bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–09–29
forty-five papers selected by
Catalina Vasilescu, Helmholz Munich
  1. CALHM2 is a mitochondrial protein import channel that regulates fatty acid metabolism.
  2. Emerging Multi-omic Approaches to the Molecular Diagnosis of Mitochondrial Disease and Available Strategies for Treatment and Prevention.
  3. Beyond MitoCarta-expanding the list of candidate proteins involved in mitochondrial functions using a biological network approach.
  4. Setting the curve: the biophysical properties of lipids in mitochondrial form and function.
  5. Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence.
  6. Primary mitochondrial diseases.
  7. A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria.
  8. The Australian Genomics Mitochondrial Flagship: A National Program Delivering Mitochondrial Diagnoses.
  9. PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis.
  10. Cytoplasmic ribosomes hitchhike on mitochondria to dendrites.
  11. Molecular Alterations in Core Subunits of Mitochondrial Complex I and Their Relation to Parkinson'S Disease.
  12. Macrophage NRF1 promotes mitochondrial protein turnover via the ubiquitin proteasome system to limit mitochondrial stress and inflammation.
  13. Retinal damage promotes mitochondrial transfer in the visual system of a mouse model of Leber hereditary optic neuropathy.
  14. Geranylgeranylated SCFFBXO10 regulates selective outer mitochondrial membrane proteostasis and function.
  15. Fast and quantitative mitophagy assessment by flow cytometry using the mito-QC reporter.
  16. Unraveling the nexus of age, epilepsy, and mitochondria: exploring the dynamics of cellular energy and excitability.
  17. Visualizing Mitochondrial Membrane Potential with FRET Probes: Integrating Fluorescence Intensity Ratio and Lifetime Imaging.
  18. Artificial targeting of the NEIL1 DNA glycosylase to the mitochondria.
  19. Saturation mutagenesis-reinforced functional assays for disease-related genes.
  20. Mitochondrial Labeling with Mulberrin-Cy3: A New Fluorescent Probe for Live Cell Visualization.
  21. Fetal and obstetrics manifestations of mitochondrial diseases.
  22. Protocol to monitor live-cell, real-time, mitochondrial respiration in mouse muscle cells using the Resipher platform.
  23. Age-induced changes in skeletal muscle mitochondrial DNA synthesis, quantity, and quality in genetically unique rats.
  24. Interferon Stimulated Gene Expression Is a Biomarker for Primary Mitochondrial Disease.
  25. Structural and Functional Characterization of the Most Frequent Pathogenic PRKN Substitution p.R275W.
  26. Mitochondrial membrane potential and oxidative stress interact to regulate Oma1-dependent processing of Opa1 and mitochondrial dynamics.
  27. Uncovering recessive alleles in rare Mendelian disorders by genome sequencing of 174 individuals with monoallelic pathogenic variants.
  28. Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I.
  29. Bi-Allelic Splicing Variant, c.153-2A > C in TOMM7 Is Associated With Leigh Syndrome.
  30. The Potential Role of Mitochondria in the Microbiota-Gut-Brain Axis: Implications for Brain Health.
  31. Investigating the prevalence of MFN2 mutations in amyotrophic lateral sclerosis: insights from an Italian cohort.
  32. Cochlear Implantation for Isoleucyl-tRNA Synthetase Mutation-Associated Mitochondrial Disease: A Case Report.
  33. Mitochondria facilitate neuronal differentiation by metabolising nuclear-encoded RNA.
  34. The mitochondrial dicarboxylate carrier mediates in vivo hepatic gluconeogenesis.
  35. MADD-like pattern of acylcarnitines associated with sertraline use.
  36. Evaluating the safety and efficiency of nanomaterials: A focus on mitochondrial health.
  37. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.
  38. The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting.
  39. An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium.
  40. Mutation in the mitochondrial chaperone TRAP1 leads to autism with more severe symptoms in males.
  41. Cytochrome c oxidase dependent respiration is essential for T cell activation, proliferation and memory formation.
  42. RAB32 mutation in Parkinson's disease.
  43. Neurological manifestations in adult patients with the m.3243A>G variant in mitochondrial DNA.
  44. Altered molecular and cellular mechanisms in KIF5A-associated neurodegenerative or neurodevelopmental disorders.
  45. Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis.
  1. Res Sq. 2024 Sep 13. pii: rs.3.rs-4985689. [Epub ahead of print]
    CALHM2 is a mitochondrial protein import channel that regulates fatty acid metabolism.
    Elizabeth Jonas, Nelli Mnatsakanyan, Felix Rivera-Molina, Andrew Robson, Alexandra MacColl Garfinkel, Amrendra Kumar, Stephen Batter, Valeria Padovano, Kaitlin Webster, Rebecca Cardone, Justin Berg, Derek Toomre, Richard Kibbey Iv, Michael Caplan, Mustafa Khokha.
      For mitochondrial metabolism to occur in the matrix, multiple proteins must be imported across the two (inner and outer) mitochondrial membranes. Classically, two protein import channels, TIM/TOM, are known to perform this function, but whether other protein import channels exist is not known. Here, using super-resolution microscopy, proteomics, and electrophysiological techniques, we identify CALHM2 as the import channel for the ECHA subunit of the mitochondrial trifunctional protein (mTFP), which catalyzes β-oxidation of fatty acids in the mitochondrial matrix. We find that CALHM2 sits specifically at the inner mitochondrial and cristae membranes and is critical for membrane morphology. Depletion of CALHM2 leads to a mislocalization of ECHA outside of the mitochondria leading to severe cellular metabolic defects. These defects include cytosolic accumulation of fatty acids, depletion of tricarboxylic acid cycle enzymes and intermediates, and reduced cellular respiration. Our data identify CALHM2 as an essential protein import channel that is critical for fatty acid- and glucose-dependent aerobic metabolism. .
    DOI:  https://doi.org/10.21203/rs.3.rs-4985689/v1
  2. Curr Genomics. 2024 ;25(5): 358-379
    Emerging Multi-omic Approaches to the Molecular Diagnosis of Mitochondrial Disease and Available Strategies for Treatment and Prevention.
    Faeze Khaghani, Mahboobeh Hemmati, Masoumeh Ebrahimi, Arash Salmaninejad.
      Mitochondria are semi-autonomous organelles present in several copies within most cells in the human body that are controlled by the precise collaboration of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) encoding mitochondrial proteins. They play important roles in numerous metabolic pathways, such as the synthesis of adenosine triphosphate (ATP), the predominant energy substrate of the cell generated through oxidative phosphorylation (OXPHOS), intracellular calcium homeostasis, metabolite biosynthesis, aging, cell cycles, and so forth. Previous studies revealed that dysfunction of these multi-functional organelles, which may arise due to mutations in either the nuclear or mitochondrial genome, leads to a diverse group of clinically and genetically heterogeneous disorders. These diseases include neurodegenerative and metabolic disorders as well as cardiac and skeletal myopathies in both adults and newborns. The plethora of phenotypes and defects displayed leads to challenges in the diagnosis and treatment of mitochondrial diseases. In this regard, the related literature proposed several diagnostic options, such as high throughput mitochondrial genomics and omics technologies, as well as numerous therapeutic options, such as pharmacological approaches, manipulating the mitochondrial genome, increasing the mitochondria content of the affected cells, and recently mitochondrial diseases transmission prevention. Therefore, the present article attempted to review the latest advances and challenges in diagnostic and therapeutic options for mitochondrial diseases.
    Keywords:  Mitochondrial disease; genomic; metabolomics; omics; proteomics; transcriptomics
    DOI:  https://doi.org/10.2174/0113892029308327240612110334
  3. NAR Genom Bioinform. 2023 Dec;5(4): lqad107
    Beyond MitoCarta-expanding the list of candidate proteins involved in mitochondrial functions using a biological network approach.
    Dmitriy Leyfer, Jessica L Fetterman.
      Mitochondrial diseases are the result of pathogenic variants in genes involved in the diverse functions of the mitochondrion. A comprehensive list of mitochondrial genes is needed to improve gene prioritization in the diagnosis of mitochondrial diseases and development of therapeutics that modulate mitochondrial function. MitoCarta is an experimentally derived catalog of proteins localized to mitochondria. We sought to expand this list of mitochondrial proteins to identify proteins that may not be localized to the mitochondria yet perform important mitochondrial functions. We used a computational approach to assign statistical significance to the overlap between STRING database gene network neighborhoods and MitoCarta proteins. Using a data-driven stringent significance threshold, 2059 proteins that were not located in MitoCarta were identified, which we termed mitochondrial proximal (MitoProximal) proteins. We identified all of the oxidative phosphorylation complex subunits and 90% of 149 genes that contain confirmed oxidative phosphorylation disease causal variants, lending validation to our methodology. Among the MitoProximal proteins, 134 are annotated to be localized to mitochondria but are not in the MitoCarta 3.0 database. We extend MitoCarta nearly 3-fold, generating a more comprehensive list of mitochondrial genes, a resource to facilitate the identification of pathogenic variants in mitochondrial and metabolic diseases.
    DOI:  https://doi.org/10.1093/nargab/lqad107
  4. J Lipid Res. 2024 Sep 18. pii: S0022-2275(24)00148-2. [Epub ahead of print] 100643
    Setting the curve: the biophysical properties of lipids in mitochondrial form and function.
    Kailash Venkatraman, Christopher T Lee, Itay Budin.
      Mitochondrial membranes are defined by their diverse functions, complex geometries, and unique lipidomes. In the inner mitochondrial membrane (IMM), highly-curved membrane folds known as cristae house the electron transport chain and are the primary sites of cellular energy production. The outer mitochondrial membrane (OMM) is flat by contrast, but is critical for the initiation and mediation of processes key to mitochondrial physiology: mitophagy, inter-organelle contacts, fission and fusion dynamics and metabolite transport. While the lipid composition of both the IMM and OMM have been characterized across a variety of cell types, a mechanistic understanding for how individual lipid classes contribute to mitochondrial structure and function remains nebulous. In this review, we address the biophysical properties of mitochondrial lipids and their related functional roles. We highlight the intrinsic curvature of the bulk mitochondrial phospholipid pool, with an emphasis on the nuances surrounding the mitochondrially-synthesized cardiolipin. We also outline emerging questions about other lipid classes, ether lipids and sterols, with potential roles in mitochondrial physiology. We propose that further investigation is warranted to elucidate the specific properties of these lipids and their influence on mitochondrial architecture and function.
