bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2024–09–22
twelve papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. TBK1 adaptor AZI2/NAP1 regulates NDP52-driven mitochondrial autophagy.
  2. Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation.
  3. Activation of parkin by a molecular glue.
  4. Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans.
  5. Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion.
  6. Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.
  7. Intercellular nanotube-mediated mitochondrial transfer enhances T cell metabolic fitness and antitumor efficacy.
  8. Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis.
  9. Serine ubiquitination of SQSTM1 regulates NFE2L2-dependent redox homeostasis.
  10. Lysosome-related organelle integrity suppresses TIR-1 aggregation to restrain toxic propagation of p38 innate immunity.
  11. ER-plasma membrane contact sites deliver ER lipids and proteins for rapid cell surface expansion.
  12. The p53 target DRAM1 modulates calcium homeostasis and ER stress by promoting contact between lysosomes and the ER through STIM1.
  1. J Biol Chem. 2024 Sep 12. pii: S0021-9258(24)02276-2. [Epub ahead of print] 107775
    TBK1 adaptor AZI2/NAP1 regulates NDP52-driven mitochondrial autophagy.
    Ryu Endo, Hiroki Kinefuchi, Momoha Sawada, Reika Kikuchi, Waka Kojima, Noriyuki Matsuda, Koji Yamano.
      Damaged mitochondria are selectively eliminated in a process called mitophagy. PINK1 and Parkin amplify ubiquitin signals on damaged mitochondria, which are then recognized by autophagy adaptors to induce local autophagosome formation. NDP52 and OPTN, two essential mitophagy adaptors, facilitate de novo synthesis of pre-autophagosomal membranes near damaged mitochondria by linking ubiquitinated mitochondria and ATG8 family proteins and by recruiting core autophagy initiation components. The multifunctional serine/threonine kinase TBK1 also plays important roles in mitophagy. OPTN directly binds TBK1 to form a positive feedback loop for isolation membrane expansion. TBK1 is also thought to indirectly interact with NDP52; however, its role in NDP52-driven mitophagy remains largely unknown. Here, we focused on two TBK1 adaptors, AZI2/NAP1 and TBKBP1/SINTBAD, that are thought to mediate the TBK1-NDP52 interaction. We found that both AZI2 and TBKBP1 are recruited to damaged mitochondria during Parkin-mediated mitophagy. Further, a series of AZI2 and TBKBP1 knockout constructs combined with an OPTN knockout showed that AZI2, but not TBKBP1, impacts NDP52-driven mitophagy. In addition, we found that AZI2 at S318 is phosphorylated during mitophagy, the impairment of which slightly inhibits mitochondrial degradation. These results suggest that AZI2, in concert with TBK1, plays an important role in NDP52-driven mitophagy.
    Keywords:  autophagy; mitochondria; mitophagy; polyubiquitin chain; serine/threonine protein kinase
    DOI:  https://doi.org/10.1016/j.jbc.2024.107775
  2. Nat Commun. 2024 Sep 14. 15(1): 8066
    Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation.
    Juan C Landoni, Semin Erkul, Tuomas Laalo, Steffi Goffart, Riikka Kivelä, Karlo Skube, Anni I Nieminen, Sara A Wickström, James Stewart, Anu Suomalainen.
      High mitochondrial DNA (mtDNA) amount has been reported to be beneficial for resistance and recovery of metabolic stress, while increased mtDNA synthesis activity can drive aging signs. The intriguing contrast of these two mtDNA boosting outcomes prompted us to jointly elevate mtDNA amount and frequency of replication in mice. We report that high activity of mtDNA synthesis inhibits perinatal metabolic maturation of the heart. The offspring of the asymptomatic parental lines are born healthy but manifest dilated cardiomyopathy and cardiac collapse during the first days of life. The pathogenesis, further enhanced by mtDNA mutagenesis, involves prenatal upregulation of mitochondrial integrated stress response and the ferroptosis-inducer MESH1, leading to cardiac fibrosis and cardiomyocyte death after birth. Our evidence indicates that the tight control of mtDNA replication is critical for early cardiac homeostasis. Importantly, ferroptosis sensitivity is a potential targetable mechanism for infantile-onset cardiomyopathy, a common manifestation of mitochondrial diseases.
