bims-mirnam 2026-06-28 papers

Issue of 2026–06–28
four papers selected by
Hana Antonicka, McGill University

Nat Commun. 2026 Jun 24. pii: 5564. [Epub ahead of print]17(1):

Pseudouridine synthase PUS1 and initiation factor mtIF2 are human mitoribosomal small subunit assembly factors.

Vivek Singh, Dmitrii Shiriaev, Lorina Bilalli, Anas Khawaja, Joanna Rorbach.

Assembly of the mitochondrial ribosome (mitoribosome) is a crucial step in mitochondrial gene expression. This process facilitates mitochondrial translation, which produces essential subunits of the oxidative phosphorylation machinery-the cell's primary energy-producing machinery. Disruptions in mitoribosome assembly can lead to severe human diseases. Given its fundamental importance, detailed structural analysis of mitoribosome assembly pathways is essential for advancing our understanding of mitochondrial function in both health and disease. In this study, we characterize twelve distinct assembly states of the mitoribosomal small subunit (mtSSU) isolated from human cells. Our findings reveal the intricate details of the final maturation stages of the mtSSU platform, decoding center, and the 3'-end of 12S rRNA. This process is governed by coordinated actions of assembly factors that ensure precise, stepwise rRNA folding and the integration of mitoribosomal proteins into the developing subunit. Our approach identifies pseudouridine synthase PUS1 and initiation factor mtIF2 as assembly factors, expanding their known roles beyond mt-tRNA maturation and translation, respectively. In addition, the identified assembly intermediates provide insight into the modular nature of mtSSU biogenesis in mitochondria and further link late-stage assembly to the acquisition of translational competence.

DOI: https://doi.org/10.1038/s41467-026-74700-x

Cells. 2026 Jun 22. pii: 1129. [Epub ahead of print]15(12):

Activity of DNA- and RNA-Guided Prokaryotic Argonautes in Human Mitochondria.

Beatrisa Rimskaya, Ekaterina Kropocheva, Iaroslava Ponomareva, Lada Karchemkina, Lidiya Lisitskaya, Daria Gelfenbein, Egor Ulashchik, Vadim Shmanai, Andrey Kulbachinskiy, Ilya Mazunin.

Precise manipulation of mitochondrial DNA (mtDNA) by CRISPR-Cas systems remains challenging, largely due to inefficient import of guide RNAs, motivating the exploration of alternative programmable nucleases. Here, we show that prokaryotic Argonaute nucleases (pAgos) of various classes can be efficiently targeted to human mitochondria. Using the Su9 mitochondrial targeting sequence from Neurospora crassa, we achieved robust mitochondrial import of four pAgos-DecAgo, CbuAgo, KmaAgo and RslAgo. As a functional readout of their activity in cells, we targeted the single-stranded D-loop region, which plays a central role in mtDNA replication and maintenance, reasoning that cleavage at this site was expected to potentially result in a reduction in mtDNA copy number. Of the four enzymes, only RNA-guided DecAgo induced a pronounced reduction in mtDNA levels, decreasing copy number approximately fivefold within 48 h. Unexpectedly, this effect occurred independently of exogenous guides, suggesting that DecAgo may utilize endogenous mitochondrial guide RNAs. These findings identify DecAgo as an active nuclease in human mitochondria and reveal a previously unrecognized mode of targeting, highlighting the need to further investigate the underlying mechanism and the potential role of endogenous guide molecules, as well as improving targeting specificity.

Keywords: D-loop; mitochondria; mtDNA copy number; prokaryotic argonautes

DOI: https://doi.org/10.3390/cells15121129

Cell Rep. 2026 Jun 26. pii: S2211-1247(26)00685-6. [Epub ahead of print]45(7): 117607

Disrupted mitochondrial dynamics activate RNA-sensing innate immunity through mitochondrial RNA release.

Tatsuki Yasuda, Aoi Ichikawa, Kenta Onoue, Emi Ogasawara, Takaya Ishihara, Hidetaka Kosako, Naotada Ishihara.

