bims-mirnam 2026-10-25 papers

Issue of 2026–10–25
four papers selected by
Hana Antonicka, McGill University

J Biol Chem. 2026 Oct 22. pii: S0021-9258(26)02542-1. [Epub ahead of print] 113670

Site-specific m1A Installation by the MTR1 Ribozyme and Modulation of Mitochondrial mRNA Translation in vitro.

Yuting Xie, Zhuoya Zhao, Jie Deng, Yingying Zhao, Bo Fu, Yuanlin He, Xiaorong Zhang, Lin Huang.

RNA modifications play essential roles in regulating RNA structure, stability, and translation. Among these, m1A is a functionally important modification that influences Watson-Crick base pairing and translational fidelity. However, approaches for site-specific installation and func tional interrogation of m1A in RNA remain limited. Here, we characterize the catalytic properties of the methyltransferase ribozyme MTR1 with a focus on donor compatibility, sequence-dependent kinetics, and activity on structured RNA substrates. We show that MTR1 catalyzes alkyl transfer from O6-methylguanine- derived donors to adenosine residues in RNA and accommodates fluorophore-conjugated donors for covalent RNA labeling. Target-site mutation and reverse transcription-based analyses further validate the adenosine-dependent specificity of MTR1-mediated transfer. Comparative kinetic analyses under mildly acidic (pH 6.0) and alkaline (pH 7.5) conditions reveal that pH is a key determinant of MTR1 catalytic efficiency across sequence contexts. Although local sequence context influences reaction rates, pH 6.0 substantially enhances catalytic activity across tested substrates, enabling efficient modification of sequences with limited activity under pH 7.5 conditions. These findings indicate that sequence preference primarily affects reaction kinetics rather than modification capability under mildly acidic conditions, expanding the practical sequence compatibility of MTR1-mediated RNA modification. We further demonstrate that MTR1 enables site-specific m1A modification in structured mitochondrial mRNAs, including mouse COX2 and human ATP8 transcripts, and that these modifications reduce translation in a cell-free mitochondrial system. Together, these results define the donor compatibility, sequence-dependent kinetics, and substrate scope of MTR1 and provide insights into ribozyme-mediated RNA alkylation chemistry.

Keywords: MTR1; Methyltransferase ribozyme; Mitochondria; RNA fluorescent labeling; RNA modification; Site-specific; m(1)A

DOI: https://doi.org/10.1016/j.jbc.2026.113670

Methods Mol Biol. 2027 ;3091 207-231

Visualization of RNA Structures and Functional Annotations Using ArcPlot.

Khoa M Dao, Anthony M Mustoe.

RNA molecules intrinsically fold into complex base-paired structures that critically shape RNA function and mechanisms. Recent innovations in chemical probing now make it straightforward to interrogate RNA structures in cells. New technologies, such as single-molecule chemical probing, further make it possible to directly measure secondary and tertiary base pairing interactions. However, visualizing and interpreting these structural data remains nontrivial. To address this challenge, we developed ArcPlot, a Python program for visualizing DMS and SHAPE reactivity data, PAIR and RING single-molecule probing data, and secondary structure arc diagrams. ArcPlot also facilitates the retrieval and juxtaposition of functional annotations of RNA elements from experiments such as enhanced crosslinking and immunoprecipitation (eCLIP). For advanced users, ArcPlot has an application programming interface (API) that can be used to generate highly customized data visualizations. We provide stepwise instructions and specific examples of different ArcPlot usage applications. The flexibility and ease of use of ArcPlot make visualization and interpretation of complex RNA structural datasets routine, broadly facilitating hypothesis generation and mechanistic understanding of RNA function.

Keywords: DMS; Data visualization; RNA structural ensembles; RNA structure; RNA–protein interactions; SHAPE ; chemical probing

DOI: https://doi.org/10.1007/978-1-0716-5627-3_13

Biol Direct. 2026 Jul 27. pii: 213. [Epub ahead of print]21(1):

Mitochondrial RNA polymerase is a critical mediator of LPS-induced inflammatory responses and septic shock.