    Keywords:  Cardiolipin; Curvature; Mitochondria; Phospholipids; Plasmalogens; Sterols
    DOI:  https://doi.org/10.1016/j.jlr.2024.100643
  5. Nat Commun. 2024 Sep 27. 15(1): 8274
    Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence.
    Abdul Haseeb Khan, Xuefang Gu, Rutvik J Patel, Prabha Chuphal, Matheus P Viana, Aidan I Brown, Brian M Zid, Tatsuhisa Tsuboi.
      A decline in mitochondrial function is a hallmark of aging and neurodegenerative diseases. It has been proposed that changes in mitochondrial morphology, including fragmentation of the tubular mitochondrial network, can lead to mitochondrial dysfunction, yet the mechanism of this loss of function is unclear. Most proteins contained within mitochondria are nuclear-encoded and must be properly targeted to the mitochondria. Here, we report that sustained mRNA localization and co-translational protein delivery leads to a heterogeneous protein distribution across fragmented mitochondria. We find that age-induced mitochondrial fragmentation drives a substantial increase in protein expression noise across fragments. Using a translational kinetic and molecular diffusion model, we find that protein expression noise is explained by the nature of stochastic compartmentalization and that co-translational protein delivery is the main contributor to increased heterogeneity. We observed that cells primarily reduce the variability in protein distribution by utilizing mitochondrial fission-fusion processes rather than relying on the mitophagy pathway. Furthermore, we are able to reduce the heterogeneity of the protein distribution by inhibiting co-translational protein targeting. This research lays the framework for a better understanding of the detrimental impact of mitochondrial fragmentation on the physiology of cells in aging and disease.
    DOI:  https://doi.org/10.1038/s41467-024-52183-y
  6. Handb Clin Neurol. 2024 ;pii: B978-0-323-99209-1.00004-1. [Epub ahead of print]204 53-76
    Primary mitochondrial diseases.
    Chiara Pizzamiglio, Michael G Hanna, Robert D S Pitceathly.
      Primary mitochondrial diseases (PMDs) are a heterogeneous group of hereditary disorders characterized by an impairment of the mitochondrial respiratory chain. They are the most common group of genetic metabolic disorders, with a prevalence of 1 in 4,300 people. The presence of leukoencephalopathy is recognized as an important feature in many PMDs and can be a manifestation of mutations in both mitochondrial DNA (classic syndromes such as mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes; myoclonic epilepsy with ragged-red fibers [RRFs]; Leigh syndrome; and Kearns-Sayre syndrome) and nuclear DNA (mutations in maintenance genes such as POLG, MPV17, and TYMP; Leigh syndrome; and mitochondrial aminoacyl-tRNA synthetase disorders). In this chapter, PMDs associated with white matter involvement are outlined, including details of clinical presentations, brain MRI features, and elements of differential diagnoses. The current approach to the diagnosis of PMDs and management strategies are also discussed. A PMD diagnosis in a subject with leukoencephalopathy should be considered in the presence of specific brain MRI features (for example, cyst-like lesions, bilateral basal ganglia lesions, and involvement of both cerebral hemispheres and cerebellum), in addition to a complex neurologic or multisystem disorder. Establishing a genetic diagnosis is crucial to ensure appropriate genetic counseling, multidisciplinary team input, and eligibility for clinical trials.
    Keywords:  Brain MRI; Kearns-Sayre syndrome; Leber hereditary optic neuropathy; Leigh disease; Leukoencephalopathy; Mitochondrial DNA maintenance disorders; Mitochondrial aminoacyl-tRNA synthetase disorders; Mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes; Mitochondrial neurogastrointestinal encephalomyopathy; Primary mitochondrial diseases
    DOI:  https://doi.org/10.1016/B978-0-323-99209-1.00004-1
  7. Cell. 2024 Sep 17. pii: S0092-8674(24)00974-7. [Epub ahead of print]
    A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria.
    Pablo Hernansanz-Agustín, Carmen Morales-Vidal, Enrique Calvo, Paolo Natale, Yolanda Martí-Mateos, Sara Natalia Jaroszewicz, José Luis Cabrera-Alarcón, Rebeca Acín-Pérez, Iván López-Montero, Jesús Vázquez, José Antonio Enríquez.
      Eukaryotic cell function and survival rely on the use of a mitochondrial H+ electrochemical gradient (Δp), which is composed of an inner mitochondrial membrane (IMM) potential (ΔΨmt) and a pH gradient (ΔpH). So far, ΔΨmt has been assumed to be composed exclusively of H+. Here, using a rainbow of mitochondrial and nuclear genetic models, we have discovered that a Na+ gradient equates with the H+ gradient and controls half of ΔΨmt in coupled-respiring mammalian mitochondria. This parallelism is controlled by the activity of the long-sought Na+-specific Na+/H+ exchanger (mNHE), which we have identified as the P-module of complex I (CI). Deregulation of this mNHE function, without affecting the canonical enzymatic activity or the assembly of CI, occurs in Leber's hereditary optic neuropathy (LHON), which has profound consequences in ΔΨmt and mitochondrial Ca2+ homeostasis and explains the previously unknown molecular pathogenesis of this neurodegenerative disease.
    Keywords:  LHON; Na(+) gradient; complex I; mitochondrial Na(+)/H(+) antiporter; ΔΨmt
    DOI:  https://doi.org/10.1016/j.cell.2024.08.045
  8. Genet Med. 2024 Sep 17. pii: S1098-3600(24)00205-3. [Epub ahead of print] 101271
    The Australian Genomics Mitochondrial Flagship: A National Program Delivering Mitochondrial Diagnoses.
    Rocio Rius, Alison G Compton, Naomi L Baker, Shanti Balasubramaniam, Stephanie Best, Kaustuv Bhattacharya, Kirsten Boggs, Tiffany Boughtwood, Jeffrey Braithwaite, Drago Bratkovic, Alessandra Bray, Marie-Jo Brion, Jo Burke, Sarah Casauria, Belinda Chong, David Coman, Shannon Cowie, Mark Cowley, Michelle G de Silva, Martin B Delatycki, Samantha Edwards, Carolyn Ellaway, Michael C Fahey, Keri Finlay, Janice Fletcher, Leah E Frajman, Ann E Frazier, Velimir Gayevskiy, Roula Ghaoui, Himanshu Goel, Ilias Goranitis, Matilda Haas, Daniella H Hock, Denise Howting, Matilda R Jackson, Maina P Kava, Madonna Kemp, Sarah King-Smith, Nicole J Lake, Phillipa J Lamont, Joy Lee, Janet C Long, Mandi MacShane, Evanthia O Madelli, Ellenore M Martin, Justine E Marum, Tessa Mattiske, Jim McGill, Alejandro Metke, Sean Murray, Julie Panetta, Liza K Phillips, Michael C J Quinn, Michael T Ryan, Sarah Schenscher, Cas Simons, Nicholas Smith, David A Stroud, Michel C Tchan, Melanie Tom, Mathew Wallis, Tyson L Ware, AnneMarie E Welch, Christine Wools, You Wu, John Christodoulou, David R Thorburn.
       PURPOSE: Families living with mitochondrial diseases (MD) often endure prolonged diagnostic journeys and invasive testing, yet many remain without a molecular diagnosis. The Australian Genomics Mitochondrial flagship, comprising clinicians, diagnostic, and research scientists, conducted a prospective national study to identify the diagnostic utility of singleton genomic sequencing using blood samples.
    METHODS: 140 children and adults living with suspected MD were recruited using modified Nijmegen criteria (MNC) and randomized to either exome + mtDNA sequencing (ES+mtDNAseq) or genome sequencing (GS).
    RESULTS: Diagnostic yield was 55% (n=77) with variants in nuclear (n=37) and mtDNA (n=18) MD genes, as well as phenocopy genes (n=22). A nuclear gene etiology was identified in 77% of diagnoses, irrespective of disease onset. Diagnostic rates were higher in pediatric-onset (71%) than adult-onset (31%) cases, and comparable in children with non-European (78%) versus European (67%) ancestry. For children, higher MNC scores correlated with increased diagnostic yield and fewer diagnoses in phenocopy genes. Additionally, three adult patients had a mtDNA deletion discovered in skeletal muscle that was not initially identified in blood.
    CONCLUSION: Genomic sequencing from blood can simplify the diagnostic pathway for individuals living with suspected MD, especially those with childhood onset diseases and high MNC scores.
    Keywords:  Genomics; Mitochondrial Disease; diagnosis; proteomics
    DOI:  https://doi.org/10.1016/j.gim.2024.101271
  9. Genet Epidemiol. 2024 Sep 24.
    PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis.
    Marie-Sophie C Ogloblinsky, Ozvan Bocher, Chaker Aloui, Anne-Louise Leutenegger, Ozan Ozisik, Anaïs Baudot, Elisabeth Tournier-Lasserve, Helen Castillo-Madeen, Daniel Lewinsohn, Donald F Conrad, Emmanuelle Génin, Gaëlle Marenne.
      The introduction of Next-Generation Sequencing technologies in the clinics has improved rare disease diagnosis. Nonetheless, for very heterogeneous or very rare diseases, more than half of cases still lack molecular diagnosis. Novel strategies are needed to prioritize variants within a single individual. The Population Sampling Probability (PSAP) method was developed to meet this aim but only for coding variants in exome data. Here, we propose an extension of the PSAP method to the non-coding genome called PSAP-genomic-regions. In this extension, instead of considering genes as testing units (PSAP-genes strategy), we use genomic regions defined over the whole genome that pinpoint potential functional constraints. We conceived an evaluation protocol for our method using artificially generated disease exomes and genomes, by inserting coding and non-coding pathogenic ClinVar variants in large data sets of exomes and genomes from the general population. PSAP-genomic-regions significantly improves the ranking of these variants compared to using a pathogenicity score alone. Using PSAP-genomic-regions, more than 50% of non-coding ClinVar variants were among the top 10 variants of the genome. On real sequencing data from six patients with Cerebral Small Vessel Disease and nine patients with male infertility, all causal variants were ranked in the top 100 variants with PSAP-genomic-regions. By revisiting the testing units used in the PSAP method to include non-coding variants, we have developed PSAP-genomic-regions, an efficient whole-genome prioritization tool which offers promising results for the diagnosis of unresolved rare diseases.