Mitochondria are dynamic organelles that continuously remodel their morphology through fusion and fission in response to cellular cues. While this dynamic behavior is essential for diverse cellular functions, how mitochondrial dynamics influence innate immune responses remains incompletely understood. Here, we show that mitochondrial hyperfusion-induced by loss of the fission factor DRP1 or by cellular stress, including cycloheximide or doxorubicin treatment-is associated with activation of a RIG-I-MAVS-dependent innate immune response and BAX-dependent cytosolic release of mitochondrial RNA. Functionally, our data suggest that this pathway contributes to enhanced susceptibility to NK cell-mediated cytotoxicity in vitro and reduced tumor growth in a xenograft model. Collectively, our findings identify mitochondrial hyperfusion-induced mtRNA release as a mechanism that engages innate immune signaling downstream of impaired mitochondrial dynamics.

Keywords: CP: immunology; DRP1; RIG-I; innate immunity; mitochondrial RNA; mitochondrial dynamics; mitochondrial hyperfusion; molecular biology

DOI: https://doi.org/10.1016/j.celrep.2026.117607

Bioorg Chem. 2026 Jun 22. pii: S0045-2068(26)00687-5. [Epub ahead of print]180 110151

The landscape of mitochondrial transfer RNA post-transcriptional modifications reveals GTPBP3-responsive mo5U in acute ischemic stroke.

Jianfeng Sun, Caiyun Wang, Hengtao Fu, Zijun Shao, Chunyuan Chen, Liping Bai, Guoyuan Zhu, Zhihong Jiang, Wei Zhang.

BACKGROUND: Mitochondrial dysfunction is central to acute ischemic stroke (AIS), but the contribution of mitochondrial transfer RNA (mt-tRNA) post-transcriptional modification changes to ischemic stress remains insufficiently defined. Therefore, a mass-spectrometry-based workflow was utilized to generate an exploratory map of mt-tRNA post-transcriptional modifications in AIS models and to functionally evaluate a candidate GTPBP3/5-methoxyuridine (mo5U) axis in OGD/R-injured PC12 cells.
METHODS: Chemical labeling-assisted liquid chromatography-tandem mass spectrometry was applied to mt-tRNAs obtained both in vivo and vitro models of AIS. Candidate modification-associated nucleosides and RNase digestion fragments were profiled. To test the functional relevance of GTPBP3, PC12 cells were transfected with empty pcDNA vector or pcDNA-GTPBP3, followed by measurement of GTPBP3 abundance, mo5U signal, cell viability, ROS, mitochondrial membrane potential (MMP), and ATP production.
RESULTS: This method achieved over 60% sequence coverage and uncovered 38 distinct modification types spanning 237 nucleotide positions. Compared with prior studies (18 modifications at 137 sites), 20 previously unannotated modification types were identified, including novel sites within underexplored variable loop regions. Remarkably, 15.33% of all nucleotide positions were modified. Both the A[mo5U]AGp digestion fragment from the anticodon loop of mt-tRNAIle(GAU) and the mo5U modification level were significantly reduced both in vitro and in vivo AIS models, accompanied by decreased GTPBP3 abundance. Curcumin treatment in PC12 cells partially restored cell viability, lowered ROS, improved MMP, and was associated with recovery of GTPBP3 abundance and A[mo5U]AGp/mo5U-related signals. Importantly, pcDNA-GTPBP3 overexpression increased GTPBP3 abundance and mo5U levels, and significantly attenuated OGD/R-induced loss of cell viability, ATP depletion, ROS accumulation, and MMP dissipation.
CONCLUSIONS: These findings provide a landscape of mammalian mt-tRNA modifications and identify candidate epitranscriptomic changes associated with AIS. Specifically, we highlight a possible GTPBP3-dependent mo5U axis in ischemia-induced mitochondrial dysfunction, which represents a promising neuroprotective target warranting further functional validation.

Keywords: Acute ischemic stroke; Curcumin; GTPBP3; Mitochondrial transfer RNAs; Post-transcriptional modification

DOI: https://doi.org/10.1016/j.bioorg.2026.110151