bims-smemid 2025-03-16 papers

on Stress metabolism in mitochondrial dysfunction

Issue of 2025–03–16
seven papers selected by
Deepti Mudartha, The International Institute of Molecular Mechanisms and Machines

Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle.
Succinate dehydrogenase activity supports de novo purine synthesis.
Engineering mtDNA deletions by reconstituting end joining in human mitochondria.
MIA40 suppresses cell death induced by apoptosis-inducing factor 1.
L- and D-Lactate: unveiling their hidden functions in disease and health.
Labeling of mitochondria for detection of intercellular mitochondrial transfer.
Mitochondrial genetics, signalling and stress responses.

Nat Commun. 2025 Mar 08. 16(1): 2338

Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle.

Simon T Bond, Emily J King, Shannen M Walker, Christine Yang, Yingying Liu, Kevin H Liu, Aowen Zhuang, Aaron W Jurrjens, Haoyun A Fang, Luke E Formosa, Artika P Nath, Sergio Ruiz Carmona, Michael Inouye, Thy Duong, Kevin Huynh, Peter J Meikle, Simon Crawford, Georg Ramm, Sheik Nadeem Elahee Doomun, David P de Souza, Danielle L Rudler, Anna C Calkin, Aleksandra Filipovska, David W Greening, Darren C Henstridge, Brian G Drew.

During mitochondrial damage, information is relayed between the mitochondria and nucleus to coordinate precise responses to preserve cellular health. One such pathway is the mitochondrial integrated stress response (mtISR), which is known to be activated by mitochondrial DNA (mtDNA) damage. However, the causal molecular signals responsible for activation of the mtISR remain mostly unknown. A gene often associated with mtDNA mutations/deletions is Polg1, which encodes the mitochondrial DNA Polymerase γ (PolG). Here, we describe an inducible, tissue specific model of PolG mutation, which in muscle specific animals leads to rapid development of mitochondrial dysfunction and muscular degeneration in male animals from ~5 months of age. Detailed molecular profiling demonstrated robust activation of the mtISR in muscles from these animals. This was accompanied by striking alterations to enzymes in the mitochondrial folate cycle that was likely driven by a specific depletion in the folate cycle metabolite 5,10 methenyl-THF, strongly implying imbalanced folate intermediates as a previously unrecognised pathology linking the mtISR and mitochondrial disease.

DOI: https://doi.org/10.1038/s41467-025-57299-3
bioRxiv. 2025 Mar 01. pii: 2025.02.26.640389. [Epub ahead of print]

Succinate dehydrogenase activity supports de novo purine synthesis.

Mushtaq A Nengroo, Austin T Klein, Heather S Carr, Olivia Vidal-Cruchez, Umakant Sahu, Daniel J McGrail, Nidhi Sahni, Peng Gao, John M Asara, Hardik Shah, Marc L Mendillo, Issam Ben-Sahra.

The de novo purine synthesis pathway is fundamental for nucleic acid production and cellular energetics, yet the role of mitochondrial metabolism in modulating this process remains underexplored. In many cancers, metabolic reprogramming supports rapid proliferation and survival, but the specific contributions of the tricarboxylic acid (TCA) cycle enzymes to nucleotide biosynthesis are not fully understood. Here, we demonstrate that the TCA cycle enzyme succinate dehydrogenase (SDH) is essential for maintaining optimal de novo purine synthesis in normal and cancer cells. Genetic or pharmacological inhibition of SDH markedly attenuates purine synthesis, leading to a significant reduction in cell proliferation. Mechanistically, SDH inhibition causes an accumulation of succinate, which directly impairs the purine biosynthetic pathway. In response, cancer cells compensate by upregulating the purine salvage pathway, a metabolic adaptation that represents a potential therapeutic vulnerability. Notably, co-inhibition of SDH and the purine salvage pathway induces pronounced antiproliferative and antitumoral effects in preclinical models. These findings not only reveal a signaling role for mitochondrial succinate in regulating nucleotide metabolism but also provide a promising therapeutic strategy for targeting metabolic dependencies in cancer.

DOI: https://doi.org/10.1101/2025.02.26.640389
Cell. 2025 Mar 05. pii: S0092-8674(25)00194-1. [Epub ahead of print]

Engineering mtDNA deletions by reconstituting end joining in human mitochondria.

Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B Thompson, Dana Pe'er, Agnel Sfeir.

  Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.

Keywords:  DOGMA-seq; end joining; mitochondrial pathologies; mtDNA; mtDNA deletion

DOI:  https://doi.org/10.1016/j.cell.2025.02.009
EMBO Rep. 2025 Mar 07.

MIA40 suppresses cell death induced by apoptosis-inducing factor 1.

Ben Hur Marins Mussulini, Klaudia K Maruszczak, Piotr Draczkowski, Mayra A Borrero-Landazabal, Selvaraj Ayyamperumal, Artur Wnorowski, Michal Wasilewski, Agnieszka Chacinska.

