bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021‒08‒08
fifty-seven papers selected by
Catalina Vasilescu
University of Helsinki
  1. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain.
  2. Mitochondria Can Cross Cell Boundaries: An Overview of the Biological Relevance, Pathophysiological Implications and Therapeutic Perspectives of Intercellular Mitochondrial Transfer.
  3. Instability in NAD+ metabolism leads to impaired cardiac mitochondrial function and communication.
  4. Role of PITRM1 in Mitochondrial Dysfunction and Neurodegeneration.
  5. Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse.
  6. Mff oligomerization is required for Drp1 activation and synergy with actin filaments during mitochondrial division.
  7. Molecular Insights into Mitochondrial Protein Translocation and Human Disease.
  8. UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae.
  9. Distinct Mitochondrial Pathologies Caused by Mutations of the Proximal Tubular Enzymes EHHADH and GATM.
  10. The Roles of Assembly Factors in Mammalian Mitoribosome Biogenesis.
  11. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder.
  12. Exploring the Ability of LARS2 Carboxy-Terminal Domain in Rescuing the MELAS Phenotype.
  13. Human Mitochondrial RNA Processing and Modifications: Overview.
  14. The Diagnostic Approach to Mitochondrial Disorders in Children in the Era of Next-Generation Sequencing: A 4-Year Cohort Study.
  15. The human cytomegalovirus protein pUL13 targets mitochondrial cristae architecture to increase cellular respiration during infection.
  16. Longitudinal tracking of neuronal mitochondria delineates PINK1/Parkin-dependent mechanisms of mitochondrial recycling and degradation.
  17. Pharmacological rescue of impaired mitophagy in Parkinson's disease-related LRRK2 G2019S knock-in mice.
  18. FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply.
  19. Apoptosis regulation at the mitochondria membrane level.
  20. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones.
  21. Functional Diversity of Mitochondrial Peptidyl-tRNA Hydrolase ICT1 in Human Cells.
  22. HPDL deficiency causes a neuromuscular disease by impairing the mitochondrial respiration.
  23. MICU1 opens the gates to cold-induced death.
  24. Mitochondrial Dynamics and Mitophagy in Skeletal Muscle Health and Aging.
  25. Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases.
  26. PTPMT1 Is Required for Embryonic Cardiac Cardiolipin Biosynthesis to Regulate Mitochondrial Morphogenesis and Heart Development.
  27. Mitochondrial Mutations in Multiple Sclerosis Patients with Atypical Optic Neuropathy.
  28. Minimal mitochondrial respiration is required to prevent cell death by inhibition of mTOR signaling in CoQ-deficient cells.
  29. Circulating Cell-Free Mitochondrial DNA in Cerebrospinal Fluid as a Biomarker for Mitochondrial Diseases.
  30. Oxidative bursts of single mitochondria mediate retrograde signaling toward the ER.
  31. iDeepSubMito: identification of protein submitochondrial localization with deep learning.
  32. Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissue.
  33. Fluorescent Materials for Monitoring Mitochondrial Biology.
  34. Molecular functions of autophagy adaptors upon ubiquitin-driven mitophagy.
  35. Mitophagy: At the heart of mitochondrial quality control in cardiac aging and frailty.
  36. Mitochondrial UPR through generations.
  37. Fis1 ablation in the male germline disrupts mitochondrial morphology and mitophagy, and arrests spermatid maturation.
  38. The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels.
  39. Clinical presentation and natural history of Barth Syndrome: An Overview.
  40. Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase.
  41. Linking genome variants to disease: Scalable approaches to test the functional impact of human mutations.
  42. Mutated CCDC51 Coding for a Mitochondrial Protein, MITOK Is a Candidate Gene Defect for Autosomal Recessive Rod-Cone Dystrophy.
  43. The Role of Voltage-Dependent Anion Channel in Mitochondrial Dysfunction and Human Disease.
  44. Targeting Mitochondrial Biogenesis with Polyphenol Compounds.
  45. A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation.
  46. Impact of aging and exercise on skeletal muscle mitochondrial capacity, energy metabolism, and physical function.
  47. Complexome Profiling: Assembly and Remodeling of Protein Complexes.
  48. Alterations in mitochondrial morphology as a key driver of immunity and host defence.
  49. Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca2+ homeostasis with adipose tissue lipolysis.
  50. Site-specific acetylation of adenine nucleotide translocase 1 at lysine 23 in human muscle.
  51. Expanding the phenotype of AFG3L2 mutations: Late-onset autosomal recessive spinocerebellar ataxia.
  52. Mammalian Target of Rapamycin Signaling Pathway Regulates Mitochondrial Quality Control of Brown Adipocytes in Mice.
  53. Selective mitochondrial antioxidant MitoTEMPO reduces renal dysfunction and systemic inflammation in experimental sepsis.
  54. Specific splice junction detection in single cells with SICILIAN.
  55. ACO2 clinicobiological dataset with extensive phenotype ontology annotation.
  56. Synergistic deoxynucleoside and gene therapies for thymidine kinase 2 deficiency.
  57. The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health.
  1. Int J Mol Sci. 2021 Aug 03. pii: 8325. [Epub ahead of print]22(15):
    Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain.
    Paola Zanfardino, Stefano Doccini, Filippo M Santorelli, Vittoria Petruzzella.
      Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
    Keywords:  OxPhos complexes; bioenergetics; genomics; mitochondria; mitochondrial DNA; mitochondrial diseases; nervous tissue; proteomics
    DOI:  https://doi.org/10.3390/ijms22158325
  2. Int J Mol Sci. 2021 Aug 02. pii: 8312. [Epub ahead of print]22(15):
    Mitochondria Can Cross Cell Boundaries: An Overview of the Biological Relevance, Pathophysiological Implications and Therapeutic Perspectives of Intercellular Mitochondrial Transfer.
    Daniela Valenti, Rosa Anna Vacca, Loredana Moro, Anna Atlante.
      Mitochondria are complex intracellular organelles traditionally identified as the powerhouses of eukaryotic cells due to their central role in bioenergetic metabolism. In recent decades, the growing interest in mitochondria research has revealed that these multifunctional organelles are more than just the cell powerhouses, playing many other key roles as signaling platforms that regulate cell metabolism, proliferation, death and immunological response. As key regulators, mitochondria, when dysfunctional, are involved in the pathogenesis of a wide range of metabolic, neurodegenerative, immune and neoplastic disorders. Far more recently, mitochondria attracted renewed attention from the scientific community for their ability of intercellular translocation that can involve whole mitochondria, mitochondrial genome or other mitochondrial components. The intercellular transport of mitochondria, defined as horizontal mitochondrial transfer, can occur in mammalian cells both in vitro and in vivo, and in physiological and pathological conditions. Mitochondrial transfer can provide an exogenous mitochondrial source, replenishing dysfunctional mitochondria, thereby improving mitochondrial faults or, as in in the case of tumor cells, changing their functional skills and response to chemotherapy. In this review, we will provide an overview of the state of the art of the up-to-date knowledge on intercellular trafficking of mitochondria by discussing its biological relevance, mode and mechanisms underlying the process and its involvement in different pathophysiological contexts, highlighting its therapeutic potential for diseases with mitochondrial dysfunction primarily involved in their pathogenesis.
    Keywords:  bioenergetics; cancer; ccf-mtDNA; extracellular mitochondria; extracellular mitovesicles; immune-metabolic regulation; intercellular mitochondria trafficking; mitochondria; mitochondrial transplantation; neurodegenerative diseases; neurodevelopmental disorders; oxidative phosphorylation; tunneling nanotubes
    DOI:  https://doi.org/10.3390/ijms22158312
  3. Elife. 2021 Aug 03. pii: e59828. [Epub ahead of print]10
    Instability in NAD+ metabolism leads to impaired cardiac mitochondrial function and communication.
    Knut H Lauritzen, Maria Belland Olsen, Mohammed Shakil Ahmed, Kuan Yang, Johanne Egge Rinholm, Linda H Bergersen, Qin Ying Esbensen, Lars Jansen Sverkeli, Mathias Ziegler, Håvard Attramadal, Bente Halvorsen, Pål Aukrust, Arne Yndestad.