    Keywords:  non‐coding variants; rare diseases; variant prioritization; whole‐genome sequencing
    DOI:  https://doi.org/10.1002/gepi.22593
  10. bioRxiv. 2024 Sep 13. pii: 2024.09.13.612863. [Epub ahead of print]
    Cytoplasmic ribosomes hitchhike on mitochondria to dendrites.
    Corbin J Renken, Susie Kim, Youjun Wu, Marc Hammarlund, Shaul Yogev.
      Neurons rely on local protein synthesis to rapidly modify the proteome of neurites distant from the cell body. A prerequisite for local protein synthesis is the presence of ribosomes in the neurite, but the mechanisms of ribosome transport in neurons remain poorly defined. Here, we find that ribosomes hitchhike on mitochondria for their delivery to the dendrite of a sensory neuron in C. elegans. Ribosomes co-transport with dendritic mitochondria, and their association requires the atypical Rho GTPase MIRO-1. Disrupting mitochondrial transport prevents ribosomes from reaching the dendrite, whereas ectopic re-localization of mitochondria results in a concomitant re-localization of ribosomes, demonstrating that mitochondria are required and sufficient for instructing ribosome distribution in dendrites. Endolysosomal organelles that are involved in mRNA transport and translation can associate with mitochondria and ribosomes but do not play a significant role in ribosome transport. These results reveal a mechanism for dendritic ribosome delivery, which is a critical upstream requirement for local protein synthesis.
    DOI:  https://doi.org/10.1101/2024.09.13.612863
  11. Mol Neurobiol. 2024 Sep 27.
    Molecular Alterations in Core Subunits of Mitochondrial Complex I and Their Relation to Parkinson'S Disease.
    Matheus Caetano Epifane-de-Assunção, Ana Gabrielle Bispo, Ândrea Ribeiro-Dos-Santos, Giovanna C Cavalcante.
      Among the myriad of neurodegenerative diseases, mitochondrial dysfunction represents a nexus regarding their pathogenic processes, in which Parkinson's disease (PD) is notable for inherent vulnerability of the dopaminergic pathway to energy deficits and oxidative stress. Underlying this dysfunction, the occurrence of defects in complex I (CI) derived from molecular alterations in its subunits has been described in the literature. However, the mechanistic understanding of the processes mediating the occurrence of mitochondrial dysfunction mediated by CI deficiency in PD remains uncertain and subject to some inconsistencies. Therefore, this review analyzed existing evidence that may explain the relationship between molecular alterations in the core subunits of CI, recognized for their direct contribution to its enzymatic performance, and the pathogenesis of PD. As a result, we discussed 47 genetic variants in the 14 core subunits of CI, which, despite some discordant results, were predominantly associated with varying degrees of deficiency in complex enzymatic activity, as well as defects in supercomplex biogenesis and CI itself. Finally, we hypothesized about the relationship of the described alterations with the pathogenesis of PD and offered some suggestions that may aid in the design of future studies aimed at elucidating the relationship between such alterations and PD.
    Keywords:  Complex I; Mitochondria; NADH ubiquinone oxidoreductase; Oxidative phosphorylation; Parkinson’s disease
    DOI:  https://doi.org/10.1007/s12035-024-04526-5
  12. Cell Rep. 2024 Sep 25. pii: S2211-1247(24)01131-8. [Epub ahead of print]43(10): 114780
    Macrophage NRF1 promotes mitochondrial protein turnover via the ubiquitin proteasome system to limit mitochondrial stress and inflammation.
    Jiawei Yan, Xin Zhang, Huiying Wang, Xinglong Jia, Ruohong Wang, Shuangyang Wu, Zheng-Jiang Zhu, Minjia Tan, Tiffany Horng.
      Macrophage elaboration of inflammatory responses is dynamically regulated, shifting from acute induction to delayed suppression during the course of infection. Here, we show that such regulation of inflammation is modulated by dynamic shifts in metabolism. In macrophages exposed to the bacterial product lipopolysaccharide (LPS), an initial induction of protein biosynthesis is followed by compensatory induction of the transcription factor nuclear factor erythroid 2-like 1 (NRF1), leading to increased flux through the ubiquitin proteasome system (UPS). A major target of NRF1-mediated UPS flux is the mitochondrial proteome, and in the absence of NRF1, ubiquitinated mitochondrial proteins accumulate to trigger severe mitochondrial stress. Such mitochondrial stress engages the integrated stress response-ATF4 axis, which limits mitochondrial translation to attenuate mitochondrial stress but amplifies inflammatory responses to augment susceptibility to septic shock. Therefore, NRF1 mediates a dynamic regulation of mitochondrial proteostasis in inflammatory macrophages that contributes to curbing inflammatory responses.
    Keywords:  CP: Metabolism; CP: Molecular biology; NRF1; immunometabolism; inflammation; integrated stress response; macrophage; mitochondria; proteostasis
    DOI:  https://doi.org/10.1016/j.celrep.2024.114780
  13. Neurobiol Dis. 2024 Sep 25. pii: S0969-9961(24)00281-X. [Epub ahead of print] 106681
    Retinal damage promotes mitochondrial transfer in the visual system of a mouse model of Leber hereditary optic neuropathy.
    Pascal Ezan, Eléonore Hardy, Alexis Bemelmans, Magali Taiel, Elena Dossi, Nathalie Rouach.
      Lenadogene nolparvovec is a gene therapy which has been developed to treat Leber hereditary optic neuropathy (LHON) caused by a point mutation in the mitochondrial NADH dehydrogenase 4 (ND4) gene. Clinical trials have demonstrated a significant improvement of visual acuity up to 5 years after treatment by lenadogene nolparvovec but, surprisingly, unilateral treatment resulted in bilateral improvement of vision. This contralateral effect - similarly observed with other gene therapy products in development for MT-ND4-LHON - is supported by the migration of viral vector genomes and their transcripts to the contralateral eye, as reported in animals, and post-mortem samples from two patients. In this study, we used an AAV2 encoding fluorescent proteins targeting mitochondria to investigate whether these organelles themselves could transfer from the treated eye to the fellow one. We found that mitochondria travel along the visual system (optic chiasm and primary visual cortex) and reach the contralateral eye (optic nerve and retina) in physiological conditions. We also observed that, in a rotenone-induced model of retinal damage mimicking LHON, mitochondrial transfer from the healthy to the damaged eye was accelerated and enhanced. Our results thus provide a further explanation for the contralateral beneficial effect observed during clinical studies with lenadogene nolparvovec.
    Keywords:  Gene therapy; Leber hereditary optic neuropathy; Mitochondrial transfer; Optic nerve; Retina; Viral vector
    DOI:  https://doi.org/10.1016/j.nbd.2024.106681
  14. Cell Rep. 2024 Sep 21. pii: S2211-1247(24)01134-3. [Epub ahead of print]43(10): 114783
    Geranylgeranylated SCFFBXO10 regulates selective outer mitochondrial membrane proteostasis and function.
    Sameer Ahmed Bhat, Zahra Vasi, Liping Jiang, Shruthi Selvaraj, Rachel Ferguson, Sanaz Salarvand, Anish Gudur, Ritika Adhikari, Veronica Castillo, Hagar Ismail, Avantika Dhabaria, Beatrix Ueberheide, Shafi Kuchay.
      Compartment-specific cellular membrane protein turnover is not well understood. We show that FBXO10, the interchangeable component of the cullin-RING-ligase 1 complex, undergoes lipid modification with geranylgeranyl isoprenoid at cysteine953, facilitating its dynamic trafficking to the outer mitochondrial membrane (OMM). FBXO10 polypeptide lacks a canonical mitochondrial targeting sequence (MTS); instead, its geranylgeranylation at C953 and interaction with two cytosolic factors, cytosolic factor-like δ subunit of type 6 phosphodiesterase (PDE6δ; a prenyl-group-binding protein) and heat shock protein 90 (HSP90; a chaperone), orchestrate specific OMM targeting of prenyl-FBXO10. The FBXO10(C953S) mutant redistributes away from the OMM, impairs mitochondrial ATP production and membrane potential, and increases fragmentation. Phosphoglycerate mutase-5 (PGAM5) was identified as a potential substrate of FBXO10 at the OMM using comparative quantitative proteomics of enriched mitochondria. FBXO10 loss or expression of prenylation-deficient FBXO10(C953S) inhibited PGAM5 degradation, disrupted mitochondrial homeostasis, and impaired myogenic differentiation of human induced pluripotent stem cells (iPSCs) and murine myoblasts. Our studies identify a mechanism for FBXO10-mediated regulation of selective mitochondrial proteostasis potentially amenable to therapeutic intervention.
    Keywords:  CP: Metabolism; CP: Molecular biology; E3-ligase; F-box protein; FBXO10; HSP90; PDE6δ; mitochondria; prenylation; trafficking; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2024.114783
  15. Front Cell Dev Biol. 2024 ;12 1460061
    Fast and quantitative mitophagy assessment by flow cytometry using the mito-QC reporter.
    Juan Ignacio Jiménez-Loygorri, Carlos Jiménez-García, Álvaro Viedma-Poyatos, Patricia Boya.
      Mitochondrial quality control is finely tuned by mitophagy, the selective degradation of mitochondria through autophagy, and mitochondrial biogenesis. Removal of damaged mitochondria is essential to preserve cellular bioenergetics and prevent detrimental events such as sustained mitoROS production, pro-apoptotic cytochrome c release or mtDNA leakage. The array of tools available to study mitophagy is very limited but in constant development. Almost a decade ago, we developed a method to assess mitophagy flux using MitoTracker Deep Red in combination with lysosomal inhibitors. Now, using the novel tandem-fluorescence reporter mito-QC (mCherry-GFP-FIS1101-152) that allows to differentiate between healthy mitochondria (mCherry+GFP+) and mitolysosomes (mCherry+GFP-), we have developed a robust and quantitative method to assess mitophagy by flow cytometry. This approach has been validated in ARPE-19 cells using PINK1/Parkin-dependent (CCCP) and PINK1/Parkin-independent (DFP) positive controls and complementary techniques. Furthermore, we show that the mito-QC reporter can be multiplexed, especially if using spectral flow cytometry, to simultaneously study other cellular parameters such as viability or ROS production. Using this technique, we evaluated and characterized two prospective mitophagy inducers and further dissected their mechanism of action. Finally, using mito-QC reporter mice, we developed a protocol to measure mitophagy levels in the retina ex vivo. This novel methodology will propel mitophagy research forward and accelerate the discovery of novel mitophagy modulators.