  Mitochondria harbor respiratory complexes that perform oxidative phosphorylation. Complex I is the first enzyme of the respiratory chain that oxidizes NADH. A dysfunction in complex I can result in higher cellular levels of NADH, which in turn strengthens the interaction between apoptosis-inducing factor 1 (AIFM1) and Mitochondrial intermembrane space import and assembly protein 40 (MIA40) in the mitochondrial intermembrane space. We investigated whether MIA40 modulates the activity of AIFM1 upon increased NADH/NAD+ balance. We found that in model cells characterized by an increase in NADH the AIFM1-MIA40 interaction is strengthened and these cells demonstrate resistance to AIFM1-induced cell death. Either silencing of MIA40, rescue of complex I, or depletion of NADH through the expression of yeast NADH-ubiquinone oxidoreductase-2 sensitized NDUFA13-KO cells to AIFM1-induced cell death. These findings indicate that the complex of MIA40 and AIFM1 suppresses AIFM1-induced cell death in a NADH-dependent manner. This study identifies an effector complex involved in regulating the programmed cell death that accommodates the metabolic changes in the cell and provides a molecular explanation for AIFM1-mediated chemoresistance of cancer cells.

Keywords:  Cancer; Metabolism; Mitochondria; Programmed Cell Death; Protein Import

DOI:  https://doi.org/10.1038/s44319-025-00406-8
Cell Commun Signal. 2025 Mar 12. 23(1): 134

L- and D-Lactate: unveiling their hidden functions in disease and health.

Jianting Li, Peng Ma, Zhizhen Liu, Jun Xie.

  Lactate, once considered a mere byproduct of anaerobic metabolism, is now recognized as a critical signaling molecule with diverse roles in physiology and pathology. There are two stereoisomers of lactate: L- and D-lactate. Recent studies have shown that disruptions in these two lactate stereoisomers have distinct effects on health and disease. L-lactate is central to glycolysis and energy transfer through the Cori cycle but also acts as the dominant lactylation isomer induced by glycolysis, influencing metabolism and cell survival. Although less studied, D-lactate is linked to metabolic disorders and plays a role in mitochondrial dysfunction and oxidative stress. This review focuses on both L- and D-lactate and examines their biosynthesis, transport, and expanding roles in physiological and pathological processes, particularly their functions in cancer, immune regulation, inflammation, neurodegeneration and other diseases. Finally, we assess the therapeutic prospects of targeting lactate metabolism, highlighting emerging strategies for intervention in clinical settings. Our review synthesizes the current understanding of L- and D-lactate, offering insights into their potential as targets for therapeutic innovation.

Keywords:  D-lactate; Epigenetic; L-lactate; Lactylation; Metabolism

DOI:  https://doi.org/10.1186/s12964-025-02132-z
Methods Cell Biol. 2025 ;pii: S0091-679X(24)00143-2. [Epub ahead of print]194 1-17

Labeling of mitochondria for detection of intercellular mitochondrial transfer.

Isamu Taiko, Chika Takano, Shingo Hayashida, Kazunori Kanemaru, Toshio Miki.

  The phenomenon of intercellular transfer of mitochondria has been reported and has attracted significant interest in recent years. The phenomena involve a range of physiological and pathological conditions, such as tumor growth, immunoregulation, and tissue regeneration. There is speculation on the potential restoration of cellular energy status through the transfer of healthy mitochondria from donor cells to cells with impaired mitochondria. Multiple mechanisms and routes of mitochondria transfer have been suggested, including direct cell-to-cell connections, extracellular vesicles, and cell fusion. However, there is limited understanding regarding the precise mechanisms behind mitochondrial transfer, particularly the initiation signals and the associated processes. In order to explore these fundamental mechanisms of mitochondrial transfer, it is imperative to employ techniques that enable direct labeling of mitochondria. Here, we present a detailed methodology utilizing fluorescent protein tagging to visualize mitochondria. The molecular biological techniques applied in this study entail the precise localization of mitochondria with reduced cytotoxicity. This approach facilitates the direct observation of transferred mitochondria through fluorescent and confocal microscopy. The described method can be readily implemented in other mammalian cell types with few modifications, enabling the continuous monitoring of mitochondrial trafficking processes over an extended period.

Keywords:  Amniotic epithelial cells; Mitochondria; Mitochondrial transfer

DOI:  https://doi.org/10.1016/bs.mcb.2024.05.001
Nat Cell Biol. 2025 Mar;27(3): 393-407

Mitochondrial genetics, signalling and stress responses.

Yasmine J Liu, Jonathan Sulc, Johan Auwerx.

Mitochondria are multifaceted organelles with crucial roles in energy generation, cellular signalling and a range of synthesis pathways. The study of mitochondrial biology is complicated by its own small genome, which is matrilineally inherited and not subject to recombination, and present in multiple, possibly different, copies. Recent methodological developments have enabled the analysis of mitochondrial DNA (mtDNA) in large-scale cohorts and highlight the far-reaching impact of mitochondrial genetic variation. Genome-editing techniques have been adapted to target mtDNA, further propelling the functional analysis of mitochondrial genes. Mitochondria are finely tuned signalling hubs, a concept that has been expanded by advances in methodologies for studying the function of mitochondrial proteins and protein complexes. Mitochondrial respiratory complexes are of dual genetic origin, requiring close coordination between mitochondrial and nuclear gene-expression systems (transcription and translation) for proper assembly and function, and recent findings highlight the importance of the mitochondria in this bidirectional signalling.

DOI: https://doi.org/10.1038/s41556-025-01625-w