      Poly(ADP-ribose) polymerase (PARP) enzymes initiate (mt)DNA repair mechanisms and use nicotinamide adenine dinucleotide (NAD+) as energy source. Prolonged PARP activity can drain cellular NAD+ reserves, leading to de-regulation of important molecular processes. Here, we provide evidence of a pathophysiological mechanism that connects mtDNA damage to cardiac dysfunction via reduced NAD+ levels and loss of mitochondrial function and communication. Using a transgenic model, we demonstrate that high levels of mice cardiomyocyte mtDNA damage cause a reduction in NAD+ levels due to extreme DNA repair activity, causing impaired activation of NAD+-dependent SIRT3. In addition, we show that myocardial mtDNA damage in combination with high dosages of nicotinamideriboside (NR) causes an inhibition of sirtuin activity due to accumulation of nicotinamide (NAM), in addition to irregular cardiac mitochondrial morphology. Consequently, high doses of NR should be used with caution, especially when cardiomyopathic symptoms are caused by mitochondrial dysfunction and instability of mtDNA.
    Keywords:  DNA repair; NAD+; SIRT3; biochemistry; cardiovascular disease; chemical biology; human; mitochondrial dna; mouse; nicotinamide riboside
    DOI:  https://doi.org/10.7554/eLife.59828
  4. Biomedicines. 2021 Jul 17. pii: 833. [Epub ahead of print]9(7):
    Role of PITRM1 in Mitochondrial Dysfunction and Neurodegeneration.
    Dario Brunetti, Alessia Catania, Carlo Viscomi, Michela Deleidi, Laurence A Bindoff, Daniele Ghezzi, Massimo Zeviani.
      Mounting evidence shows a link between mitochondrial dysfunction and neurodegenerative disorders, including Alzheimer Disease. Increased oxidative stress, defective mitodynamics, and impaired oxidative phosphorylation leading to decreased ATP production, can determine synaptic dysfunction, apoptosis, and neurodegeneration. Furthermore, mitochondrial proteostasis and the protease-mediated quality control system, carrying out degradation of potentially toxic peptides and misfolded or damaged proteins inside mitochondria, are emerging as potential pathogenetic mechanisms. The enzyme pitrilysin metallopeptidase 1 (PITRM1) is a key player in these processes; it is responsible for degrading mitochondrial targeting sequences that are cleaved off from the imported precursor proteins and for digesting a mitochondrial fraction of amyloid beta (Aβ). In this review, we present current evidence obtained from patients with PITRM1 mutations, as well as the different cellular and animal models of PITRM1 deficiency, which points toward PITRM1 as a possible driving factor of several neurodegenerative conditions. Finally, we point out the prospect of new diagnostic and therapeutic approaches.
    Keywords:  Alzheimer Disease; PITRM1; mitochondrial dysfunction; mitochondrial protein quality control; mitochondrial proteostasis; neurodegeneration; neurodegenerative dementia; neurodegenerative diseases; pitrilysin metallopeptidase 1; protein aggregation; spinocerebellar ataxia
    DOI:  https://doi.org/10.3390/biomedicines9070833
  5. Neurogenetics. 2021 Aug 03.
    Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse.
    Antonia Maletzko, Jana Key, Ilka Wittig, Suzana Gispert, Gabriele Koepf, Júlia Canet-Pons, Sylvia Torres-Odio, A Phillip West, Georg Auburger.
      Mitochondrial dysfunction may activate innate immunity, e.g. upon abnormal handling of mitochondrial DNA in TFAM mutants or in altered mitophagy. Recent reports showed that also deletion of mitochondrial matrix peptidase ClpP in mice triggers transcriptional upregulation of inflammatory factors. Here, we studied ClpP-null mouse brain at two ages and mouse embryonal fibroblasts, to identify which signaling pathways are responsible, employing mass spectrometry, subcellular fractionation, immunoblots, and reverse transcriptase polymerase chain reaction. Several mitochondrial unfolded protein response factors showed accumulation and altered migration in blue-native gels, prominently the co-chaperone DNAJA3. Its mitochondrial dysregulation increased also its extra-mitochondrial abundance in the nucleus, a relevant observation given that DNAJA3 modulates innate immunity. Similar observations were made for STAT1, a putative DNAJA3 interactor. Elevated expression was observed not only for the transcription factors Stat1/2, but also for two interferon-stimulated genes (Ifi44, Gbp3). Inflammatory responses were strongest for the RLR pattern recognition receptors (Ddx58, Ifih1, Oasl2, Trim25) and several cytosolic nucleic acid sensors (Ifit1, Ifit3, Oas1b, Ifi204, Mnda). The consistent dysregulation of these factors from an early age might influence also human Perrault syndrome, where ClpP loss-of-function leads to early infertility and deafness, with subsequent widespread neurodegeneration.
    Keywords:  Ataxia; Leukodystrophy; MTRNR1; Mitochondrial amino acid tRNA synthetases; POLG; PRLTS3; Release of mtDNA and mtRNA; TWINKLE; cGAS-STING
    DOI:  https://doi.org/10.1007/s10048-021-00657-2
  6. Mol Biol Cell. 2021 Aug 04. mbcE21040224
    Mff oligomerization is required for Drp1 activation and synergy with actin filaments during mitochondrial division.
    Ao Liu, Frieda Kage, Henry N Higgs.
      Mitochondrial division is an important cellular process in both normal and pathological conditions. The dynamin GTPase Drp1 is a central mitochondrial division protein, driving constriction of the outer mitochondrial membrane. In mammals, the outer mitochondrial membrane protein Mff is a key receptor for recruiting Drp1 from the cytosol to the mitochondrion. Actin filaments are also important in Drp1 recruitment and activation. The manner in which Mff and actin work together in Drp1 activation is unknown. Here, we show that Mff is an oligomer (most likely a trimer) that dynamically associates and disassociates through its C-terminal coiled-coil, with a Kd in the range of 10 µM. Dynamic Mff oligomerization is required for Drp1 activation. While not binding Mff directly, actin filaments enhance Mff-mediated Drp1 activation by lowering the effective Mff concentration 10-fold. Total internal reflection microscopy assays using purified proteins show that Mff interacts with Drp1 on actin filaments in a manner dependent on Mff oligomerization. In U2OS cells, oligomerization-defective Mff does not effectively rescue three defects in Mff knock-out cells: mitochondrial division, mitochondrial Drp1 recruitment, and peroxisome division. The ability of Mff to assemble into puncta on mitochondria depends on its oligomerization, as well as on actin filaments and Drp1.
    DOI:  https://doi.org/10.1091/mbc.E21-04-0224
  7. Genes (Basel). 2021 Jul 01. pii: 1031. [Epub ahead of print]12(7):
    Molecular Insights into Mitochondrial Protein Translocation and Human Disease.
    Eduardo Ruiz-Pesini, Julio Montoya, David Pacheu-Grau.
      In human mitochondria, mtDNA encodes for only 13 proteins, all components of the OXPHOS system. The rest of the mitochondrial components, which make up approximately 99% of its proteome, are encoded in the nuclear genome, synthesized in cytosolic ribosomes and imported into mitochondria. Different import machineries translocate mitochondrial precursors, depending on their nature and the final destination inside the organelle. The proper and coordinated function of these molecular pathways is critical for mitochondrial homeostasis. Here, we will review molecular details about these pathways, which components have been linked to human disease and future perspectives on the field to expand the genetic landscape of mitochondrial diseases.
    Keywords:  disease; mitochondria; protein import
    DOI:  https://doi.org/10.3390/genes12071031
  8. Nat Commun. 2021 Aug 06. 12(1): 4769
    UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae.
    Zachary A Kemmerer, Kyle P Robinson, Jonathan M Schmitz, Mateusz Manicki, Brett R Paulson, Adam Jochem, Paul D Hutchins, Joshua J Coon, David J Pagliarini.
      Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is mobilized from its site of synthesis on the inner mitochondrial membrane to other sites of action remains a longstanding mystery. Here, using a combination of Saccharomyces cerevisiae genetics, biochemical fractionation, and lipid profiling, we identify two highly conserved but poorly characterized mitochondrial proteins, Ypl109c (Cqd1) and Ylr253w (Cqd2), that reciprocally affect this process. Loss of Cqd1 skews cellular CoQ distribution away from mitochondria, resulting in markedly enhanced resistance to oxidative stress caused by exogenous polyunsaturated fatty acids, whereas loss of Cqd2 promotes the opposite effects. The activities of both proteins rely on their atypical kinase/ATPase domains, which they share with Coq8-an essential auxiliary protein for CoQ biosynthesis. Overall, our results reveal protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.
    DOI:  https://doi.org/10.1038/s41467-021-25084-7
  9. Front Physiol. 2021 ;12 715485
    Distinct Mitochondrial Pathologies Caused by Mutations of the Proximal Tubular Enzymes EHHADH and GATM.
    Anna-Lena Forst, Markus Reichold, Robert Kleta, Richard Warth.
      The mitochondria of the proximal tubule are essential for providing energy in this nephron segment, whose ATP generation is almost exclusively oxygen dependent. In addition, mitochondria are involved in a variety of metabolic processes and complex signaling networks. Proximal tubular mitochondrial dysfunction can therefore affect renal function in very different ways. Two autosomal dominantly inherited forms of renal Fanconi syndrome illustrate how multifaceted mitochondrial pathology can be: Mutation of EHHADH, an enzyme in fatty acid metabolism, results in decreased ATP synthesis and a consecutive transport defect. In contrast, mutations of GATM, an enzyme in the creatine biosynthetic pathway, leave ATP synthesis unaffected but do lead to mitochondrial protein aggregates, inflammasome activation, and renal fibrosis with progressive renal failure. In this review article, the distinct pathophysiological mechanisms of these two diseases are presented, which are examples of the spectrum of proximal tubular mitochondrial diseases.
    Keywords:  autosomal dominant mutation; inflammasome; mitochondrial damage associated molecular patterns; peroxisome; protein aggregates; renal fibrosis
    DOI:  https://doi.org/10.3389/fphys.2021.715485
  10. Mitochondrion. 2021 Jul 30. pii: S1567-7249(21)00101-X. [Epub ahead of print]
    The Roles of Assembly Factors in Mammalian Mitoribosome Biogenesis.
    Taru Hilander, Christopher B Jackson, Marius Robciuc, Tanzeela Bashir, Hongxia Zhao.
      As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
    Keywords:  mitochondrial translation; mitoribosome assembly factors; mitoribosome biogenesis
    DOI:  https://doi.org/10.1016/j.mito.2021.07.008
  11. EMBO Rep. 2021 Aug 05. e51991
    The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder.
    Esther Nuebel, Jeffrey T Morgan, Sarah Fogarty, Jacob M Winter, Sandra Lettlova, Jordan A Berg, Yu-Chan Chen, Chelsea U Kidwell, J Alan Maschek, Katie J Clowers, Catherine Argyriou, Lingxiao Chen, Ilka Wittig, James E Cox, Minna Roh-Johnson, Nancy Braverman, Joshua Bonkowsky, Steven P Gygi, Jared Rutter.
      Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.
    Keywords:  mitochondria; mitochondrial quality control; peroxisomal biogenesis disorder; peroxisomal import; peroxisomes
    DOI:  https://doi.org/10.15252/embr.202051991
  12. Life (Basel). 2021 Jul 10. pii: 674. [Epub ahead of print]11(7):
    Exploring the Ability of LARS2 Carboxy-Terminal Domain in Rescuing the MELAS Phenotype.
    Francesco Capriglia, Francesca Rizzo, Giuseppe Petrosillo, Veronica Morea, Giulia d'Amati, Palmiro Cantatore, Marina Roberti, Paola Loguercio Polosa, Francesco Bruni.
      The m.3243A>G mutation within the mitochondrial mt-tRNALeu(UUR) gene is the most prevalent variant linked to mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome. This pathogenic mutation causes severe impairment of mitochondrial protein synthesis due to alterations of the mutated tRNA, such as reduced aminoacylation and a lack of post-transcriptional modification. In transmitochondrial cybrids, overexpression of human mitochondrial leucyl-tRNA synthetase (LARS2) has proven effective in rescuing the phenotype associated with m.3243A>G substitution. The rescuing activity resides in the carboxy-terminal domain (Cterm) of the enzyme; however, the precise molecular mechanisms underlying this process have not been fully elucidated. To deepen our knowledge on the rescuing mechanisms, we demonstrated the interactions of the Cterm with mutated mt-tRNALeu(UUR) and its precursor in MELAS cybrids. Further, the effect of Cterm expression on mitochondrial functions was evaluated. We found that Cterm ameliorates de novo mitochondrial protein synthesis, whilst it has no effect on mt-tRNALeu(UUR) steady-state levels and aminoacylation. Despite the complete recovery of cell viability and the increase in mitochondrial translation, Cterm-overexpressing cybrids were not able to recover bioenergetic competence. These data suggest that, in our MELAS cell model, the beneficial effect of Cterm may be mediated by factors that are independent of the mitochondrial bioenergetics.
    Keywords:  Cterm; LARS2; MELAS; aminoacyl-tRNA synthetases; mitochondrial disease; therapeutic peptides; transmitochondrial cybrids
    DOI:  https://doi.org/10.3390/life11070674
  13. Int J Mol Sci. 2021 Jul 27. pii: 7999. [Epub ahead of print]22(15):
    Human Mitochondrial RNA Processing and Modifications: Overview.
    Marta Jedynak-Slyvka, Agata Jabczynska, Roman J Szczesny.
      Mitochondria, often referred to as the powerhouses of cells, are vital organelles that are present in almost all eukaryotic organisms, including humans. They are the key energy suppliers as the site of adenosine triphosphate production, and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune response. Abnormalities occurring in mitochondria, such as mitochondrial DNA (mtDNA) mutations and disturbances at any stage of mitochondrial RNA (mtRNA) processing and translation, usually lead to severe mitochondrial diseases. A fundamental line of investigation is to understand the processes that occur in these organelles and their physiological consequences. Despite substantial progress that has been made in the field of mtRNA processing and its regulation, many unknowns and controversies remain. The present review discusses the current state of knowledge of RNA processing in human mitochondria and sheds some light on the unresolved issues.
    Keywords:  RNA decay; RNA modifications; RNA processing; mitochondria; mitochondrial genome; mitochondrial transcription
    DOI:  https://doi.org/10.3390/ijms22157999
  14. J Clin Med. 2021 Jul 22. pii: 3222. [Epub ahead of print]10(15):
    The Diagnostic Approach to Mitochondrial Disorders in Children in the Era of Next-Generation Sequencing: A 4-Year Cohort Study.
    Deborah Tolomeo, Daniele Orsucci, Claudia Nesti, Jacopo Baldacci, Roberta Battini, Claudio Bruno, Giorgia Bruno, Denise Cassandrini, Stefano Doccini, M Alice Donati, Annarita Ferrari, Simona Fiori, Chiara Fiorillo, Renzo Guerrini, Francesco Mari, Martino Montomoli, Francesca Pochiero, Elena Procopio, Lucia Ruggiero, Simone Sampaolo, Federico Sicca, Chiara Ticci, Anna Rubegni, Filippo M Santorelli.
