bims-protra 2025-06-29 papers

Issue of 2025–06–29
four papers selected by
Marius d’Hervé, McGill University

Viruses. 2025 May 28. pii: 766. [Epub ahead of print]17(6):

Viral Strategies and Cellular Countermeasures That Regulate mRNA Access to the Translation Apparatus.

The papers introduced in the Commentary present new insights and review aspects of current knowledge concerning the competition between viruses and their hosts for the cellular translation apparatus. Viruses depend on this apparatus and utilize diverse mechanisms to usurp it for the translation of viral mRNAs and to suppress synthesis of cellular proteins. Virus-induced modification of translation factors, selective abrogation of mRNA binding to ribosomes and degradation of cellular mRNAs all impair elements of the innate immune response, thereby undermining host defenses against infection. Various cellular mechanisms prevent translation of viral mRNAs, by modifying components of the translation apparatus to effect a generalized shut-off of translation or by binding of host proteins to viral mRNAs to induce their degradation or to prevent their engagement with the translation apparatus. Viruses have in turn evolved countermeasures to evade these defenses, for example by encoding proteins that impair the activity of host factors or via alterations in the sequence and structure of viral mRNAs. Such changes enable viral mRNAs to avoid recognition by host factors or to support translation initiation by specialized mechanisms that involve only a subset of the factors that are required by cellular mRNAs.

Keywords: IRES; ITAF; Shiftless; calicivirus; coronavirus; interferon-stimulated gene; mRNA translation; picornavirus; poxvirus; translational control

DOI: https://doi.org/10.3390/v17060766

PLoS One. 2025 ;20(6): e0324462

rbpTransformer: A novel deep learning model for prediction of piRNA and mRNA bindings.

Ahmet Gürhanlı.

An important issue in biotechnology is predicting whether a piRNA and an mRNA will or will not bind. Research and treatment of diseases, drug discovery, and the silencing and regulation of genes, transposons, and genomic stability may all benefit from accurate binding predictions. The literature offers numerous deep-learning models for piRNA and mRNA binding prediction. However, a proper adjustment of the effective transformer model and the impact of important design alternatives has not been evaluated thoroughly. This paper summarizes the models available in the literature, briefly introduces transformers, then offers a novel deep learning model and evaluates various design alternatives, including k-mer size, number of core modules, choice of optimization algorithm, and whether to use self-attention. The results show that rbpTransformer can be a good candidate for building deep AI models to predict the binding of piRNA and mRNA sequences with an AUC value of 94.38%. The test results also reveal how the design affects the model's accuracy.

DOI: https://doi.org/10.1371/journal.pone.0324462

Cells. 2025 Jun 08. pii: 866. [Epub ahead of print]14(12):

5' DREDGE: Direct Repeat-Enabled Downregulation of Gene Expression via the 5' UTR of Target Genes.

Sagar J Parikh, Heather M Terron, Luke A Burgard, Dylan D Butler, Frank M LaFerla, Shelley Lane, Malcolm A Leissring.

Despite the availability of numerous methods for controlling gene expression, there remains a strong need for technologies that maximize two key properties: selectivity and reversibility. To this end, we developed a novel approach that exploits the highly sequence-specific nature of CRISPR-associated endoribonucleases (Cas RNases), which recognize and cleave short RNA sequences known as direct repeats (DRs). In this approach, referred to as DREDGE (direct repeat-enabled downregulation of gene expression), selective control of gene expression is enabled by introducing one or more DRs into the untranslated regions (UTRs) of target mRNAs, which can then be cleaved upon expression of the cognate Cas RNase. We previously demonstrated that the expression of target genes with DRs in their 3' UTRs are efficiently controlled by the DNase-dead version of Cas12a (dCas12a) with a high degree of selectivity and complete reversibility. Here, we assess the feasibility of using DREDGE to regulate the expression of genes with DRs inserted in their 5' UTRs. Among the five different Cas RNases tested, Csy4 was found to be the most efficient in this context, yielding robust downregulation with rapid onset in doxycycline-regulatable systems targeting either a stably expressed fluorescent protein or an endogenous gene, both in a fully reversible manner. Unexpectedly, dCas12a was also found to be modestly effective despite binding essentially irreversibly to the cut mRNA on its 5' end and thereby boosting mRNA levels. Our results expand the utility of DREDGE as an attractive method for regulating gene expression in a targeted, highly selective, and fully reversible manner.

Keywords: CRISPR; DREDGE; direct repeat; endoribonuclease; gene regulation

DOI: https://doi.org/10.3390/cells14120866

Biophys J. 2025 Jun 19. pii: S0006-3495(25)00381-9. [Epub ahead of print]

Denaturation of firefly luciferase at heat shock temperatures captured in silico.

Vishal D Lashkari, Piotr E Marszalek.

Firefly luciferase (Fluc) is a bioluminescent protein that is widely used in cell and molecular biology research. Specifically, it is a gold standard substrate in chaperone protein studies because its bioluminescence decrease and recovery are related to Fluc misfolding and chaperone-assisted refolding, respectively. Fluc is moderately stable at room temperature but quickly loses bioluminescent activity at elevated temperatures as a stable, misfolded conformation is induced which persists upon cooling Fluc to room temperature. The heat shock protein 70 chaperone system can revert such structural changes, restoring bioluminescent activity. While thermal denaturation of Fluc is often used in chaperone-assisted refolding reactions, little is known about the specific structural alterations that occur in Fluc at heat shock temperatures. In this study, we use comprehensive all-atom molecular dynamics simulations to investigate the structural dynamics of Fluc at room (∼25 °C) and heat shock temperatures (∼42 °C). We conduct simulations totaling over 100 μs across replicates which allows a misfolded equilibrium to be approached. We find that at heat shock temperatures, Fluc undergoes subtle but long-lasting and reproducible conformational changes, namely the complete and irreversible denaturation of the α-helix at residues 405-411. We show the potential for this discrete change to inhibit Fluc bioluminescent activity. This consistent α-helix denaturation, along with other small secondary structure changes outlined in this work, are potential targets for chaperone systems known to restore Fluc activity after thermal denaturation. Therefore, our results inform a refined mechanism for chaperone-assisted refolding in which chaperone proteins may restore protein function by fixing localized structural perturbations as opposed to refolding an entirely denatured polypeptide chain.

Keywords: bioluminescence; chaperone proteins; luciferase; molecular dynamics; protein folding; thermal denaturation

DOI: https://doi.org/10.1016/j.bpj.2025.06.021