    Keywords:  FACS; Fisetin; SI; autophagy; mitochondria; phenanthroline; retina
    DOI:  https://doi.org/10.3389/fcell.2024.1460061
  16. Front Pharmacol. 2024 ;15 1469053
    Unraveling the nexus of age, epilepsy, and mitochondria: exploring the dynamics of cellular energy and excitability.
    Wen Xie, Sushruta Koppula, Mayur B Kale, Lashin S Ali, Nitu L Wankhede, Mohit D Umare, Aman B Upaganlawar, Ahmed Abdeen, Elturabi E Ebrahim, Mohamed El-Sherbiny, Tapan Behl, Bairong Shen, Rajeev K Singla.
      Epilepsy, a complex neurological condition marked by recurring seizures, is increasingly recognized for its intricate relationship with mitochondria, the cellular powerhouses responsible for energy production and calcium regulation. This review offers an in-depth examination of the interplay between epilepsy, mitochondrial function, and aging. Many factors might account for the correlation between epilepsy and aging. Mitochondria, integral to cellular energy dynamics and neuronal excitability, perform a critical role in the pathophysiology of epilepsy. The mechanisms linking epilepsy and mitochondria are multifaceted, involving mitochondrial dysfunction, reactive oxygen species (ROS), and mitochondrial dynamics. Mitochondrial dysfunction can trigger seizures by compromising ATP production, increasing glutamate release, and altering ion channel function. ROS, natural byproducts of mitochondrial respiration, contribute to oxidative stress and neuroinflammation, critical factors in epileptogenesis. Mitochondrial dynamics govern fusion and fission processes, influence seizure threshold and calcium buffering, and impact seizure propagation. Energy demands during seizures highlight the critical role of mitochondrial ATP generation in maintaining neuronal membrane potential. Mitochondrial calcium handling dynamically modulates neuronal excitability, affecting synaptic transmission and action potential generation. Dysregulated mitochondrial calcium handling is a hallmark of epilepsy, contributing to excitotoxicity. Epigenetic modifications in epilepsy influence mitochondrial function through histone modifications, DNA methylation, and non-coding RNA expression. Potential therapeutic avenues targeting mitochondria in epilepsy include mitochondria-targeted antioxidants, ketogenic diets, and metabolic therapies. The review concludes by outlining future directions in epilepsy research, emphasizing integrative approaches, advancements in mitochondrial research, and ethical considerations. Mitochondria emerge as central players in the complex narrative of epilepsy, offering profound insights and therapeutic potential for this challenging neurological disorder.
    Keywords:  ageing; epigenetic modification; epilepsy; ketogenic diet; mitochondria targeted therapy
    DOI:  https://doi.org/10.3389/fphar.2024.1469053
  17. J Fluoresc. 2024 Sep 25.
    Visualizing Mitochondrial Membrane Potential with FRET Probes: Integrating Fluorescence Intensity Ratio and Lifetime Imaging.
    Fei Peng, Xiangnan Ai, Xiaoyu Bu, Zixuan Zhao, Baoxiang Gao.
      Mitochondrial membrane potential (MMP) is crucial for mitochondrial function and serves as a key indicator of cellular health and metabolic activity. Traditional lipophilic cationic fluorescence intensity probes are unavoidably influenced by probe concentration, laser intensity, and photobleaching, limiting their accuracy. To address these issues, we designed and synthesized a pair of fluorescence molecules, OR-C8 and SiR-BA, based on the Förster Resonance Energy Transfer (FRET) mechanism, for dual-modality visualization of MMP. OR-C8 anchors to the inner mitochondrial membrane through strong hydrophobic interactions, while SiR-BA is expelled from mitochondria when MMP decreases, thereby regulating the FRET process. During MMP reduction, the fluorescence intensity and lifetime of OR-C8 increase, while the fluorescence intensity of SiR-BA decreases. By combining changes in fluorescence intensity ratio and fluorescence lifetime, dual-modality visualization of MMP was achieved. This method not only accurately reflects MMP changes but also provides a novel tool for in-depth studies of mitochondrial function and related disease mechanisms, offering significant potential for advancing mitochondrial research and therapeutic development.
    Keywords:  Dual-modality; FRET; Fluorescence intensity; Fluorescence lifetime; Mitochondrial membrane potential
    DOI:  https://doi.org/10.1007/s10895-024-03929-w
  18. Environ Mol Mutagen. 2024 Sep 26.
    Artificial targeting of the NEIL1 DNA glycosylase to the mitochondria.
    Marlo K Thompson, Mark H Eggers, Ryan G Benton, Tom Johnsten, Aishwarya Prakash.
      The human NEIL1 DNA glycosylase is one of 11 mammalian glycosylases that initiate base excision repair. While substrate preference, catalytic mechanism, and structural information of NEIL1's ordered residues are available, limited information on its subcellular localization, compounded by relatively low endogenous expression levels, have impeded our understanding of NEIL1. Here, we employed a previously developed computational framework to optimize the mitochondrial localization signal of NEIL1, enabling the visualization of its specific targeting to the mitochondrion via confocal microscopy. While we observed clear mitochondrial localization and increased glycosylase/lyase activity in mitochondrial extracts from low-moderate NEIL1 expression, high NEIL1 mitochondrial expression levels proved harmful, potentially leading to cell death.
    Keywords:  NEIL1 DNA glycosylase; computational framework; confocal microscopy; mitochondrial localization
    DOI:  https://doi.org/10.1002/em.22632
  19. Cell. 2024 Sep 19. pii: S0092-8674(24)00976-0. [Epub ahead of print]
    Saturation mutagenesis-reinforced functional assays for disease-related genes.
    Kaiyue Ma, Shushu Huang, Kenneth K Ng, Nicole J Lake, Soumya Joseph, Jenny Xu, Angela Lek, Lin Ge, Keryn G Woodman, Katherine E Koczwara, Justin Cohen, Vincent Ho, Christine L O'Connor, Melinda A Brindley, Kevin P Campbell, Monkol Lek.
      Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.
    Keywords:  cost-effective variant interpretation; deep mutational scanning; diagnostics; dystroglycanopathies; genetic diseases; high-throughput functional assays; muscular dystrophies; saturation mutagenesis; variant effect prediction; variants of uncertain significance
    DOI:  https://doi.org/10.1016/j.cell.2024.08.047
  20. Biosensors (Basel). 2024 Sep 05. pii: 428. [Epub ahead of print]14(9):
    Mitochondrial Labeling with Mulberrin-Cy3: A New Fluorescent Probe for Live Cell Visualization.
    Gangxiang Yuan, Yiwei Luo, Peng Qian, Ningjia He.
      Mitochondria, crucial intracellular organelles, are central to energy metabolism, signal transduction, apoptosis, calcium homeostasis, and a myriad of other biological processes, making them a focal point in diverse research fields. The capacity to fluorescently label and visually track mitochondria is crucial for understanding their biological roles. We present mulberrin-Cy3, a novel small molecule fluorescent probe that selectively labels mitochondria in animal cells, including cancer cells, with relative ease. This protocol details the synthesis of mulberrin-Cy3 and its use for visualizing mitochondria in living cells. The synthesis is straightforward and time-efficient, and the labeling method is more accessible than traditional approaches, providing a cost-effective option for mitochondrial visualization at room temperature. The labeling is rapid, with effective labeling achieved within 5 min of incubation. The fluorescent signal is stable and brighter, offering a significant advantage over existing methods. Mulberrin-Cy3 represents a promising mitochondrial labeling compound, providing researchers with a novel experimental tool to explore the complex biological functions of mitochondria. This innovation has the potential to significantly advance our comprehension of mitochondrial dynamics and their role in cellular health and disease.
    Keywords:  fluorescent labeling; mitochondria; mulberrin-Cy3; probe
    DOI:  https://doi.org/10.3390/bios14090428
  21. J Transl Med. 2024 Sep 23. 22(1): 853
    Fetal and obstetrics manifestations of mitochondrial diseases.
    Adelizzi Alessia, Giri Anastasia, Di Donfrancesco Alessia, Boito Simona, Prigione Alessandro, Bottani Emanuela, Bollati Valentina, Tiranti Valeria, Persico Nicola, Brunetti Dario.
      During embryonic and neonatal development, mitochondria have essential effects on metabolic and energetic regulation, shaping cell fate decisions and leading to significant short- and long-term effects on embryonic and offspring health. Therefore, perturbation on mitochondrial function can have a pathological effect on pregnancy. Several shreds of evidence collected in preclinical models revealed that severe mitochondrial dysfunction is incompatible with life or leads to critical developmental defects, highlighting the importance of correct mitochondrial function during embryo-fetal development. The mechanism impairing the correct development is unknown and may include a dysfunctional metabolic switch in differentiating cells due to decreased ATP production or altered apoptotic signalling. Given the central role of mitochondria in embryonic and fetal development, the mitochondrial dysfunction typical of Mitochondrial Diseases (MDs) should, in principle, be detectable during pregnancy. However, little is known about the clinical manifestations of MDs in embryonic and fetal development. In this manuscript, we review preclinical and clinical evidence suggesting that MDs may affect fetal development and highlight the fetal and maternal outcomes that may provide a wake-up call for targeted genetic diagnosis.
    DOI:  https://doi.org/10.1186/s12967-024-05633-6
  22. STAR Protoc. 2024 Sep 20. pii: S2666-1667(24)00495-7. [Epub ahead of print]5(4): 103330
    Protocol to monitor live-cell, real-time, mitochondrial respiration in mouse muscle cells using the Resipher platform.
    Matthew Triolo, Mireille Khacho.
      Mitochondrial function is typically assessed by measuring oxygen consumption at a given time point. However, this approach cannot monitor respiratory changes that occur over time. Here, we present a protocol to measure mitochondrial respiration in freshly isolated muscle stem cells, primary skeletal muscle, and immortalized C2C12 myoblasts in real time using the Resipher platform. We describe steps for preparing and plating cells, performing media changes, setting up the software and device, and analyzing data. This method can be adapted to other cell types. For complete details on the use and execution of this protocol, please refer to Triolo et al.1.