      Mitochondrial diseases (MDs) are a large group of genetically determined multisystem disorders, characterized by extreme phenotypic heterogeneity, attributable in part to the dual genomic control (nuclear and mitochondrial DNA) of the mitochondrial proteome. Advances in next-generation sequencing technologies over the past two decades have presented clinicians with a challenge: to select the candidate disease-causing variants among the huge number of data provided. Unfortunately, the clinical tools available to support genetic interpretations still lack specificity and sensitivity. For this reason, the diagnosis of MDs continues to be difficult, with the new "genotype first" approach still failing to diagnose a large group of patients. With the aim of investigating possible relationships between clinical and/or biochemical phenotypes and definitive molecular diagnoses, we performed a retrospective multicenter study of 111 pediatric patients with clinical suspicion of MD. In this cohort, the strongest predictor of a molecular (in particular an mtDNA-related) diagnosis of MD was neuroimaging evidence of basal ganglia (BG) involvement. Regression analysis confirmed that normal BG imaging predicted negative genetic studies for MD. Psychomotor regression was confirmed as an independent predictor of a definitive diagnosis of MD. The findings of this study corroborate previous data supporting a role for neuroimaging in the diagnostic approach to MDs and reinforce the idea that mtDNA sequencing should be considered for first-line testing, at least in specific groups of children.
    Keywords:  MRI; basal ganglia; diagnostic approach; mitochondrial disorders; mtDNA; muscle biopsy; nDNA; next-generation sequencing
    DOI:  https://doi.org/10.3390/jcm10153222
  15. Proc Natl Acad Sci U S A. 2021 Aug 10. pii: e2101675118. [Epub ahead of print]118(32):
    The human cytomegalovirus protein pUL13 targets mitochondrial cristae architecture to increase cellular respiration during infection.
    Cora N Betsinger, Connor S R Jankowski, William A Hofstadter, Joel D Federspiel, Clayton J Otter, Pierre M Jean Beltran, Ileana M Cristea.
      Viruses modulate mitochondrial processes during infection to increase biosynthetic precursors and energy output, fueling virus replication. In a surprising fashion, although it triggers mitochondrial fragmentation, the prevalent pathogen human cytomegalovirus (HCMV) increases mitochondrial metabolism through a yet-unknown mechanism. Here, we integrate molecular virology, metabolic assays, quantitative proteomics, and superresolution confocal microscopy to define this mechanism. We establish that the previously uncharacterized viral protein pUL13 is required for productive HCMV replication, targets the mitochondria, and functions to increase oxidative phosphorylation during infection. We demonstrate that pUL13 forms temporally tuned interactions with the mitochondrial contact site and cristae organizing system (MICOS) complex, a critical regulator of cristae architecture and electron transport chain (ETC) function. Stimulated emission depletion superresolution microscopy shows that expression of pUL13 alters cristae architecture. Indeed, using live-cell Seahorse assays, we establish that pUL13 alone is sufficient to increase cellular respiration, not requiring the presence of other viral proteins. Our findings address the outstanding question of how HCMV targets mitochondria to increase bioenergetic output and expands the knowledge of the intricate connection between mitochondrial architecture and ETC function.
    Keywords:  HCMV; metabolism; mitochondria; pUL13; proteomics
    DOI:  https://doi.org/10.1073/pnas.2101675118
  16. Sci Adv. 2021 Aug;pii: eabf6580. [Epub ahead of print]7(32):
    Longitudinal tracking of neuronal mitochondria delineates PINK1/Parkin-dependent mechanisms of mitochondrial recycling and degradation.
    Huihui Li, Zak Doric, Amandine Berthet, Danielle M Jorgens, Mai K Nguyen, Ivy Hsieh, Julia Margulis, Rebecca Fang, Jayanta Debnath, Hiromi Sesaki, Steve Finkbeiner, Eric Huang, Ken Nakamura.
      Altered mitochondrial quality control and dynamics may contribute to neurodegenerative diseases, including Parkinson's disease, but we understand little about these processes in neurons. We combined time-lapse microscopy and correlative light and electron microscopy to track individual mitochondria in neurons lacking the fission-promoting protein dynamin-related protein 1 (Drp1) and delineate the kinetics of PINK1-dependent pathways of mitochondrial quality control. Depolarized mitochondria recruit Parkin to the outer mitochondrial membrane, triggering autophagosome formation, rapid lysosomal fusion, and Parkin redistribution. Unexpectedly, these mitolysosomes are dynamic and persist for hours. Some are engulfed by healthy mitochondria, and others are deacidified before bursting. In other cases, Parkin is directly recruited to the matrix of polarized mitochondria. Loss of PINK1 blocks Parkin recruitment, causes LC3 accumulation within mitochondria, and exacerbates Drp1KO toxicity to dopamine neurons. These results define a distinct neuronal mitochondrial life cycle, revealing potential mechanisms of mitochondrial recycling and signaling relevant to neurodegeneration.
    DOI:  https://doi.org/10.1126/sciadv.abf6580
  17. Elife. 2021 Aug 03. pii: e67604. [Epub ahead of print]10
    Pharmacological rescue of impaired mitophagy in Parkinson's disease-related LRRK2 G2019S knock-in mice.
    Francois Singh, Alan R Prescott, Philippa Rosewell, Graeme Ball, Alastair D Reith, Ian G Ganley.
      Parkinson's disease (PD) is a major and progressive neurodegenerative disorder, yet the biological mechanisms involved in its aetiology are poorly understood. Evidence links this disorder with mitochondrial dysfunction and/or impaired lysosomal degradation - key features of the autophagy of mitochondria, known as mitophagy. Here, we investigated the role of LRRK2, a protein kinase frequently mutated in PD, in this process in vivo. Using mitophagy and autophagy reporter mice, bearing either knockout of LRRK2 or expressing the pathogenic kinase-activating G2019S LRRK2 mutation, we found that basal mitophagy was specifically altered in clinically relevant cells and tissues. Our data show that basal mitophagy inversely correlates with LRRK2 kinase activity in vivo. In support of this, use of distinct LRRK2 kinase inhibitors in cells increased basal mitophagy, and a CNS penetrant LRRK2 kinase inhibitor, GSK3357679A, rescued the mitophagy defects observed in LRRK2 G2019S mice. This study provides the first in vivo evidence that pathogenic LRRK2 directly impairs basal mitophagy, a process with strong links to idiopathic Parkinson's disease, and demonstrates that pharmacological inhibition of LRRK2 is a rational mitophagy-rescue approach and potential PD therapy.
    Keywords:  LRRK2; Mitophagy; cell biology; kinase inhibitor; mito-QC; mouse; neuroscience; parkinson's disease
    DOI:  https://doi.org/10.7554/eLife.67604
  18. J Cell Biol. 2021 Oct 04. pii: e201912077. [Epub ahead of print]220(10):
    FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply.
    Himanish Basu, Gulcin Pekkurnaz, Jill Falk, Wei Wei, Morven Chin, Judith Steen, Thomas L Schwarz.
      Mitochondrial movement and distribution are fundamental to their function. Here we report a mechanism that regulates mitochondrial movement by anchoring mitochondria to the F-actin cytoskeleton. This mechanism is activated by an increase in glucose influx and the consequent O-GlcNAcylation of TRAK (Milton), a component of the mitochondrial motor-adaptor complex. The protein four and a half LIM domains protein 2 (FHL2) serves as the anchor. FHL2 associates with O-GlcNAcylated TRAK and is both necessary and sufficient to drive the accumulation of F-actin around mitochondria and to arrest mitochondrial movement by anchoring to F-actin. Disruption of F-actin restores mitochondrial movement that had been arrested by either TRAK O-GlcNAcylation or forced direction of FHL2 to mitochondria. This pathway for mitochondrial immobilization is present in both neurons and non-neuronal cells and can thereby adapt mitochondrial dynamics to changes in glucose availability.
    DOI:  https://doi.org/10.1083/jcb.201912077
  19. Biochim Biophys Acta Biomembr. 2021 Jul 31. pii: S0005-2736(21)00164-4. [Epub ahead of print] 183716
    Apoptosis regulation at the mitochondria membrane level.
    Shashank Dadsena, Louise E King, Ana J García-Sáez.
      Mitochondrial outer membrane permeabilization (MOMP) is a key checkpoint in apoptosis that activates the caspase cascade and irreversibly causes the majority of cells to die. The proteins of the Bcl-2 family are master regulators of apoptosis that form a complex interaction network within the mitochondrial membrane that determines the induction of MOMP. This culminates in the activation of the effector members Bax and Bak, which permeabilize the mitochondrial outer membrane to mediate MOMP. Although the key role of Bax and Bak has been established, many questions remain unresolved regarding molecular mechanisms that control the apoptotic pore. In this review, we discuss the recent progress in our understanding of the regulation of Bax/Bak activity within the mitochondrial membrane.