Jie Qiong Ping, Tao Guo, Shi Wei Zhang, Cheng Kong, Xiang Yu Gao, Hong Peng Li.

Sepsis, particularly septic shock, is a life-threatening condition driven by a dysregulated inflammatory response. Mitochondria are vital for orchestrating the LPS (lipopolysaccharide)-induced innate immune response. At the core of mitochondrial functionality lies mitochondrial RNA Polymerase (POLRMT). This study delineates POLRMT's functional role and underlying mechanisms in LPS-induced pro-inflammatory responses across various macrophage models and in vivo. Through multiple genetic strategies, including stable shRNA-mediated knockdown and CRISPR/Cas9-mediated ablation, we demonstrated that POLRMT deficiency in THP-1 human macrophages, peripheral blood mononuclear cells (PBMCs), and murine bone marrow-derived macrophages (BMDMs) consistently attenuated LPS-induced transcriptional upregulation and secretion of key pro-inflammatory cytokines (IL-1β, TNF-α, IL-6). Conversely, POLRMT overexpression in THP-1 cells augmented these inflammatory responses. LPS-induced enhancements in mitochondrial Complex I activity and ATP content, alongside NFκB activation, were dependent on POLRMT expression. Genetic perturbation of POLRMT directly correlated with altered mitochondrial function and NFκB activity. Pharmacological inhibition of POLRMT with a specific inhibitor IMT1 also suppressed LPS-induced cytokine production, mitochondrial activation, and NFκB activity in vitro. The in vivo studies revealed that knockdown of POLRMT in CD68-expressing cells protected mice from LPS-induced septic shock, reducing mortality and systemic cytokine levels. Oral administration of IMT1 similarly conferred protection against septic shock, correlating with diminished circulating pro-inflammatory cytokines and reduced NFκB activity in murine PBMCs. Collectively, these findings establish POLRMT as a mediator of LPS-induced inflammatory responses in macrophages/monocytes.

DOI: https://doi.org/10.1186/s13062-026-00917-x

J Phys Chem B. 2026 Oct 22. 130(42): 11103-11114

Flexibility of the TRMT10C N-Terminal Domain Helix Explored by Molecular Dynamics Simulations.

Gia Linh Hoang, Giulia Rossetti, Carine Tisné, Paolo Carloni.

The human mitochondrial tRNA methyltransferase TRMT10C contains a 41-residue long positively charged α-helix in its N-terminal domain, interacting with tRNAs from the anticodon to the T-loops. Here, we investigated the flexibility of this N-terminal long α-helix using comparative molecular dynamics simulations in explicit solvent with three different force fields/water model combinations, alongside two helices of identical length but different sequences: a polyalanine helix and an AEEEKRK repeat helix. We also expanded our simulations to three additional helices belonging to the Trm10 family. Five independent 1-μs simulations were performed for each system. The human TRMT10C helix turned out to display heterogeneous dynamics, with a stable α-helical segment (residues 132-139) embedded within more flexible regions and this trend was also observed in the human Trm10 family members. This relatively rigid segment is more hydrophobic, whereas the remaining portion is enriched in charged residues and shows higher conformational variability. The rigid region corresponds to the portion interacting with the cavity formed by tRNA and TRMT10C N-terminal domain. Additional simulations using alternative force-field and water-model combinations supported the robustness of the overall flexibility ranking for the AEEEKRK repeat helix and the TRMT10C helix, but it gave force-field-dependent results for the structural dynamics of the polyalanine helix. Simulations of the N-terminal helices of other TRMT10C homologues revealed similar flexibility profiles, suggesting that the observed trends are generalizable across the family. Based on our results, we suggest that the human TRMT10C helix is tuned to combine localized rigidity to provide localized structural support that helps present the fragile mitochondrial tRNA to the maturation enzymes with overall flexibility for conformational adaptation, facilitating tRNA positioning and efficient catalysis.

DOI: https://doi.org/10.1021/acs.jpcb.6c03249