    Keywords:  Cell Biology; Metabolism; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2024.103330
  23. Geroscience. 2024 Sep 23.
    Age-induced changes in skeletal muscle mitochondrial DNA synthesis, quantity, and quality in genetically unique rats.
    Robert V Musci, Jordan D Fuqua, Frederick F Peelor, Hoang Van Michelle Nguyen, Arlan Richardson, Solbie Choi, Benjamin F Miller, Jonathan Wanagat.
      Mitochondrial genomic integrity is a key element of physiological processes and health. Changes in the half-life of the mitochondrial genome are implicated in the generation and accumulation of age-induced mitochondrial DNA (mtDNA) mutations, which are implicated in skeletal muscle aging and sarcopenia. There are conflicting data on the half-life of mtDNA, and there is limited information on how aging affects half-life in skeletal muscle. We hypothesized that skeletal muscle mtDNA synthesis rates would decrease with age in both female and male rats concomitant with changes in mtDNA integrity reflected in mtDNA copy number and mutation frequency. We measured mitochondrial genome half-life using stable isotope labeling over a period of 14 days and assessed mtDNA copy number and deletion mutation frequency using digital PCR in the quadriceps muscle of 9-month-old and 26-month-old male and female OKC-HET rats. We found a significant age-related increase in mtDNA half-life, from 132 days at 9 months to 216 days at 26 months of age in OKC-HET quadriceps. Concomitant with the increase in mtDNA half-life, we found an age-related increase in mtDNA deletion mutation frequency in both male and female rats. Notably, 26-month-old female rats had a lower mutation frequency than male rats, and there were no changes in mtDNA copy number with sex, age, or mitochondrial genotype. These data reveal several key findings: (1) mtDNA turnover in rat skeletal muscle decreases with age, (2) mtDNA half-lives in skeletal muscle are approximately an order of magnitude longer than what is reported for other tissues, and (3) muscle mtDNA turnover differs significantly from the turnover of other mitochondrial macromolecules including components of the mitochondrial nucleoid. These findings provide insight into the factors driving age-induced mtDNA mutation accumulation, which contribute to losses of mitochondrial genomic integrity and may play a role in skeletal muscle dysfunction.
    Keywords:  Aging; Deuterium oxide; Mitochondrial DNA; Mutation; Rats; Skeletal muscle
    DOI:  https://doi.org/10.1007/s11357-024-01344-4
  24. Ann Neurol. 2024 Sep 25.
    Interferon Stimulated Gene Expression Is a Biomarker for Primary Mitochondrial Disease.
    Nandaki Keshavan, Lana Mhaldien, Kimberly Gilmour, Shamima Rahman.
       OBJECTIVE: Mitochondria are implicated in regulation of the innate immune response. We hypothesized that abnormalities in interferon signaling may contribute to pathophysiology in patients with primary mitochondrial disease (PMD).
    METHODS: Expression of interferon stimulated genes (ISGs) was measured by real-time polymerase chain reaction (PCR) in whole blood samples from a cohort of patients with PMD.
    RESULTS: Upregulated ISG expression was observed in a high proportion (41/55, 75%) of patients with PMD on at least 1 occasion, most frequently IFI27 upregulation, seen in 50% of the samples. Some patients had extremely high IFI27 levels, similar to those seen in patients with primary interferonopathies. A statistically significant correlation was observed between elevated IFI27 gene expression and PMD, but not between IFI27 and secondary mitochondrial dysfunction, suggesting that ISG upregulation is a biomarker of PMD. In some patients with PMD, ISG abnormalities persisted on repeat measurement over several years, indicative of ongoing chronic inflammation. Subgroup analyses suggested common ISG signatures in patients with similar mitochondrial disease mechanisms and positive correlations with disease severity among patients with identical genetic diagnoses.
    INTERPRETATION: Dysregulated interferon signaling is frequently seen in patients with PMD suggesting that interferon dysregulation is a contributor to pathophysiology. This may indicate a role for repurposing of immunomodulatory therapies for the treatment of PMDs by targeting interferon signaling. ANN NEUROL 2024.
    DOI:  https://doi.org/10.1002/ana.27081
  25. Cells. 2024 Sep 13. pii: 1540. [Epub ahead of print]13(18):
    Structural and Functional Characterization of the Most Frequent Pathogenic PRKN Substitution p.R275W.
    Bernardo A Bustillos, Liam T Cocker, Mathew A Coban, Caleb A Weber, Jenny M Bredenberg, Paige K Boneski, Joanna Siuda, Jaroslaw Slawek, Andreas Puschmann, Derek P Narendra, Neill R Graff-Radford, Zbigniew K Wszolek, Dennis W Dickson, Owen A Ross, Thomas R Caulfield, Wolfdieter Springer, Fabienne C Fiesel.
      Mutations in the PINK1 and PRKN genes are the most frequent genetic cause of early-onset Parkinson disease. The pathogenic p.R275W substitution in PRKN is the most frequent substitution observed in patients, and thus far has been characterized mostly through overexpression models that suggest a possible gain of toxic misfunction. However, its effects under endogenous conditions are largely unknown. We used patient fibroblasts, isogenic neurons, and post-mortem human brain samples from carriers with and without PRKN p.R275W to assess functional impact. Immunoblot analysis and immunofluorescence were used to study mitophagy activation, and mitophagy execution was analyzed by flow cytometry of the reporter mitoKeima. The functional analysis was accompanied by structural investigation of PRKN p.R275W. We observed lower PRKN protein in fibroblasts with compound heterozygous p.R275W mutations. Isogenic neurons showed an allele-dose dependent decrease in PRKN protein. Lower PRKN protein levels were accompanied by diminished phosphorylated ubiquitin and decreased MFN2 modification. Mitochondrial degradation was also allele-dose dependently impaired. Consistently, PRKN protein levels were drastically reduced in human brain samples from p.R275W carriers. Finally, structural simulations showed significant changes in the closed form of PRKN p.R275W. Our data suggest that under endogenous conditions the p.R275W mutation results in a loss-of-function by destabilizing PRKN.
    Keywords:  PINK1; PRKN; Parkinson disease; mitophagy; parkin; ubiquitin
    DOI:  https://doi.org/10.3390/cells13181540
  26. FASEB J. 2024 Sep 30. 38(18): e70066
    Mitochondrial membrane potential and oxidative stress interact to regulate Oma1-dependent processing of Opa1 and mitochondrial dynamics.
    Garrett M Fogo, Sarita Raghunayakula, Katlynn J Emaus, Francisco J Torres Torres, Joseph M Wider, Thomas H Sanderson.
      Mitochondrial form and function are regulated by the opposing forces of mitochondrial dynamics: fission and fusion. Mitochondrial dynamics are highly active and consequential during neuronal ischemia/reperfusion (I/R) injury. Mitochondrial fusion is executed at the mitochondrial inner membrane by Opa1. The balance of long (L-Opa1) and proteolytically cleaved short (S-Opa1) isoforms is critical for efficient fusion. Oma1 is the predominant stress-responsive protease for Opa1 processing. In neuronal cell models, we assessed Oma1 and Opa1 regulation during mitochondrial stress. In an immortalized mouse hippocampal neuron line (HT22), Oma1 was sensitive to mitochondrial membrane potential depolarization (rotenone, FCCP) and hyperpolarization (oligomycin). Further, oxidative stress was sufficient to increase Oma1 activity and necessary for depolarization-induced proteolysis. We generated Oma1 knockout (KO) HT22 cells that displayed normal mitochondrial morphology and fusion capabilities. FCCP-induced mitochondrial fragmentation was exacerbated in Oma1 KO cells. However, Oma1 KO cells were better equipped to perform restorative fusion after fragmentation, presumably due to preserved L-Opa1. We extended our investigations to a combinatorial stress of neuronal oxygen-glucose deprivation and reoxygenation (OGD/R), where we found that Opa1 processing and Oma1 activation were initiated during OGD in an ROS-dependent manner. These findings highlight a novel dependence of Oma1 on oxidative stress in response to depolarization. Further, we demonstrate contrasting fission/fusion roles for Oma1 in the acute response and recovery stages of mitochondrial stress. Collectively, our results add intersectionality and nuance to the previously proposed models of Oma1 activity.
    Keywords:  membrane fusion; membrane potential; mitochondria; mitochondrial dynamics; proteostasis; reactive oxygen species
    DOI:  https://doi.org/10.1096/fj.202400313R
  27. Eur J Hum Genet. 2024 Sep 27.
    Uncovering recessive alleles in rare Mendelian disorders by genome sequencing of 174 individuals with monoallelic pathogenic variants.
    Gaby Schobers, Maartje Pennings, Juliette de Vries, Michael Kwint, Jeroen van Reeuwijk, Jordi Corominas Galbany, Ronald van Beek, Eveline Kamping, Raoul Timmermans, Erik-Jan Kamsteeg, Lonneke Haer-Wigman, Frans P M Cremers, Susanne Roosing, Christian Gilissen, Hannie Kremer, Han G Brunner, Helger G Yntema, Lisenka E L M Vissers.
      Clinical exome sequencing (ES) has facilitated genetic diagnosis in individuals with a rare genetic disorder by analysis of all protein-coding sequences in a single experiment. However, in 40-60% of patients, a conclusive diagnosis remains elusive. In 2-5% of these individuals, ES does identify a disease-associated monoallelic variant in a recessive disorder. We hypothesized that short-read genome sequencing (GS) might uncover a pathogenic variant on the second allele, thereby increasing diagnostic yield. We performed GS for 174 individuals in whom ES identified a monoallelic pathogenic variant in a gene associated with recessive disease related to their phenotype. GS interpretation was limited to the (non-)coding parts of the gene in which this first pathogenic variant was identified, focusing on splice-disrupting variants. Firstly, we uncovered a second pathogenic variant affecting coding sequence in five individuals, including two SNV/indel variants, two copy number variants, and one insertion. Secondly, for 24 individuals, we identified a total of 31 rare non-coding intronic SNV/indel variants, all predicted to disrupt splicing. Using functional follow-up assays, we confirmed an effect on splicing for three of these variants (in ABCA4, POLR3A and COL4A4) in three individuals. In summary, we identified a (likely) pathogenic second variant in 4.6% (8/174), and a possible diagnosis for 12.1% (21/174) of our cohort. Hence, when performing GS as first-tier diagnostic test, including the interpretation of SVs and rare intronic variants in known recessive disease genes, the overall diagnostic yield of rare disease will increase. The added diagnostic value of GS for recessive disease In our cohort of 174 individuals (84 males and 90 females) with a monoallelic pathogenic variant in genes associated with a wide and diverse range of recessive diseases (pie chart), using genome sequencing (GS) and a systematic approach (methods), we identified eight new diagnoses (4.6%). We identified a second likely pathogenic variant in eight individuals (results); In two a second coding variant was found, in three others, a rare non-coding SNV anticipated to disrupt splicing was uncovered, and in three individuals a structural rearrangement was identified (two copy number variants (CNV), and one structural variant (SV)).