    Keywords:  Apoptosis; BCL-2 proteins; Lipids; MOMP; Membrane dynamics; Protein-protein interaction
    DOI:  https://doi.org/10.1016/j.bbamem.2021.183716
  20. Mol Genet Genomic Med. 2021 Aug 04. e1749
    Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones.
    M Reza Jabalameli, Fiona M Fitzpatrick, Roberto Colombo, Sarah A Howles, Gary Leggatt, Valerie Walker, Akira Wiberg, Edmund R S Kunji, Sarah Ennis.
      BACKGROUND: Calcium kidney stones are common and recurrences are often not preventable by available empiric remedies. Their etiology is multifactorial and polygenic, and an increasing number of genes are implicated. Their identification will enable improved management.METHODS: DNA from three stone-formers in a Southampton family (UK) and two from an Italian family were analyzed independently by whole exome sequencing and selected variants were genotyped across all available members of both pedigrees. A disease variant of SLC25A25 (OMIM 608745), encoding the mitochondrial ATP-Mg/Pi carrier 3 (APC3) was identified, and analyzed structurally and functionally with respect to its calcium-regulated transport activity.
    RESULTS: All five patients had a heterozygous dominant SLC25A25 variant (rs140777921; GRCh37.p13: chr 9 130868670 G>C; p.Gln349His; Reference Sequence NM_001006641.3). Non-stone formers also carried the variant indicating incomplete penetrance. Modeling suggests that the variant lacks a conserved polar interaction, which may cause structural instability. Calcium-regulated ATP transport was reduced to ~20% of the wild type, showing a large reduction in function.
    CONCLUSION: The transporter is important in regulating mitochondrial ATP production. This rare variant may increase urine lithogenicity through impaired provision of ATP for solute transport processes in the kidney, and/or for purinergic signaling. Variants found in other genes may compound this abnormality.
    Keywords:  calcium kidney stones; calcium signaling; mitochondrial adenine nucleotide metastasis; mitochondrial transporter; purinergic signaling
    DOI:  https://doi.org/10.1002/mgg3.1749
  21. Front Mol Biosci. 2021 ;8 716885
    Functional Diversity of Mitochondrial Peptidyl-tRNA Hydrolase ICT1 in Human Cells.
    I V Chicherin, S V Dukhalin, R A Khannanov, M V Baleva, S A Levitskii, M V Patrushev, P V Sergiev, P Kamenski.
      Mitochondria are energy producing organelles of the eukaryotic cell, involved in the synthesis of key metabolites, calcium homeostasis and apoptosis. Protein biosynthesis in these organelles is a relic of its endosymbiotic origin. While mitochondrial translational factors have homologues among prokaryotes, they possess a number of unique traits. Remarkably as many as four mammalian mitochondrial proteins possess a clear similarity with translation termination factors. The review focuses on the ICT1, which combines several functions. It is a non-canonical termination factor for protein biosynthesis, a rescue factor for stalled mitochondrial ribosomes, a structural protein and a regulator of proliferation, cell cycle, and apoptosis. Such a diversity of roles demonstrates the high functionality of mitochondrial translation associated proteins and their relationship with numerous processes occurring in a living cell.
    Keywords:  apoptosis; cell cycle; mitochondria; proliferation; regulation; ribosome, signaling; termination; translation
    DOI:  https://doi.org/10.3389/fmolb.2021.716885
  22. J Genet Genomics. 2021 Jun 17. pii: S1673-8527(21)00162-4. [Epub ahead of print]
    HPDL deficiency causes a neuromuscular disease by impairing the mitochondrial respiration.
    Yu Sun, Xiujuan Wei, Fang Fang, Yiping Shen, Haiyan Wei, Jiuwei Li, Xianglai Ye, Yongkun Zhan, Xiantao Ye, Xiaomin Liu, Wei Yang, Yuhua Li, Xiangju Geng, Xuelin Huang, Yiyan Ruan, Zailong Qin, Shang Yi, Jianxin Lyu, Hezhi Fang, Yongguo Yu.
      Mitochondrial diseases are caused by variants in both mitochondrial and nuclear genomes. A nuclear gene HPDL (4-hydroxyphenylpyruvate dioxygenase-like), which encodes an intermembrane mitochondrial protein, has been recently implicated in causing a neurodegenerative disease characterized by pediatric-onset spastic movement phenotypes. Here, we report six Chinese patients with bi-allelic HPDL pathogenic variants from four unrelated families showing neuropathic symptoms of variable severity, including developmental delay/intellectual disability, spasm, and hypertonia. Seven different pathogenic variants are identified, of which five are novel. Both fibroblasts and immortalized lymphocytes derived from patients show impaired mitochondrial respiratory function, which is also observed in HPDL-knockdown (KD) HeLa cells. In these HeLa cells, overexpression of a wild-type HPDL gene can rescue the respiratory phenotype of oxygen consumption rate. In addition, a decreased activity of the oxidative phosphorylation (OXPHOS) complex II is observed in patient-derived lymphocytes and HPDL-KD HeLa cells, further supporting an essential role of HPDL in the mitochondrial respiratory chain. Collectively, our data expand the clinical and mutational spectra of this mitochondrial neuropathy and further delineate the possible disease mechanism involving the impairment of the OXPHOS complex II activity due to the bi-allelic inactivations of HPDL.
    Keywords:  HPDL gene; Mitochondrial disease; OXPHOS; Respiration chain complex II; Respiration impairment
    DOI:  https://doi.org/10.1016/j.jgg.2021.01.009
  23. Cell Calcium. 2021 Jul 27. pii: S0143-4160(21)00105-6. [Epub ahead of print]98 102451
    MICU1 opens the gates to cold-induced death.
    Felicia Dietsche, Li Zhang, John W Elrod, Axel Methner.
      Nakamura et al. recently discovered that the mitochondrial calcium uniporter gatekeeper, MICU1, is required for cold-induced ferroptotic cell death by modulating mitochondrial membrane potential. This function appears to be independent of its Ca2+-sensing ability. Here, we discuss their findings and suggest next steps to define MICU1's role in ferroptotic cell death.
    DOI:  https://doi.org/10.1016/j.ceca.2021.102451
  24. Int J Mol Sci. 2021 Jul 30. pii: 8179. [Epub ahead of print]22(15):
    Mitochondrial Dynamics and Mitophagy in Skeletal Muscle Health and Aging.
    Jean-Philippe Leduc-Gaudet, Sabah N A Hussain, Esther Barreiro, Gilles Gouspillou.
      The maintenance of mitochondrial integrity is critical for muscle health. Mitochondria, indeed, play vital roles in a wide range of cellular processes, including energy supply, Ca2+ homeostasis, retrograde signaling, cell death, and many others. All mitochondria-containing cells, including skeletal muscle cells, dispose of several pathways to maintain mitochondrial health, including mitochondrial biogenesis, mitochondrial-derived vesicles, mitochondrial dynamics (fusion and fission process shaping mitochondrial morphology), and mitophagy-the process in charge of the removal of mitochondria though autophagy. The loss of skeletal muscle mass (atrophy) is a major health problem worldwide, especially in older people. Currently, there is no treatment to counteract the progressive decline in skeletal muscle mass and strength that occurs with aging, a process termed sarcopenia. There is increasing data, including our own, suggesting that accumulation of dysfunctional mitochondria contributes to the development of sarcopenia. Impairments in mitochondrial dynamics and mitophagy were recently proposed to contribute to sarcopenia. This review summarizes the current state of knowledge on the role played by mitochondrial dynamics and mitophagy in skeletal muscle health and in the development of sarcopenia. We also highlight recent studies showing that enhancing mitophagy in skeletal muscle is a promising therapeutic target to prevent or even treat skeletal muscle dysfunction in the elderly.