    DOI:  https://doi.org/10.1038/s41467-024-52164-1
  3. Nat Commun. 2024 Sep 19. 15(1): 7707
    Activation of parkin by a molecular glue.
    Véronique Sauvé, Eric Stefan, Nathalie Croteau, Thomas Goiran, Rayan Fakih, Nupur Bansal, Adelajda Hadzipasic, Jing Fang, Paramasivam Murugan, Shimin Chen, Edward A Fon, Warren D Hirst, Laura F Silvian, Jean-François Trempe, Kalle Gehring.
      Mutations in parkin and PINK1 cause early-onset Parkinson's disease (EOPD). The ubiquitin ligase parkin is recruited to damaged mitochondria and activated by PINK1, a kinase that phosphorylates ubiquitin and the ubiquitin-like domain of parkin. Activated phospho-parkin then ubiquitinates mitochondrial proteins to target the damaged organelle for degradation. Here, we present the mechanism of activation of a new class of small molecule allosteric modulators that enhance parkin activity. The compounds act as molecular glues to enhance the ability of phospho-ubiquitin (pUb) to activate parkin. Ubiquitination assays and isothermal titration calorimetry with the most active compound (BIO-2007817) identify the mechanism of action. We present the crystal structure of a closely related compound (BIO-1975900) bound to a complex of parkin and two pUb molecules. The compound binds next to pUb on RING0 and contacts both proteins. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments confirm that activation occurs through release of the catalytic Rcat domain. In organello and mitophagy assays demonstrate that BIO-2007817 partially rescues the activity of parkin EOPD mutants, R42P and V56E, offering a basis for the design of activators as therapeutics for Parkinson's disease.
    DOI:  https://doi.org/10.1038/s41467-024-51889-3
  4. Nat Commun. 2024 Sep 19. 15(1): 8237
    Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans.
    Bryan L Gitschlag, Claudia V Pereira, James P Held, David M McCandlish, Maulik R Patel.
      Cells possess multiple mitochondrial DNA (mtDNA) copies, which undergo semi-autonomous replication and stochastic inheritance. This enables mutant mtDNA variants to arise and selfishly compete with cooperative (wildtype) mtDNA. Selfish mitochondrial genomes are subject to selection at different levels: they compete against wildtype mtDNA directly within hosts and indirectly through organism-level selection. However, determining the relative contributions of selection at different levels has proven challenging. We overcome this challenge by combining mathematical modeling with experiments designed to isolate the levels of selection. Applying this approach to many selfish mitochondrial genotypes in Caenorhabditis elegans reveals an unexpected diversity of evolutionary mechanisms. Some mutant genomes persist at high frequency for many generations, despite a host fitness cost, by aggressively outcompeting cooperative genomes within hosts. Conversely, some mutant genomes persist by evading inter-organismal selection. Strikingly, the mutant genomes vary dramatically in their susceptibility to genetic drift. Although different mechanisms can cause high frequency of selfish mtDNA, we show how they give rise to characteristically different distributions of mutant frequency among individuals. Given that heteroplasmic frequency represents a key determinant of phenotypic severity, this work outlines an evolutionary theoretic framework for predicting the distribution of phenotypic consequences among individuals carrying a selfish mitochondrial genome.
    DOI:  https://doi.org/10.1038/s41467-024-52596-9
  5. Structure. 2024 Sep 12. pii: S0969-2126(24)00334-4. [Epub ahead of print]
    Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion.
    Raphaëlle Versini, Marc Baaden, Laetitia Cavellini, Mickaël M Cohen, Antoine Taly, Patrick F J Fuchs.
      Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.
    Keywords:  Fzo1; Lys716; mitofusin; molecular modeling; outer mitochondrial membrane fusion; transmembrane domain
    DOI:  https://doi.org/10.1016/j.str.2024.08.017
  6. JCI Insight. 2024 Sep 17. pii: e178645. [Epub ahead of print]
    Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.
    Sandrina P Correia, Marco F Moedas, Lucie S Taylor, Karin Naess, Albert Z Lim, Robert McFarland, Zuzanna Kazior, Anastasia Rumyantseva, Rolf Wibom, Martin Engvall, Helene Bruhn, Nicole Lesko, Ákos Végvári, Lukas Käll, Matthias Trost, Charlotte L Alston, Christoph Freyer, Robert W Taylor, Anna Wedell, Anna Wredenberg.