    DOI:  https://doi.org/10.1038/s41431-024-01694-9
  28. Biochim Biophys Acta Bioenerg. 2024 Sep 24. pii: S0005-2728(24)00482-1. [Epub ahead of print] 149512
    Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I.
    Jonathan Lasham, Amina Djurabekova, Georgios Kolypetris, Volker Zickermann, Janet Vonck, Vivek Sharma.
      The charge states of titratable amino acid residues play a key role in the function of membrane-bound bioenergetic proteins. However, determination of these charge states both through experimental and computational approaches is extremely challenging. Cryo-EM density maps can provide insights on the charge states of titratable amino acid residues. By performing classical atomistic molecular dynamics simulations on the high resolution cryo-EM structures of respiratory complex I from Yarrowia lipolytica, we analyze the conformational and charge states of a key acidic residue in its ND1 subunit, aspartic acid D203, which is also a mitochondrial disease mutation locus. We suggest that in the native state of respiratory complex I, D203 is negatively charged and maintains a stable hydrogen bond to a conserved arginine residue. Alternatively, upon conformational change in the turnover state of the enzyme, its sidechain attains a charge-neutral status. We discuss the implications of this analysis on the molecular mechanism of respiratory complex I.
    Keywords:  Charge transfer; Conformational dynamics; Coupling mechanism; Electrostatics; Proton pump; Protonation states
    DOI:  https://doi.org/10.1016/j.bbabio.2024.149512
  29. Am J Med Genet A. 2024 Sep 27. e63892
    Bi-Allelic Splicing Variant, c.153-2A > C in TOMM7 Is Associated With Leigh Syndrome.
    Mayuri Yeole, Purvi Majethia, Shahyan Siddiqui, Katta Mohan Girisha, Anju Shukla, Periyasamy Radhakrishnan, Vivekananda Bhat.
      Translocase of the outer mitochondrial membrane (TOMM) complex plays an important role in the transport of proteins from the cytoplasm into the mitochondria. TOMM7, one of the subunits of the TOMM complex, modulates its assembly and stability. Bi-allelic disease-causing variants in TOMM7 (MIM* 607980) have been previously reported in two unrelated families with a diverse phenotype of short stature, lipodystrophy, progeria, developmental delay, hypotonia, and skeletal dysplasia. We report a 4-month-old female child significantly affected with neonatal-onset hypotonia, lactic acidosis, optic atrophy, and neuroimaging findings suggestive of Leigh disease with a novel canonical splice variant, c.153-2A > C in TOMM7 (NM_019059.5). Further work done on cDNA of parents revealed the presence of shorter transcripts secondary to aberrant splicing.
    Keywords:  Garg‐Mishra progeroid syndrome; TOMM complex; elevated lactate; mitochondria
    DOI:  https://doi.org/10.1002/ajmg.a.63892
  30. Pharmacol Res. 2024 Sep 25. pii: S1043-6618(24)00379-7. [Epub ahead of print] 107434
    The Potential Role of Mitochondria in the Microbiota-Gut-Brain Axis: Implications for Brain Health.
    Lei Qiao, Ge Yang, Peng Wang, Chunlan Xu.
      Mitochondria are crucial organelles that regulate cellular energy metabolism, calcium homeostasis, and oxidative stress responses, playing pivotal roles in brain development and neurodegeneration. Concurrently, the gut microbiota has emerged as a key modulator of brain physiology and pathology through the microbiota-gut-brain axis. Recent evidence suggests an intricate crosstalk between the gut microbiota and mitochondrial function, mediated by microbial metabolites that can influence mitochondrial activities in the brain. This review aims to provide a comprehensive overview of the emerging role of mitochondria as critical mediators in the microbiota-gut-brain axis, shaping brain health and neurological disease pathogenesis. We discuss how gut microbial metabolites such as short-chain fatty acids, secondary bile acids, tryptophan metabolites, and trimethylamine N-oxide can traverse the blood-brain barrier and modulate mitochondrial processes including energy production, calcium regulation, mitophagy, and oxidative stress in neurons and glial cells. Additionally, we proposed targeting the mitochondria through diet, prebiotics, probiotics, or microbial metabolites as a promising potential therapeutic approach to maintain brain health by optimizing mitochondrial fitness. Overall, further investigations into how the gut microbiota and its metabolites regulate mitochondrial bioenergetics, dynamics, and stress responses will provide valuable insights into the microbiota-gut-brain axis in both health and disease states.
    Keywords:  Brain; Gut microbiota; Microbiota-gut-brain axis; Mitochondria; Neurodegenerative diseases; Redox processes
    DOI:  https://doi.org/10.1016/j.phrs.2024.107434
  31. Brain Commun. 2024 ;6(5): fcae312
    Investigating the prevalence of MFN2 mutations in amyotrophic lateral sclerosis: insights from an Italian cohort.
    Elena Abati, Delia Gagliardi, Arianna Manini, Roberto Del Bo, Dario Ronchi, Megi Meneri, Francesca Beretta, Annalisa Sarno, Federica Rizzo, Edoardo Monfrini, Alessio Di Fonzo, Maria Teresa Pellecchia, Alberto Brusati, Vincenzo Silani, Giacomo Pietro Comi, Antonia Ratti, Federico Verde, Nicola Ticozzi, Stefania Corti.
      The MFN2 gene encodes mitofusin 2, a key protein for mitochondrial fusion, transport, maintenance and cell communication. MFN2 mutations are primarily linked to Charcot-Marie-Tooth disease type 2A. However, a few cases of amyotrophic lateral sclerosis and amyotrophic lateral sclerosis/frontotemporal dementia phenotypes with concomitant MFN2 mutations have been previously reported. This study examines the clinical and genetic characteristics of an Italian cohort of amyotrophic lateral sclerosis patients with rare, non-synonymous MFN2 mutations. A group of patients (n = 385) diagnosed with amyotrophic lateral sclerosis at our Neurology Units between 2008 and 2023 underwent comprehensive molecular testing, including MFN2. After excluding pathogenic mutations in the main amyotrophic lateral sclerosis-related genes (i.e. C9orf72, SOD1, FUS and TARDBP), MFN2 variants were classified based on the American College of Medical Genetics and Genomics guidelines, and demographic and clinical data of MFN2-mutated patients were retrieved. We identified 12 rare, heterozygous, non-synonymous MFN2 variants in 19 individuals (4.9%). Eight of these variants, carried by nine patients (2.3%), were either pathogenic, likely pathogenic or variants of unknown significance according to the American College of Medical Genetics and Genomics guidelines. Among these patients, four exhibited a familial pattern of inheritance. The observed phenotypes included classic and bulbar amyotrophic lateral sclerosis, amyotrophic lateral sclerosis/frontotemporal dementia, flail arm, flail leg and progressive muscular atrophy. Median survival after disease onset was extremely variable, ranging from less than 1 to 13 years. This study investigates the prevalence of rare, non-synonymous MFN2 variants within an Italian cohort of amyotrophic lateral sclerosis patients, who have been extensively investigated, enhancing our knowledge of the underlying phenotypic spectrum. Further research is needed to understand whether MFN2 mutations contribute to motor neuron disease and to what extent. Improving our knowledge regarding the genetic basis of amyotrophic lateral sclerosis is crucial both in a diagnostic and therapeutic perspective.
    Keywords:  amyotrophic lateral sclerosis; genetics; mitochondria; mitofusin 2
    DOI:  https://doi.org/10.1093/braincomms/fcae312
  32. Cureus. 2024 Aug;16(8): e67760
    Cochlear Implantation for Isoleucyl-tRNA Synthetase Mutation-Associated Mitochondrial Disease: A Case Report.
    Masaomi Motegi, Yuika Sakurai, Yasushi Mio, Toya Ohashi.
      Biallelic missense mutations in the nuclear-encoded, cytosolic isoleucyl-tRNA synthetase (IARS) gene are associated with a rare and complex multisystemic phenotype, including growth retardation, intellectual disability, muscular hypotonia, diabetes mellitus, and deafness. These mutations impact the cytosolic isoform of IARS, which plays a crucial role in protein synthesis. The pathogenesis involves mitochondrial dysfunction, despite IARS being primarily a cytosolic enzyme, potentially linking it to the observed clinical manifestations. The efficacy of cochlear implantation for deafness due to IARS mutations and the safety of general anesthesia in such patients remain unclear. This report describes a rare case of progressive sensorineural hearing loss caused by IARS mutation-associated mitochondrial disease, which was successfully treated with cochlear implantation. Additionally, we discuss the safety of general anesthesia in this patient. A Japanese woman with IARS mutation-associated mitochondrial disease was diagnosed with severe bilateral sensorineural hearing loss at five years of age and immediately received hearing aids. Her hearing progressively deteriorated to profound impairment, necessitating cochlear implantation at 26 years of age, which resulted in satisfactory hearing. Furthermore, no perioperative general anesthesia-related adverse events were reported. Our case demonstrates that cochlear implantation can effectively restore hearing. This suggests that sensorineural hearing loss caused by IARS deficiency is primarily due to cochlear dysfunction. This case demonstrated that hearing loss is a crucial feature of IARS mutation-associated mitochondrial disease, which can be mitigated by cochlear implantation. While general anesthesia can be safely administered, careful consideration of anesthetic choices, such as avoiding depolarizing muscle relaxants and prolonged use of propofol, is essential to prevent complications. In this case, general anesthesia was well tolerated without perioperative events, providing valuable insight into the potential safety of such procedures in similar patients. Nevertheless, further studies are needed to confirm these findings across a broader population.
    Keywords:  anesthesia complication; cochlear implantation; diabetes mellitus; general anesthesia; intellectual disability; iras mutation; mitochondrial disease; profound sensorineural hearing loss
    DOI:  https://doi.org/10.7759/cureus.67760
  33. Cell Commun Signal. 2024 Sep 26. 22(1): 450
    Mitochondria facilitate neuronal differentiation by metabolising nuclear-encoded RNA.