    Keywords:  aging; autophagy; mitochondrial dynamics; mitophagy; sarcopenia; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms22158179
  25. Int J Mol Sci. 2021 Jul 28. pii: 8077. [Epub ahead of print]22(15):
    Mitochondrial HSP70 Chaperone System-The Influence of Post-Translational Modifications and Involvement in Human Diseases.
    Henrieta Havalová, Gabriela Ondrovičová, Barbora Keresztesová, Jacob A Bauer, Vladimír Pevala, Eva Kutejová, Nina Kunová.
      Since their discovery, heat shock proteins (HSPs) have been identified in all domains of life, which demonstrates their importance and conserved functional role in maintaining protein homeostasis. Mitochondria possess several members of the major HSP sub-families that perform essential tasks for keeping the organelle in a fully functional and healthy state. In humans, the mitochondrial HSP70 chaperone system comprises a central molecular chaperone, mtHSP70 or mortalin (HSPA9), which is actively involved in stabilizing and importing nuclear gene products and in refolding mitochondrial precursor proteins, and three co-chaperones (HSP70-escort protein 1-HEP1, tumorous imaginal disc protein 1-TID-1, and Gro-P like protein E-GRPE), which regulate and accelerate its protein folding functions. In this review, we summarize the roles of mitochondrial molecular chaperones with particular focus on the human mtHsp70 and its co-chaperones, whose deregulated expression, mutations, and post-translational modifications are often considered to be the main cause of neurological disorders, genetic diseases, and malignant growth.
    Keywords:  GRPE; HEP1; TID-1; cancer; mitochondrial chaperones; mortalin; mtHSP70; neurodegenerative disorders; post-translational modification; protein quality control
    DOI:  https://doi.org/10.3390/ijms22158077
  26. Circulation. 2021 Aug 03. 144(5): 403-406
    PTPMT1 Is Required for Embryonic Cardiac Cardiolipin Biosynthesis to Regulate Mitochondrial Morphogenesis and Heart Development.
    Ze'e Chen, Siting Zhu, Hong Wang, Li Wang, Jianlin Zhang, Yusu Gu, Changming Tan, Mehul Dhanani, Eric Wever, Xinru Wang, Boyu Xie, Shijia Wang, Lei Huang, Antoine H C van Kampen, Jie Liu, Zhen Han, Hemal H Patel, Frédéric M Vaz, Xi Fang, Ju Chen, Kunfu Ouyang.
      
    Keywords:  cardiolipins; mitochondria; mitochondrial membranes; myocytes, cardiac; protein tyrosine phosphatases
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.121.054768
  27. Mult Scler Relat Disord. 2021 Jul 25. pii: S2211-0348(21)00433-8. [Epub ahead of print]55 103166
    Mitochondrial Mutations in Multiple Sclerosis Patients with Atypical Optic Neuropathy.
    Yesim Beckmann, Cihat Uzunköprü, Aslı Subaşıoğlu.
      BACKGROUND: Multiple sclerosis-related optic neuritis is mostly associated with good recovery. The aim of this study was to investigate the causes of progressive visual worsening in multiple sclerosis patients despite treatment.METHODS: We retrospectively reviewed the medical records of multiple sclerosis patients with optic neuritis admitted to the ward of our Neurology Department between 2001 and 2020. The patients with unilateral/bilateral progressive visual loss or non-substantial recovery of visual acuity were screened for genetic testing for Leber's hereditary optic neuropathy.
    RESULTS: Of 1014 multiple sclerosis patients, 411 (39%) reported having optic neuritis. During follow-up, 11 patients manifested atypical characteristics of multiple sclerosis-related optic neuritis (presence of one of the following clinical findings: bilateral simultaneous or sequential eye involvement, progressive visual loss, or no response to corticosteroids during hospitalization), while others presented with typical multiple sclerosis-related optic neuritis. Those multiple sclerosis patients with atypical characteristics of optic neuritis were screened for other possible etiologies of optic neuropathy. We found pathogenic mitochondrial mutations in 5 patients with multiple sclerosis in our study group.
    CONCLUSION: In our study group, the prevalence of mitochondrial mutations among all multiple sclerosis patients with optic neuritis was 0.12%. We strongly recommend investigating Leber's hereditary optic neuropathy mutations in MS patients if they suffer from severe or bilateral visual loss without recovery during follow-up. Because Leber's hereditary optic neuropathy mitochondrial mutations indicate relatively poor visual prognosis and have important implications for genetic counseling.
    Keywords:  Harding's syndrome; Leber's hereditary optic neuropathy; Multiple sclerosis
    DOI:  https://doi.org/10.1016/j.msard.2021.103166
  28. Cell Death Discov. 2021 Aug 04. 7(1): 201
    Minimal mitochondrial respiration is required to prevent cell death by inhibition of mTOR signaling in CoQ-deficient cells.
    Ying Wang, Siegfried Hekimi.
      Coenzyme Q (CoQ) is a lipid-like mobile electron transporter of the mitochondrial respiratory chain. Patients with partial loss-of-function mutations in the CoQ biosynthesis pathway suffer from partial primary CoQ deficiency (MIM 607426). This leads to mitochondrial dysfunction, which presents like mitochondrial disease syndrome (MDS). In addition, many other conditions, including MDS itself, lead to secondary CoQ deficiency. We sought to identify drugs that can alleviate the consequences of the mitochondrial dysfunction that is associated with CoQ deficiency. Loss of the CoQ-biosynthetic enzyme COQ7 prevents CoQ synthesis but leads to the accumulation of the biosynthetic intermediate demethoxyubiquinone (DMQ). Coq7-knockout mouse embryonic fibroblasts (MEFs) die when rapid ATP generation from glycolysis is prevented. We screened for drugs that could rescue cell death under these conditions. All compounds that were identified inhibit mTOR signaling. In the CoQ-deficient cells, the beneficial action mTOR inhibition appears to be mediated by inhibition of protein translation rather than by stimulation of autophagy. We further studied the Coq7-knockout cells to better determine under which conditions mTOR inhibition could be beneficial. We established that Coq7-knockout cells remain capable of a low level of mitochondrial respiration mediated by DMQ. To obtain more profound mitochondrial dysfunction, we created double-knockout mutant MEFs lacking both Coq7, as well as Pdss2, which is required for sidechain synthesis. These cells make neither CoQ nor DMQ, and their extremely small residual respiration depends on uptake of CoQ from the culture medium. Although these cells are healthy in the presence of sufficient glucose for glycolysis and do not require uridine or pyruvate supplementation, mTOR inhibitors were unable to prevent their death in the absence of sufficient glycolysis. We conclude that, for reasons that remain to be elucidated, the energy-sparing benefits of the inhibition of mTOR signaling require a minimally functional respiratory chain.
    DOI:  https://doi.org/10.1038/s41420-021-00591-0
  29. Clin Chem. 2021 Aug 05. 67(8): 1113-1121
    Circulating Cell-Free Mitochondrial DNA in Cerebrospinal Fluid as a Biomarker for Mitochondrial Diseases.
    Selena Trifunov, Abraham J Paredes-Fuentes, Carmen Badosa, Anna Codina, Julio Montoya, Eduardo Ruiz-Pesini, Cristina Jou, Glòria Garrabou, Josep M Grau-Junyent, Dèlia Yubero, Raquel Montero, Jordi Muchart, Juan D Ortigoza-Escobar, Maria M O'Callaghan, Andrés Nascimento, Albert Català, Àngels Garcia-Cazorla, Cecilia Jimenez-Mallebrera, Rafael Artuch.
      BACKGROUND: Mitochondrial diseases (MD) are genetic metabolic disorders that impair normal mitochondrial structure or function. The aim of this study was to investigate the status of circulating cell-free mitochondrial DNA (ccfmtDNA) in cerebrospinal fluid (CSF), together with other biomarkers (growth differentiation factor-15 [GDF-15], alanine, and lactate), in a cohort of 25 patients with a molecular diagnosis of MD.METHODS: Measurement of ccfmtDNA was performed by using droplet digital PCR.