       BACKGROUND: Mitochondrial diseases belong to the group of inborn errors of metabolism (IEM), with a prevalence of 1:2,000-1:5,000. They are the most common form of IEM, but despite advances in next-generation sequencing technologies, almost half of the patients are left genetically undiagnosed.
    METHODS: We investigated a cohort of 61 patients with defined mitochondrial disease to improve diagnostics, identify biomarkers, and correlate metabolic pathways to specific disease groups. Clinical presentations were structured using human phenotype ontology terms, and mass spectrometry-based proteomics was performed on primary fibroblasts. Additionally, we integrated six patients carrying variants of uncertain significance (VUS) to test proteomics as a diagnostic expansion.
    RESULTS: Proteomic profiles from patient samples could be classified according to their biochemical and genetic characteristics, with the expression of five proteins (GPX4, MORF4L1, MOXD1, MSRA and TMED9) correlating with the disease cohort, and thus, acting as putative biomarkers. Pathway analysis showed a deregulation of inflammatory and mitochondrial stress responses. This included the upregulation of glycosphingolipid metabolism and mitochondrial protein import, as well as the downregulation of arachidonic acid metabolism. Furthermore, we could assign pathogenicity to a VUS in MRPS23 by demonstrating the loss of associated mitochondrial ribosome subunits.
    CONCLUSION: We established mass spectrometry-based proteomics on patient fibroblasts as a viable and versatile tool for diagnosing patients with mitochondrial disease.
    FUNDING: The NovoNordisk Foundation, Knut and Alice Wallenberg Foundation, Wellcome Centre for Mitochondrial Research, UK Medical Research Council, and the UK NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and Children.
    Keywords:  Metabolism; Mitochondria; Molecular diagnosis; Proteomics
    DOI:  https://doi.org/10.1172/jci.insight.178645
  7. Cell. 2024 Sep 12. pii: S0092-8674(24)00956-5. [Epub ahead of print]
    Intercellular nanotube-mediated mitochondrial transfer enhances T cell metabolic fitness and antitumor efficacy.
    Jeremy G Baldwin, Christoph Heuser-Loy, Tanmoy Saha, Roland C Schelker, Dragana Slavkovic-Lukic, Nicholas Strieder, Inmaculada Hernandez-Lopez, Nisha Rana, Markus Barden, Fabio Mastrogiovanni, Azucena Martín-Santos, Andrea Raimondi, Philip Brohawn, Brandon W Higgs, Claudia Gebhard, Veena Kapoor, William G Telford, Sanjivan Gautam, Maria Xydia, Philipp Beckhove, Sina Frischholz, Kilian Schober, Zacharias Kontarakis, Jacob E Corn, Matteo Iannacone, Donato Inverso, Michael Rehli, Jessica Fioravanti, Shiladitya Sengupta, Luca Gattinoni.
      Mitochondrial loss and dysfunction drive T cell exhaustion, representing major barriers to successful T cell-based immunotherapies. Here, we describe an innovative platform to supply exogenous mitochondria to T cells, overcoming these limitations. We found that bone marrow stromal cells establish nanotubular connections with T cells and leverage these intercellular highways to transplant stromal cell mitochondria into CD8+ T cells. Optimal mitochondrial transfer required Talin 2 on both donor and recipient cells. CD8+ T cells with donated mitochondria displayed enhanced mitochondrial respiration and spare respiratory capacity. When transferred into tumor-bearing hosts, these supercharged T cells expanded more robustly, infiltrated the tumor more efficiently, and exhibited fewer signs of exhaustion compared with T cells that did not take up mitochondria. As a result, mitochondria-boosted CD8+ T cells mediated superior antitumor responses, prolonging animal survival. These findings establish intercellular mitochondrial transfer as a prototype of organelle medicine, opening avenues to next-generation cell therapies.
    Keywords:  CAR T therapy; CD8(+) T cells; TCR-T therapy; TIL therapy; Talin 2; bone marrow stromal cells; cancer immunotherapy; immune metabolism; mitochondrial transfer; nanotubes
    DOI:  https://doi.org/10.1016/j.cell.2024.08.029
  8. Proc Natl Acad Sci U S A. 2024 Sep 24. 121(39): e2320611121
    Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis.
