bims-protra 2025-07-20 papers

Issue of 2025–07–20
four papers selected by
Marius d’Hervé, McGill University

bioRxiv. 2025 Jun 09. pii: 2025.06.08.658532. [Epub ahead of print]

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

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

In eukaryotes, regulation of mRNA translation initiation greatly impacts gene expression, and is critical for cellular stress responses. DDX3X is a ubiquitous DEAD-box RNA helicase whose precise role in 5' UTR scanning and start codon decoding in non-stressed and stressed cells is still elusive. Here we show that DDX3X engages with thousands of mRNAs as part of the eIF4F-mediated 48S scanning complex, simultaneously acting to promote or suppress translation of select mRNAs in non-stressed conditions, and switches this regulation in opposite directions in acute ER stress. We find distinct DDX3X binding patterns of differentially regulated mRNAs, which lead us to identify N4-acetylation of cytidines surrounding the start codon as an accompanying feature of mRNAs subject to DDX3X-mediated selective dual regulation. Our findings illuminate the role of DDX3X in stress response and highlight a novel connection between an RNA helicase and a post-transcriptional modification in regulating mRNA translation.

DOI: https://doi.org/10.1101/2025.06.08.658532

J Biol Chem. 2025 Jul 10. pii: S0021-9258(25)02319-1. [Epub ahead of print] 110469

Interpreting ribosome dynamics during mRNA translation.

Saori Uematsu, Shu-Bing Qian.

Translation takes a central position in gene expression, its swift response to environmental stress is evolutionarily conserved. Upon chemical damage to the messenger RNA (mRNA) or the lack of building blocks, the ribosome stalls during elongation and halts the production line. Even under normal growth conditions, the translation machinery encounters constant hinderances such as varied codon composition or nascent chains with distinct features. However, it is challenging to define these kinetics experimentally partly due to the inherent variations of ribosome behavior during mRNA translation. To ensure the flow of ribosomal traffic, cells employ several mechanisms to circumvent the traffic jam. When the roadblock is not resolved timely, trailing ribosomes can collide with stalled ribosomes. However, the boundary between physiological queuing and pathological collision is often blurred, representing a fundamental gap in our understanding of ribosome dynamics. To cope with translational barriers, several signaling pathways are activated to adjust the rate of global translation and rescue the local stalled ribosome. Deficiencies of cellular response to translational stress have been associated with a wide array of human diseases. In this review, we focus on fundamental aspects of the ribosome dynamics during mRNA translation. We provide an overview of causes, outcomes, and cellular responses to ribosome stalling and collision on mRNA. We highlight questions that may clarify the biological roles of distinct ribosome behavior during mRNA translation and emphasize the mechanistic connection between altered ribosome dynamics and human diseases.

DOI: https://doi.org/10.1016/j.jbc.2025.110469

bioRxiv. 2025 Jun 27. pii: 2025.06.26.660926. [Epub ahead of print]

Dynamics and Regulation of mRNA Cap Recognition by Human eIF4F.

Hea Jin Hong, Matthew G Guevara, Siyu Li, Yankang Liu, Alexandra N Huang, Eric Lin, Arrmund Neal, Duo Xu, Rong Hai, Roya Zandi, Seán E O'Leary.

Efficient eukaryotic messenger RNA translation requires dynamic collaboration between the three subunits of initiation factor 4F (eIF4F, eIF4E•G•A), which recognises and activates mRNA at its 5' cap structure for ribosome recruitment. Despite its high biological and pharmacological importance, the dynamics of full human eIF4F-mRNA engagement remain largely uncharacterised, hindering mechanistic understanding of translation initiation and its regulation. Here we observed human eIF4F activity with single-molecule fluorescence assays that directly visualise mRNA cap recognition by its eIF4E subunit. Unexpectedly, we find that inherently transient eIF4E-cap binding is repressed by full-length human eIF4G, predominantly through its C-terminus, representing an unanticipated role for eIF4G as a central rate-limiting factor in the eIF4F complex. This repression is relieved by nucleotide-bound eIF4A in the eIF4F heterotrimer, placing eIF4A as a crucial determinant of efficient cap recognition for translation. Molecular dynamics simulations reveal that electrostatic modulation of eIF4E-mRNA interaction allows eIF4G to control the cap-recognition frequency. Our findings also indicate that intrinsic eIF4F- mRNA dynamics are insufficient to support cap-tethered ribosomal scanning to locate translation start sites. They illuminate fundamental design-principle differences for the overall mechanism and division of labour among eIF4F subunits during mRNA recognition in humans and yeast.

DOI: https://doi.org/10.1101/2025.06.26.660926

bioRxiv. 2025 Jun 28. pii: 2025.06.25.661590. [Epub ahead of print]

Chaperone saturation mediates translation and protein folding efficiency.

Andrew T Martens, Vincent J Hilser.

Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question (Chaney and Clark, 2015; Deane and Saunders, 2011; Levinthal, 1968; Marin, 2008; Sauna and Kimchi-Sarfaty, 2011; Spencer and Barral, 2012; Tsai et al., 2008; Zhang and Ignatova, 2011). Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones (Siller et al., 2010; Spencer et al., 2012), which in Escherichia coli are induced by unfolded protein (Parsell and Sauer, 1989) via σ 32 (Craig and Gross, 1991). The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. Using ribosome profiling (Ingolia et al., 2009) and protein quantitation, we show that synonymous changes to Firefly Luciferase ( Luc ) mRNA have a direct effect on its translation efficiency. These changes alone cause up to a 70-fold difference in Luc protein levels. However, increased Luc protein is met with at most a ∼2-fold increase in chaperone levels, revealing that the σ 32 transcriptional response has saturable properties. This response is found to be poised near its midpoint (where it is most sensitive to perturbation) when Luc mRNA has an intermediate translation efficiency. These results suggest not only that chaperone saturation limits the ability of cells to maintain protein folding homeostasis when challenged with highly efficient translation, but that translation efficiency and protein folding efficiency evolved for mutual sensitivity.

DOI: https://doi.org/10.1101/2025.06.25.661590