporter mRNAs. We generated lipoplexes containing the aforementioned reporter mRNAs and liposomes composed of cationic lipid 2X3 (1,26-bis(cholest-5-en-3beta-yloxycarbonylamino)-7,11,16,20-tetraazahexacosane tetrahydrochloride) and helper lipid DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine). For in vivo experiments, the liposomes were decorated with 2 % of 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (DSPE- PEG2000). The translation efficiency of mRNAs was found to be superior for the novel UTR combination compared with HBB gene UTRs, both in vitro and in vivo. When mRNA is administered intramuscularly, the proposed combination of UTRs provides lasting expression for more than 4 days. The results demonstrated that the novel UTR pair combination could be useful in the development of artificial mRNAs with enhanced translation efficiency, potentially reducing the dose for mRNA-based therapeutics.

Keywords: RNA delivery; lipid nanoparticle; nucleotide modifications; synthetic mRNA; untranslated region

DOI: https://doi.org/10.18699/vjgb-25-81