    Peter Rodriguez, Vrinda Kalia, Cristina Fenollar-Ferrer, Chelsea L Gibson, Zayna Gichi, Andre Rajoo, Carson D Matier, Aidan T Pezacki, Tong Xiao, Lucia Carvelli, Christopher J Chang, Gary W Miller, Andy V Khamoui, Jana Boerner, Randy D Blakely.
      Cuprous copper [Cu(I)] is an essential cofactor for enzymes that support many fundamental cellular functions including mitochondrial respiration and suppression of oxidative stress. Neurons are particularly reliant on mitochondrial production of ATP, with many neurodegenerative diseases, including Parkinson's disease, associated with diminished mitochondrial function. The gene MBLAC1 encodes a ribonuclease that targets pre-mRNA of replication-dependent histones, proteins recently found in yeast to reduce Cu(II) to Cu(I), and when mutated disrupt ATP production, elevates oxidative stress, and severely impacts cell growth. Whether this process supports neuronal and/or systemic physiology in higher eukaryotes is unknown. Previously, we identified swip-10, the putative Caenorhabditis elegans ortholog of MBLAC1, establishing a role for glial swip-10 in limiting dopamine (DA) neuron excitability and sustaining DA neuron viability. Here, we provide evidence from computational modeling that SWIP-10 protein structure mirrors that of MBLAC1 and locates a loss of function coding mutation at a site expected to disrupt histone RNA hydrolysis. Moreover, we find through genetic, biochemical, and pharmacological studies that deletion of swip-10 in worms negatively impacts systemic Cu(I) levels, leading to deficits in mitochondrial respiration and ATP production, increased oxidative stress, and neurodegeneration. These phenotypes can be offset in swip-10 mutants by the Cu(I) enhancing molecule elesclomol and through glial expression of wildtype swip-10. Together, these studies reveal a glial-expressed pathway that supports systemic mitochondrial function and neuronal health via regulation of Cu(I) homeostasis, a mechanism that may lend itself to therapeutic strategies to treat devastating neurodegenerative diseases.
    Keywords:  C. elegans; copper; glia; neurodegeneration; swip-10
    DOI:  https://doi.org/10.1073/pnas.2320611121
  9. Autophagy. 2024 Sep 18.
    Serine ubiquitination of SQSTM1 regulates NFE2L2-dependent redox homeostasis.
    Rukmini Mukherjee, Anshu Bhattacharya, João Mello-Vieira, Santosh Kumar Kuncha, Marina Hoffmann, Alexis Gonzalez, Rajeshwari Rathore, Attinder Chadha, Donghyuk Shin, Thomas Colby, Ivan Matic, Shaeri Mukherjee, Mohit Misra, Ivan Dikic.
      The KEAP1-NFE2L2 axis is essential for the cellular response against metabolic and oxidative stress. KEAP1 is an adaptor protein of CUL3 (cullin 3) ubiquitin ligase that controls the cellular levels of NFE2L2, a critical transcription factor of several cytoprotective genes. Oxidative stress, defective autophagy and pathogenic infections activate NFE2L2 signaling through phosphorylation of the autophagy receptor protein SQSTM1, which competes with NFE2L2 for binding to KEAP1. Here we show that phosphoribosyl-linked serine ubiquitination of SQSTM1 catalyzed by SidE effectors of Legionella pneumophila controls NFE2L2 signaling and cell metabolism upon Legionella infection. Serine ubiquitination of SQSTM1 sterically blocks its binding to KEAP1, resulting in NFE2L2 ubiquitination and degradation. This reduces NFE2L2-dependent antioxidant synthesis in the early phase of infection. Levels of serine ubiquitinated SQSTM1 diminish in the later stage of infection allowing the expression of NFE2L2-target genes; causing a differential regulation of the host metabolome and proteome in a NFE2L2-dependent manner.
    Keywords:  Antioxidants; KEAP1; bacterial infection; legionella pneumophila; oxidative stress; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2024.2404375
  10. Cell Rep. 2024 Sep 13. pii: S2211-1247(24)01025-8. [Epub ahead of print] 114674
    Lysosome-related organelle integrity suppresses TIR-1 aggregation to restrain toxic propagation of p38 innate immunity.