    RESULTS: The mean copy number of ccfmtDNA was approximately 6 times higher in the MD cohort compared to the control group; patients with mitochondrial deletion and depletion syndromes (MDD) had the higher levels. We also detected the presence of both wild-type mtDNA and mtDNA deletions in CSF samples of patients with single deletions. Patients with MDD with single deletions had significantly higher concentrations of GDF-15 in CSF than controls, whereas patients with point mutations in mitochondrial DNA presented no statistically significant differences. Additionally, we found a significant positive correlation between ccfmtDNA levels and GDF-15 concentrations (r = 0.59, P = 0.016).
    CONCLUSION: CSF ccfmtDNA levels are significantly higher in patients with MD in comparison to controls and, thus, they can be used as a novel biomarker for MD research. Our results could also be valuable to support the clinical outcome assessment of MD patients.
    Keywords:  cerebrospinal fluid; circulating cell-free mitochondrial DNA; droplet digital PCR; mitochondrial deletion and depletion syndromes; mitochondrial diseases
    DOI:  https://doi.org/10.1093/clinchem/hvab091
  30. Mol Cell. 2021 Jul 27. pii: S1097-2765(21)00583-9. [Epub ahead of print]
    Oxidative bursts of single mitochondria mediate retrograde signaling toward the ER.
    David M Booth, Péter Várnai, Suresh K Joseph, György Hajnóczky.
      The emerging role of mitochondria as signaling organelles raises the question of whether individual mitochondria can initiate heterotypic communication with neighboring organelles. Using fluorescent probes targeted to the endoplasmic-reticulum-mitochondrial interface, we demonstrate that single mitochondria generate oxidative bursts, rapid redox oscillations, confined to the nanoscale environment of the interorganellar contact sites. Using probes fused to inositol 1,4,5-trisphosphate receptors (IP3Rs), we show that Ca2+ channels directly sense oxidative bursts and respond with Ca2+ transients adjacent to active mitochondria. Application of specific mitochondrial stressors or apoptotic stimuli dramatically increases the frequency and amplitude of the oxidative bursts by enhancing transient permeability transition pore openings. Conversely, blocking interface Ca2+ transport via elimination of IP3Rs or mitochondrial calcium uniporter channels suppresses ER-mitochondrial Ca2+ feedback and cell death. Thus, single mitochondria initiate local retrograde signaling by miniature oxidative bursts and, upon metabolic or apoptotic stress, may also amplify signals to the rest of the cell.
    Keywords:  Ca2+ microdomain; Inositol-1,4,5-trisphosphate receptor; Mitochondrial retrograde signaling; Organelle contacts; Redox nanodomain
    DOI:  https://doi.org/10.1016/j.molcel.2021.07.014
  31. Brief Bioinform. 2021 Jul 30. pii: bbab288. [Epub ahead of print]
    iDeepSubMito: identification of protein submitochondrial localization with deep learning.
    Zilong Hou, Yuning Yang, Hui Li, Ka-Chun Wong, Xiangtao Li.
      Mitochondria are membrane-bound organelles containing over 1000 different proteins involved in mitochondrial function, gene expression and metabolic processes. Accurate localization of those proteins in the mitochondrial compartments is critical to their operation. A few computational methods have been developed for predicting submitochondrial localization from the protein sequences. Unfortunately, most of these computational methods focus on employing biological features or evolutionary information to extract sequence features, which greatly limits the performance of subsequent identification. Moreover, the efficiency of most computational models is still under explored, especially the deep learning feature, which is promising but requires improvement. To address these limitations, we propose a novel computational method called iDeepSubMito to predict the location of mitochondrial proteins to the submitochondrial compartments. First, we adopted a coding scheme using the ProteinELMo to model the probability distribution over the protein sequences and then represent the protein sequences as continuous vectors. Then, we proposed and implemented convolutional neural network architecture based on the bidirectional LSTM with self-attention mechanism, to effectively explore the contextual information and protein sequence semantic features. To demonstrate the effectiveness of our proposed iDeepSubMito, we performed cross-validation on two datasets containing 424 proteins and 570 proteins respectively, and consisting of four different mitochondrial compartments (matrix, inner membrane, outer membrane and intermembrane regions). Experimental results revealed that our method outperformed other computational methods. In addition, we tested iDeepSubMito on the M187, M983 and MitoCarta3.0 to further verify the efficiency of our method. Finally, the motif analysis and the interpretability analysis were conducted to reveal novel insights into subcellular biological functions of mitochondrial proteins. iDeepSubMito source code is available on GitHub at https://github.com/houzl3416/iDeepSubMito.
    Keywords:  deep learning; protein sequences; protein submitochondrial localization
    DOI:  https://doi.org/10.1093/bib/bbab288
  32. Cell Rep. 2021 Aug 03. pii: S2211-1247(21)00915-3. [Epub ahead of print]36(5): 109488
    Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissue.
    Althea N Waldhart, Brejnev Muhire, Ben Johnson, Dean Pettinga, Zachary B Madaj, Emily Wolfrum, Holly Dykstra, Vanessa Wegert, J Andrew Pospisilik, Xianlin Han, Ning Wu.
      Hyperglycemia affects over 400 million individuals worldwide. The detrimental health effects are well studied at the tissue level, but the in vivo effects at the organelle level are poorly understood. To establish such an in vivo model, we used mice lacking TXNIP, a negative regulator of glucose uptake. Examining mitochondrial function in brown adipose tissue, we find that TXNIP KO mice have a lower content of polyunsaturated fatty acids (PUFAs) in their membrane lipids, which affects mitochondrial integrity and electron transport chain efficiency and ultimately results in lower mitochondrial heat output. This phenotype can be rescued by a ketogenic diet, confirming the usefulness of this model and highlighting one facet of early cellular damage caused by excess glucose influx.
    Keywords:  BAT; PUFA; TXNIP; cold stress; glucose; ketogenic diet; lipid; mitochondria
    DOI:  https://doi.org/10.1016/j.celrep.2021.109488
  33. Materials (Basel). 2021 Jul 27. pii: 4180. [Epub ahead of print]14(15):
    Fluorescent Materials for Monitoring Mitochondrial Biology.
    Yeonjeong Chu, Jisoo Park, Eunha Kim, Sanghee Lee.
      Mitochondria play important roles in diverse cellular processes such as energy production, cellular metabolism, and apoptosis to promote cell death. To investigate mitochondria-associated biological processes such as structure, dynamics, morphological change, metabolism, and mitophagy, there exists a continuous demand for visualizing and monitoring techniques elucidating mitochondrial biology and disease-relevancy. Due to the advantages of high sensitivity and practicality, fluorescence phenomena have been most widely used as scientific techniques for the visualization of biological phenomena and systems. In this review, we briefly overview the different types of fluorescent materials such as chemical probes, peptide- or protein-based probes, and nanomaterials for monitoring mitochondrial biology.
    Keywords:  fluorescence imaging; fluorescent chemical probes; fluorescent nanosensors; mitochondria; mitochondria-targeting peptides
    DOI:  https://doi.org/10.3390/ma14154180
  34. Biochim Biophys Acta Gen Subj. 2021 Jul 28. pii: S0304-4165(21)00131-8. [Epub ahead of print]1865(10): 129972
    Molecular functions of autophagy adaptors upon ubiquitin-driven mitophagy.
    Koji Yamano, Waka Kojima.
      BACKGROUND: Perturbations in organellar health can lead to an accumulation of unwanted and/or damaged organelles that are toxic to the cell and which can contribute to the onset of neurodegenerative diseases such as Parkinson's disease. Mitochondrial health is particularly critical given the indispensable role the organelle has not only in adenosine triphosphate production but also other metabolic processes. Byproducts of oxidative respiration, such as reactive oxygen species, however, can negatively impact mitochondrial fitness. Consequently, selective degradation of damaged mitochondria, which occurs via a specific autophagic process termed mitophagy, is essential for normal cell maintenance.SCOPE OF REVIEW: Recent accumulating evidence has shown that autophagy adaptors (also referred to as autophagy receptors) play critical roles in connecting ubiquitinated mitochondria with the autophagic machinery of the autophagy-lysosome pathway that is required for degradation. In this review, we focus on our current understanding of the autophagy adaptor mechanisms underlying PINK1/Parkin-driven mitophagy.