    Filip Vujovic, Mary Simonian, William E Hughes, Claire E Shepherd, Neil Hunter, Ramin M Farahani.
      Mitochondrial activity directs neuronal differentiation dynamics during brain development. In this context, the long-established metabolic coupling of mitochondria and the eukaryotic host falls short of a satisfactory mechanistic explanation, hinting at an undisclosed facet of mitochondrial function. Here, we reveal an RNA-based inter-organellar communication mode that complements metabolic coupling of host-mitochondria and underpins neuronal differentiation. We show that within minutes of exposure to differentiation cues and activation of the electron transport chain, the mitochondrial outer membrane transiently fuses with the nuclear membrane of neural progenitors, leading to efflux of nuclear-encoded RNAs (neRNA) into the positively charged mitochondrial intermembrane space. Subsequent degradation of mitochondrial neRNAs by Polynucleotide phosphorylase 1 (PNPase) located in the intermembrane space curbs the transcriptomic memory of progenitor cells. Further, acquisition of neRNA by mitochondria leads to a collapse of proton motive force, suppression of ATP production, and a resultant amplification of autophagic flux that attenuates proteomic memory. Collectively, these events force the progenitor cells towards a "tipping point" characterised by emergence of a competing neuronal differentiation program. It appears that neuronal differentiation is a consequence of reprogrammed coupling of metabolomic and transcriptomic landscapes of progenitor cells, with mitochondria emerging as key "reprogrammers" that operate by acquiring and metabolising neRNAs. However, the documented role of mitochondria as "reprogrammers" of differentiation remains to be validated in other neuronal lineages and in vivo.
    DOI:  https://doi.org/10.1186/s12964-024-01825-1
  34. bioRxiv. 2024 Sep 13. pii: 2024.09.12.612761. [Epub ahead of print]
    The mitochondrial dicarboxylate carrier mediates in vivo hepatic gluconeogenesis.
    Daniel J Pape, Kelly C Falls-Hubert, Ronald A Merrill, Adnan Ahmed, Qingwen Qian, Gavin R McGivney, Paulina Sobieralski, Adam J Rauckhorst, Ling Yang, Eric B Taylor.
      Hepatic gluconeogenesis (GNG) is essential for maintaining euglycemia during prolonged fasting. However, GNG becomes pathologically elevated and drives chronic hyperglycemia in type 2 diabetes (T2D). Lactate/pyruvate is a major GNG substrate known to be imported into mitochondria for GNG. Yet, the subsequent mitochondrial carbon export mechanisms required to supply the extra-mitochondrial canonical GNG pathway have not been genetically delineated. Here, we evaluated the role of the mitochondrial dicarboxylate carrier (DiC) in mediating GNG from lactate/pyruvate. We generated liver-specific DiC knockout (DiC LivKO) mice. During lactate/pyruvate tolerance tests, DiC LivKO decreased plasma glucose excursion and 13 C-lactate/-pyruvate flux into hepatic and plasma glucose. In a Western diet (WD) feeding model of T2D, acute DiC LivKO after induction of obesity decreased lactate/pyruvate-driven GNG, hyperglycemia, and hyperinsulinemia. Our results show that mitochondrial carbon export through the DiC mediates GNG and that the DiC contributes to impaired glucose homeostasis in a mouse model of T2D.
    DOI:  https://doi.org/10.1101/2024.09.12.612761
  35. Mol Genet Metab Rep. 2024 Dec;41 101142
    MADD-like pattern of acylcarnitines associated with sertraline use.
    Filippo Ingoglia, Mohsen Tanfous, Benjamin Ellezam, Katherine J Anderson, Marzia Pasquali, Lorenzo D Botto.
      Multiple acyl-CoA dehydrogenase deficiency (MADD) is a primary mitochondrial dysfunction affecting mitochondrial fatty acid and protein metabolism, caused by biallelic pathogenic variants in ETFA, ETFB, or ETFDH genes. The heterogeneous phenotypes associated with MADD have been classified into three groups: neonatal onset with congenital anomalies (type 1), neonatal onset without congenital anomalies (type 2), and attenuated and/or later onset (type 3). Here, we present two cases with biochemical profiles mimicking late-onset MADD but negative genetic testing, associated with the use of sertraline, a commonly used antidepressant. Case 1 is a 22 yo woman diagnosed with depression and profound fatigue who was referred to the metabolic clinic because of carnitine deficiency and a plasma acylcarnitine profile with a MADD-like pattern. Case 2 is a 61 yo woman with a history of chronic fatigue who was admitted to the emergency department with difficulty swallowing, metabolic acidosis, and mild rhabdomyolysis. Plasma acylcarnitine profile showed a MADD-like pattern. The muscle biopsy revealed lipid droplet accumulation and proliferation of mitochondria with abnormal osmiophilic inclusions, and a biochemical assay of the respiratory chain showed a deficit in complex II activity. In both cases, urine organic acid profile was normal, and genetic tests did not detect variants in the genes involved in MADD. Sertraline was on their list of medications and considering its association with inhibition of mitochondrial function and rhabdomyolysis, the team recommended the discontinuation under medical supervision. In Case 1 after discontinuation, the plasma acylcarnitine test normalized, only to return abnormal when the patient resumed sertraline. In Case 2, after sertraline was discontinued rhabdomyolysis resolved, and the muscle biopsy and biochemical assay of the respiratory chain normalized. Although sertraline is considered a safe drug, these two cases suggest that the use of sertraline may be associated with a potentially reversible form of mitochondrial dysfunction mimicking MADD. Further studies are needed to confirm and estimate the risk of MADD-like presentations with the use of sertraline, as well as identifying additional contributing factors, including genetic factors. Metabolic physicians should consider sertraline use in the differential diagnosis of MADD, particularly when genetic testing is negative.
    Keywords:  Antidepressant medications; Mitochondrial dysfunction; Multiple acyl-CoA dehydrogenase deficiency (MADD); Sertraline
    DOI:  https://doi.org/10.1016/j.ymgmr.2024.101142
  36. Biomed Pharmacother. 2024 Sep 23. pii: S0753-3322(24)01370-2. [Epub ahead of print]180 117484
    Evaluating the safety and efficiency of nanomaterials: A focus on mitochondrial health.
    Liu Siquan, Cheng Weilin, Chen Xiuwen, Zou Meiyan, Guo Weihong, Feng Xiaoli.
      Nanomaterials (NMs) have extensive application potential in drug delivery, tissue engineering, and various other domains, attributable to their exceptional physical and chemical properties. Nevertheless, an increasing body of literature underscores the diverse safety risks are associated with NMs upon interaction with the human body, including oxidative stress and programmed cell death. Mitochondria, serving as cellular energy factories, play a pivotal role in energy metabolism and the regulation of cell fate. Organs with substantial energy demands, including the heart and brain, are highly sensitive to mitochondrial integrity, with mitochondrial impairment potentially resulting in significant dysfunction and pathologies such as as heart failure and neurodegenerative disease. This review elucidates the pathways by which NMs translocate into mitochondria, their intracellular dynamics, and their impact on mitochondrial morphology, respiratory chain activity, and metabolic processes. We further investigate associated molecular mechanisms, including mitochondrial dynamic imbalance, calcium overload, and oxidative stress, and elucidate the pivotal roles of mitochondria in different forms of programmed cell death such as apoptosis and autophagy. Finally, we offer recommendations regarding the safety and efficacy of NMs for medical applications. By systematically analyzing the interactions and molecular mechanisms between NMs and mitochondria, this paper aims to enhance the toxicological evaluation framework of NMs and provide a foundational reference and theoretical basis for their clinical utilization.
    Keywords:  Diabetes; Mitochondria; MtDNA; Nanomaterials; Neurodegenerative disease; Oxidative stress; Respiratory chain; Safety risk
    DOI:  https://doi.org/10.1016/j.biopha.2024.117484
  37. Nat Commun. 2024 Sep 27. 15(1): 8268
    A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.
    Arthur S Lee, Lauren J Ayers, Michael Kosicki, Wai-Man Chan, Lydia N Fozo, Brandon M Pratt, Thomas E Collins, Boxun Zhao, Matthew F Rose, Alba Sanchis-Juan, Jack M Fu, Isaac Wong, Xuefang Zhao, Alan P Tenney, Cassia Lee, Kristen M Laricchia, Brenda J Barry, Victoria R Bradford, Julie A Jurgens, Eleina M England, Monkol Lek, Daniel G MacArthur, Eunjung Alice Lee, Michael E Talkowski, Harrison Brand, Len A Pennacchio, Elizabeth C Engle.
      Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1, and EBF3 - as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.
    DOI:  https://doi.org/10.1038/s41467-024-52463-7
  38. Elife. 2024 Sep 26. pii: RP90293. [Epub ahead of print]12
    The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting.
    Vineeth Vengayil, Shreyas Niphadkar, Swagata Adhikary, Sriram Varahan, Sunil Laxman.
      Many cells in high glucose repress mitochondrial respiration, as observed in the Crabtree and Warburg effects. Our understanding of biochemical constraints for mitochondrial activation is limited. Using a Saccharomyces cerevisiae screen, we identified the conserved deubiquitinase Ubp3 (Usp10), as necessary for mitochondrial repression. Ubp3 mutants have increased mitochondrial activity despite abundant glucose, along with decreased glycolytic enzymes, and a rewired glucose metabolic network with increased trehalose production. Utilizing ∆ubp3 cells, along with orthogonal approaches, we establish that the high glycolytic flux in glucose continuously consumes free Pi. This restricts mitochondrial access to inorganic phosphate (Pi), and prevents mitochondrial activation. Contrastingly, rewired glucose metabolism with enhanced trehalose production and reduced GAPDH (as in ∆ubp3 cells) restores Pi. This collectively results in increased mitochondrial Pi and derepression, while restricting mitochondrial Pi transport prevents activation. We therefore suggest that glycolytic flux-dependent intracellular Pi budgeting is a key constraint for mitochondrial repression.
    Keywords:  GAPDH; S. cerevisiae; biochemistry; cancer biology; chemical biology; glycolysis; inorganic phosphate; metabolic flux; mitochondria; trehalose
    DOI:  https://doi.org/10.7554/eLife.90293
  39. Structure. 2024 Sep 17. pii: S0969-2126(24)00363-0. [Epub ahead of print]
    An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium.