    Samantha Y Tse-Kang, Read Pukkila-Worley.
      Innate immunity in bacteria, plants, and animals requires the specialized subset of Toll/interleukin-1/resistance gene (TIR) domain proteins that are nicotinamide adenine dinucleotide (NAD+) hydrolases. Aggregation of these TIR proteins engages their enzymatic activity, but it is unknown how this protein multimerization is regulated. Here, we discover that TIR oligomerization is controlled to prevent immune toxicity. We find that p38 propagates its own activation in a positive feedback loop, which promotes the aggregation of the lone enzymatic TIR protein in the nematode C. elegans (TIR-1, homologous to human sterile alpha and TIR motif-containing 1 [SARM1]). We perform a forward genetic screen to determine how the p38 positive feedback loop is regulated. We discover that the integrity of the specific lysosomal subcompartment that expresses TIR-1 is actively maintained to limit inappropriate TIR-1 aggregation on the membranes of these organelles, which restrains toxic propagation of p38 innate immunity. Thus, innate immunity in C. elegans intestinal epithelial cells is regulated by specific control of TIR-1 multimerization.
    Keywords:  CP: Immunology; Caenorhabditis elegans; Pseudomonas aeruginosa; SARM1; TIR-1; intestinal immunity; lysosome-related organelles; p38
    DOI:  https://doi.org/10.1016/j.celrep.2024.114674
  11. J Cell Biol. 2024 Dec 02. pii: e202308137. [Epub ahead of print]223(12):
    ER-plasma membrane contact sites deliver ER lipids and proteins for rapid cell surface expansion.
    Madison Smith, Lincoln Gay, Markus Babst.
      As a consequence of hypoosmotic shock, yeast cells swell rapidly and increase the surface area by ∼20% in 20 s. Approximately, 35% of this surface increase is mediated by the ER-plasma membrane contact sites, specifically the tricalbins, which are required for the delivery of both lipids and the GPI-anchored protein Crh2 from the cortical ER to the plasma membrane. Therefore, we propose a new function for the tricalbins: mediating the fusion of the ER to the plasma membrane at contact sites. This proposed fusion is triggered by calcium influx via the stretch-gated channel Cch1 and is supported by the anoctamin Ist2.
    DOI:  https://doi.org/10.1083/jcb.202308137
  12. Proc Natl Acad Sci U S A. 2024 Sep 24. 121(39): e2400531121
    The p53 target DRAM1 modulates calcium homeostasis and ER stress by promoting contact between lysosomes and the ER through STIM1.
    Xiying Wang, Ji Geng, Suman Rimal, Yuxiu Sui, Jie Pan, Zhenghong Qin, Bingwei Lu.
      It is well established that DNA Damage Regulated Autophagy Modulator 1 (DRAM1), a lysosomal protein and a target of p53, participates in autophagy. The cellular functions of DRAM1 beyond autophagy remain elusive. Here, we show p53-dependent upregulation of DRAM1 in mitochondrial damage-induced Parkinson's disease (PD) models and exacerbation of disease phenotypes by DRAM1. We find that the lysosomal location of DRAM1 relies on its intact structure including the cytosol-facing C-terminal domain. Excess DRAM1 disrupts endoplasmic reticulum (ER) structure, triggers ER stress, and induces protective ER-phagy. Mechanistically, DRAM1 interacts with stromal interacting molecule 1 (STIM1) to tether lysosomes to the ER and perturb STIM1 function in maintaining intracellular calcium homeostasis. STIM1 overexpression promotes cellular health by restoring calcium homeostasis, ER stress response, ER-phagy, and AMP-activated protein kinase (AMPK)-Unc-51 like autophagy activating kinase 1 (ULK1) signaling in cells with excess DRAM1. Thus, by promoting organelle contact between lysosomes and the ER, DRAM1 modulates ER structure and function and cell survival under stress. Our results suggest that DRAM1 as a lysosomal protein performs diverse roles in cellular homeostasis and stress response. These findings may have significant implications for our understanding of the role of the p53/DRAM1 axis in human diseases, from cancer to neurodegenerative diseases.
    Keywords:  DRAM1; ER; ER-phagy; calcium homeostasis; lysosome
    DOI:  https://doi.org/10.1073/pnas.2400531121
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