bims-mitran 2025-01-05 papers

Issue of 2025–01–05
three papers selected by
Andreas Kohler, Umeå University

Nat Struct Mol Biol. 2025 Jan 02.

Molecular basis of human nuclear and mitochondrial tRNA 3' processing.

Arjun Bhatta, Bernhard Kuhle, Ryan D Yu, Lucas Spanaus, Katja Ditter, Katherine E Bohnsack, Hauke S Hillen.

Eukaryotic transfer RNA (tRNA) precursors undergo sequential processing steps to become mature tRNAs. In humans, ELAC2 carries out 3' end processing of both nucleus-encoded (nu-tRNAs) and mitochondria-encoded (mt-tRNAs) tRNAs. ELAC2 is self-sufficient for processing of nu-tRNAs but requires TRMT10C and SDR5C1 to process most mt-tRNAs. Here we show that TRMT10C and SDR5C1 specifically facilitate processing of structurally degenerate mt-tRNAs lacking the canonical elbow. Structures of ELAC2 in complex with TRMT10C, SDR5C1 and two divergent mt-tRNA substrates reveal two distinct mechanisms of pre-tRNA recognition. While canonical nu-tRNAs and mt-tRNAs are recognized by direct ELAC2-RNA interactions, processing of noncanonical mt-tRNAs depends on protein-protein interactions between ELAC2 and TRMT10C. These results provide the molecular basis for tRNA 3' processing in both the nucleus and the mitochondria and explain the organelle-specific requirement for additional factors. Moreover, they suggest that TRMT10C-SDR5C1 evolved as a mitochondrial tRNA maturation platform to compensate for the structural erosion of mt-tRNAs in bilaterian animals.

DOI: https://doi.org/10.1038/s41594-024-01445-w

Front Cell Dev Biol. 2024 ;12 1497652

Flow-cytometry reveals mitochondrial DNA accumulation in Saccharomyces cerevisiae cells during cell cycle arrest.

Elena Yu Potapenko, Nataliia D Kashko, Dmitry A Knorre.

Mitochondria are semi-autonomous organelles containing their own DNA (mtDNA), which is replicated independently of nuclear DNA (nDNA). While cell cycle arrest halts nDNA replication, mtDNA replication continues. In Saccharomyces cerevisiae, flow cytometry enables semi-quantitative estimation of mtDNA levels by measuring the difference in signals between cells lacking mtDNA and those containing mtDNA. In this study, we used flow cytometry to investigate mtDNA accumulation in yeast cells under G1 and G2 phase cell cycle arrest conditions utilising thermosensitive mutants cdc4-3 and cdc15-2. In line with the previous studies, cell cycle arrest induced a several-fold accumulation of mtDNA in both mutants. The total DNA levels in arrested cells correlated with cell forward scattering, suggesting a relationship between individual cell mtDNA quantity and size. In cell cycle-arrested cells, we observed no correlation between cell size and intercellular mtDNA copy number variability. This implies that as cell size increases during arrest, the mtDNA content remains within a specific limited range for each size class. This observation suggests that mtDNA quantity control mechanisms can function in cell cycle-arrested cells.

Keywords: cell cycle arrest; cell cycle defect; mtDNA; mtDNA copy number; mtDNA copy number control; yeast

DOI: https://doi.org/10.3389/fcell.2024.1497652

Anal Chem. 2024 Dec 31.

Mitochondria-Nucleus Migration Probe for Ultrasensitive Monitoring of mtDNA Damage in Living Cells.

Zhen-Qing Yu, Wenjing Pan, Xiaofeng Yang, Minggang Tian, Jing Zhang, Hongwen Liu, Lei Yang, Xingjiang Liu, Mei Yan, Shuai Xu.

Mitochondrial DNA (mtDNA) damage is a prevalent phenomenon that has been proven to be implicated in a wide spectrum of diseases. However, the progressive attenuation of probe signals in response to mtDNA damage within living cells inherently limits the sensitivity and precision of current probes for detecting mtDNA damage. Herein, we employ an innovative organelle signal ratio imaging approach, utilizing the mitochondria-nucleus migration probe MCQ, to achieve unparalleled sensitivity in detecting mtDNA damage in living cells. MCQ exhibited an initial preferential binding to mtDNA, facilitated by its cationic quinolinium moiety, but migrated to the nucleus upon mtDNA damage. This unique migration behavior not only enhanced the spatial identifiability of mtDNA damage but also amplified detection sensitivity and precision significantly by harnessing the intensified nucleus signal against the attenuated mitochondrial signal. This innovative approach established a positive correlation between the signal and mtDNA damage, enabling the detection of even subtle mtDNA damage at the early stage of apoptosis with a remarkable 23-fold enhancement following just 5 min H2O2 induction in living cells, whereas conventional methods relying solely on the fading of mitochondrial signals proved insufficient. Furthermore, MCQ's ability to monitor the occurrence of mtDNA damage achieved the intricate differentiation between apoptosis and ferroptosis. By monitoring mtDNA damage, drug-induced apoptosis in cancer cells was further conducted using MCQ to evaluate the therapeutic efficacy of four anticancer drugs at very low concentrations. This innovative strategy not only paves the way for ultrasensitive detection of mtDNA damage but also holds immense promise for early monitoring of mtDNA damage-associated diseases.

DOI: https://doi.org/10.1021/acs.analchem.4c04862