    Qi-Tong Lin, Danielle M Colussi, Taylor Lake, Peter B Stathopulos.
      AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca2+) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+, respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand.
    Keywords:  AI/NMR-hybrid structure; AlphaFold; Ca(2+)/H(+) antiporter; F-EF-hand domain; LETM1; calcium sensor; leucine zipper EF-hand containing transmembrane protein-1; oligomerization; pH sensor; solution NMR structure
    DOI:  https://doi.org/10.1016/j.str.2024.08.020
  40. EMBO Mol Med. 2024 Sep 27.
    Mutation in the mitochondrial chaperone TRAP1 leads to autism with more severe symptoms in males.
    Małgorzata Rydzanicz, Bozena Kuzniewska, Marta Magnowska, Tomasz Wójtowicz, Aleksandra Stawikowska, Anna Hojka, Ewa Borsuk, Ksenia Meyza, Olga Gewartowska, Jakub Gruchota, Jacek Miłek, Patrycja Wardaszka, Izabela Chojnicka, Ludwika Kondrakiewicz, Dorota Dymkowska, Alicja Puścian, Ewelina Knapska, Andrzej Dziembowski, Rafał Płoski, Magdalena Dziembowska.
      There is increasing evidence of mitochondrial dysfunction in autism spectrum disorders (ASD), but the causal relationships are unclear. In an ASD patient whose identical twin was unaffected, we identified a postzygotic mosaic mutation p.Q639* in the TRAP1 gene, which encodes a mitochondrial chaperone of the HSP90 family. Additional screening of 176 unrelated ASD probands revealed an identical TRAP1 variant in a male patient who had inherited it from a healthy mother. Notably, newly generated knock-in Trap1 p.Q641* mice display ASD-related behavioral abnormalities that are more pronounced in males than in females. Accordingly, Trap1 p.Q641* mutation also resulted in sex-specific changes in synaptic plasticity, the number of presynaptic mitochondria, and mitochondrial respiration. Thus, the TRAP1 p.Q639* mutation is the first example of a monogenic ASD caused by impaired mitochondrial protein homeostasis.
    Keywords:  Autism; Mitochondria; Mouse Model; Synapses; Trap1
    DOI:  https://doi.org/10.1038/s44321-024-00147-6
  41. Res Sq. 2024 Sep 16. pii: rs.3.rs-4875322. [Epub ahead of print]
    Cytochrome c oxidase dependent respiration is essential for T cell activation, proliferation and memory formation.
    Peter McGuire, Tatiana Tarasenko, Emily Warren, Amanda Fuchs, Bharati Singh, Jose Marin, Marten Szibor.
      T cell activation, proliferation, and differentiation are fundamentally driven by shifts in cellular metabolism, with mitochondria playing a central role. Cytochrome c oxidase (COX, complex IV) is a key player in this process, as its activity is crucial for apoptosis, mtDNA maintenance, mitochondrial transcription, and mitochondrial respiration (MR), all of which influence T cell fate and function. Despite its known roles, the specific functions of COX required for T cell activity in vivo remain unclear. To isolate the role of MR in T cell function, we reintroduced this capability in COX-deficient T cells using an alternative oxidase (AOX) from Ciona intestinalis. Our findings demonstrate that MR is vital for maintaining metabolic balance during T cell activation by alleviating electron pressure from metabolic reprogramming and preserving redox homeostasis. We further showed that AOX mitigates apoptosis, prevents metabolic disruptions in glycolysis and the tricarboxylic acid cycle, and improves mtDNA maintenance and transcription, indicating that these disturbances are secondary to impaired MR in the absence of COX. Most importantly, the introduction of AOX restored robust effector and memory T cell generation and function in COX-deficient cells. These results highlight the essential role of COX-dependent MR in ensuring cellular health and underscore its pivotal role in T cell proliferation and differentiation.
    DOI:  https://doi.org/10.21203/rs.3.rs-4875322/v2
  42. Lancet Neurol. 2024 Oct;pii: S1474-4422(24)00323-5. [Epub ahead of print]23(10): 961
    RAB32 mutation in Parkinson's disease.
    ROPAD Study Group
      
    DOI:  https://doi.org/10.1016/S1474-4422(24)00323-5
  43. BMJ Neurol Open. 2024 ;6(2): e000825
    Neurological manifestations in adult patients with the m.3243A>G variant in mitochondrial DNA.
    Kari Majamaa, Mikko Kärppä, Jukka S Moilanen.
       ABSTRACT:
    Background: The m.3243A>G variant in mitochondrial DNA (mtDNA) is the most common cause of the MELAS (Mitochondrial encephalopathy, lactic acidosis and stroke-like episodes) syndrome usually commencing in childhood or adolescence. In adults, the variant presents with versatile and mostly neurological phenotypes, but MELAS may not be common.
    Objective: To examine the frequency of phenotypes in adults with m.3243A>G in a population-based cohort and in a meta-analysis of reported case series.
    Methods: We clinically examined 51 adult patients with m.3243A>G to determine the frequency of phenotypes and to analyse the contribution of variant heteroplasmy, age, sex and mtDNA haplogroup to the phenotypes. The frequencies of neurological features were also assessed in a meta-analysis on 25 published case series reporting 1314 patients.
    Results: Sensorineural hearing impairment (HI), cognitive impairment and myopathy were the most common manifestations, whereas stroke-like episodes were infrequent. Variant heteroplasmy and age were only modest predictors of the phenotypes, although heteroplasmy correlated significantly with disability and Kaplan-Meier analysis showed progression of phenotypes with age. Male sex predicted more severe disability, whereas haplogroup UK was associated with no significant disability. Meta-analysis revealed substantial heterogeneity of phenotype frequencies and preferential inclusion of the MELAS phenotype.
    Discussion: In adult patients with m.3243A>G sensorineural HI, cognitive impairment and myopathy are common manifestations with lifetime prevalences approaching unity. Stroke-like episodes are rare. Variant heteroplasmy, age, sex and mtDNA haplogroup contribute to the severity of the disease. Meta-analysis provided a solid estimate of the various neurological symptoms in adults with m.3243A>G.
    Keywords:  CLINICAL NEUROLOGY; GENETICS; META-ANALYSIS; MITOCHONDRIAL DISORDERS; SYSTEMATIC REVIEWS
    DOI:  https://doi.org/10.1136/bmjno-2024-000825
  44. Cell Death Dis. 2024 Sep 27. 15(9): 692
    Altered molecular and cellular mechanisms in KIF5A-associated neurodegenerative or neurodevelopmental disorders.
    Marta Cozzi, Stefania Magri, Barbara Tedesco, Guglielmo Patelli, Veronica Ferrari, Elena Casarotto, Marta Chierichetti, Paola Pramaggiore, Laura Cornaggia, Margherita Piccolella, Mariarita Galbiati, Paola Rusmini, Valeria Crippa, Jessica Mandrioli, Davide Pareyson, Chiara Pisciotta, Stefano D'Arrigo, Antonia Ratti, Lorenzo Nanetti, Caterina Mariotti, Elisa Sarto, Viviana Pensato, Cinzia Gellera, Daniela Di Bella, Riccardo M Cristofani, Franco Taroni, Angelo Poletti.
      Mutations targeting distinct domains of the neuron-specific kinesin KIF5A associate with different neurodegenerative/neurodevelopmental disorders, but the molecular bases of this clinical heterogeneity are unknown. We characterised five key mutants covering the whole spectrum of KIF5A-related phenotypes: spastic paraplegia (SPG, R17Q and R280C), Charcot-Marie-Tooth disease (CMT, R864*), amyotrophic lateral sclerosis (ALS, N999Vfs*40), and neonatal intractable myoclonus (NEIMY, C975Vfs*73) KIF5A mutants. CMT-R864*-KIF5A and ALS-N999Vfs*40-KIF5A showed impaired autoinhibition and peripheral localisation accompanied by altered mitochondrial distribution, suggesting transport competence disruption. ALS-N999Vfs*40-KIF5A formed SQSTM1/p62-positive inclusions sequestering WT-KIF5A, indicating a gain of toxic function. SPG-R17Q-KIF5A and ALS-N999Vfs*40-KIF5A evidenced a shorter half-life compared to WT-KIF5A, and proteasomal blockage determined their accumulation into detergent-insoluble inclusions. Interestingly, SPG-R280C-KIF5A and ALS-N999Vfs*40-KIF5A both competed for degradation with proteasomal substrates. Finally, NEIMY-C975Vfs*73-KIF5A displayed a similar, but more severe aberrant behaviour compared to ALS-N999Vfs*40-KIF5A; these two mutants share an abnormal tail but cause disorders on the opposite end of KIF5A-linked phenotypic spectrum. Thus, our observations support the pathogenicity of novel KIF5A mutants, highlight abnormalities of recurrent variants, and demonstrate that both unique and shared mechanisms underpin KIF5A-related diseases.
    DOI:  https://doi.org/10.1038/s41419-024-07096-5
  45. Nat Commun. 2024 Sep 27. 15(1): 8301
    Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis.
    Katherine Labbé, Lauren LeBon, Bryan King, Ngoc Vu, Emily H Stoops, Nina Ly, Austin E Y T Lefebvre, Phillip Seitzer, Swathi Krishnan, Jin-Mi Heo, Bryson Bennett, Carmela Sidrauski.
      The integrated stress response (ISR) enables cells to cope with a variety of insults, but its specific contribution to downstream cellular outputs remains unclear. Using a synthetic tool, we selectively activate the ISR without co-activation of parallel pathways and define the resulting cellular state with multi-omics profiling. We identify time- and dose-dependent gene expression modules, with ATF4 driving only a small but sensitive subgroup that includes amino acid metabolic enzymes. This ATF4 response affects cellular bioenergetics, rerouting carbon utilization towards amino acid production and away from the tricarboxylic acid cycle and fatty acid synthesis. We also find an ATF4-independent reorganization of the lipidome that promotes DGAT-dependent triglyceride synthesis and accumulation of lipid droplets. While DGAT1 is the main driver of lipid droplet biogenesis, DGAT2 plays an essential role in buffering stress and maintaining cell survival. Together, we demonstrate the sufficiency of the ISR in promoting a previously unappreciated metabolic state.
    DOI:  https://doi.org/10.1038/s41467-024-52538-5
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