    MAJOR CONCLUSIONS: Although autophagy adaptors are canonically defined as proteins that possess ubiquitin-binding domains and ATG8s-binding motifs, the recent identification of novel binding partners has contributed to the development of a more sophisticated model for how autophagy adaptors contribute to the molecular hub that organizes autophagic cargo-degradation.
    GENERAL SIGNIFICANCE: Although mitophagy is recognized as one of the selective autophagy pathways that removes dysfunctional mitochondria, a more nuanced understanding of the interactions connecting autophagy adaptors and their associated proteins is needed to gain deeper insights into the fundamental biological processes underlying human diseases, including neurodegenerative disorders. This review is part of a Special Issue entitled Mitophagy.
    DOI:  https://doi.org/10.1016/j.bbagen.2021.129972
  35. Exp Gerontol. 2021 Aug 03. pii: S0531-5565(21)00290-4. [Epub ahead of print] 111508
    Mitophagy: At the heart of mitochondrial quality control in cardiac aging and frailty.
    Anna Picca, Riccardo Calvani, Hélio José Coelho-Júnior, Emanuele Marzetti.
      Cardiovascular disease is highly prevalent among older adults and poses a huge burden on morbidity, disability, and mortality. The age-related increased vulnerability of the cardiovascular system towards stressors is as a pathophysiological trait of cardiovascular disease. This has been associated with a progressive deterioration of blood vessels and decline in heart function during aging. Cardiomyocytes rely mostly on oxidative metabolism for deploying their activities and mitochondrial metabolism is crucial to this purpose. Dysmorphic, inefficient, and oxidant-producing mitochondria have been identified in aged cardiomyocytes in the setting of cardiac structural and functional alterations. These aberrant organelles are thought to arise from inefficient mitochondrial quality control, which has therefore been place in the spotlight as a relevant mechanism of cardiac aging. As a result of alterations in mitochondrial quality control and imbalanced oxidant defense, mitochondrial damage accumulates and contributes to cardiac frailty. Herein, we discuss the contribution of defective mitochondrial quality control pathways to cardiac frailty. Emerging findings pointing towards the exploitation of these pathways as therapeutic targets against cardiac aging and cardiovascular disease will also be illustrated.
    Keywords:  Autophagy; Cardioprotection; Extracellular vesicles; Mitochondrial derived vesicles; Mitochondrial quality control; Therapeutics
    DOI:  https://doi.org/10.1016/j.exger.2021.111508
  36. Nat Cell Biol. 2021 Aug 02.
    Mitochondrial UPR through generations.
    Mooncheol Park, Meng C Wang.
      
    DOI:  https://doi.org/10.1038/s41556-021-00729-3
  37. Development. 2021 Aug 06. pii: dev.199686. [Epub ahead of print]
    Fis1 ablation in the male germline disrupts mitochondrial morphology and mitophagy, and arrests spermatid maturation.
    Grigor Varuzhanyan, Mark S Ladinsky, Shun-Ichi Yamashita, Manabu Abe, Kenji Sakimura, Tomotake Kanki, David C Chan.
      Male germline development involves choreographed changes to mitochondrial number, morphology, and organization. Mitochondrial reorganization during spermatogenesis was recently shown to require mitochondrial fusion and fission. Mitophagy, the autophagic degradation of mitochondria, is another mechanism for controlling mitochondrial number and physiology, but its role during spermatogenesis is largely unknown. During post-meiotic spermatid development, restructuring of the mitochondrial network results in packing of mitochondria into a tight array in the sperm midpiece to fuel motility. Here, we show that disruption of mouse Fis1 in the male germline results in early spermatid arrest that is associated with increased mitochondrial content. Mutant spermatids coalesce into multinucleated giant cells (GCs) that accumulate mitochondria of aberrant ultrastructure and numerous mitophagic and autophagic intermediates, suggesting a defect in mitophagy. We conclude that Fis1 regulates mitochondrial morphology and turnover to promote spermatid maturation.
    Keywords:  Autophagy; Mitochondrial dynamics; Mitophagy; Spermatid; Spermatogenesis
    DOI:  https://doi.org/10.1242/dev.199686
  38. Nat Cell Biol. 2021 Aug 02.
    The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels.
    Qian Zhang, Zihao Wang, Wenfeng Zhang, Qingbo Wen, Xinyu Li, Jun Zhou, Xueying Wu, Yongqing Guo, Yangli Liu, Changshuo Wei, Wenfeng Qian, Ye Tian.
      The memory of stresses experienced by parents can be passed on to descendants as a forecast of the challenges to come. Here, we discovered that the neuronal mitochondrial perturbation-induced systemic mitochondrial unfolded protein response (UPRmt) in Caenorhabditis elegans can be transmitted to offspring over multiple generations. The transgenerational activation of UPRmt is mediated by maternal inheritance of elevated levels of mitochondrial DNA (mtDNA), which causes the proteostasis stress within mitochondria. Furthermore, results from intercrossing studies using wild C. elegans strains further support that maternal inheritance of higher levels of mtDNA can induce the UPRmt in descendants. The mitokine Wnt signalling pathway is required for the transmission of elevated mtDNA levels across generations, thereby conferring lifespan extension and stress resistance to offspring. Collectively, our results reveal that the nervous system can transmit stress signals across generations by increasing mtDNA in the germline, enabling descendants to better cope with anticipated challenges.
    DOI:  https://doi.org/10.1038/s41556-021-00724-8
  39. J Inherit Metab Dis. 2021 Aug 06.
    Clinical presentation and natural history of Barth Syndrome: An Overview.
    Carolyn Taylor, Emily S Rao, Germaine Pierre, Estathia Chronopoulou, Brittany Hornby, Andrea Heyman, Hilary J Vernon.
      Barth Syndrome is a rare X-linked disorder caused by pathogenic variants in the gene TAFAZZIN, which encodes for an enzyme involved in the remodeling of cardiolipin, a phospholipid primarily localized to the inner mitochondrial membrane. Barth syndrome is characterized by cardiomyopathy, skeletal myopathy, neutropenia and growth abnormalities, among other features. In this review, we will discuss the clinical presentation and natural history of Barth Syndrome, review key features of this disease, and introduce less common clinical associations. Recognition and understanding of the natural history of Barth Syndrome are important for ongoing patient management and developing endpoints for the demonstration of efficacy of new and emerging therapies. This article is protected by copyright. All rights reserved.
    Keywords:  Barth Syndrome; Cardiolipin; Cardiomyopathy; TAFAZZIN
    DOI:  https://doi.org/10.1002/jimd.12422
  40. Int J Mol Sci. 2021 Jul 21. pii: 7779. [Epub ahead of print]22(15):
    Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase.
    Minu Chaudhuri, Anuj Tripathi, Fidel Soto Gonzalez.
      Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca2+ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are integrated into the signaling network to maintain cellular homeostasis under stress. Mitochondria require hundreds of proteins to perform all these functions. Since the mitochondrial genome only encodes a handful of proteins, most mitochondrial proteins are imported from the cytosol via receptor/translocase complexes on the mitochondrial outer and inner membranes known as TOMs and TIMs. Many of the subunits of these protein complexes are essential for cell survival in model yeast and other unicellular eukaryotes. Defects in the mitochondrial import machineries are also associated with various metabolic, developmental, and neurodegenerative disorders in multicellular organisms. In addition to their canonical functions, these protein translocases also help maintain mitochondrial structure and dynamics, lipid metabolism, and stress response. This review focuses on the role of Tim50, the receptor component of one of the TIM complexes, in different cellular functions, with an emphasis on the Tim50 homologue in parasitic protozoan Trypanosoma brucei.
    Keywords:  HAD-phosphatase family; TIM; TIMM50; TOM; Tim50; Trypanosoma
    DOI:  https://doi.org/10.3390/ijms22157779
  41. Hum Mol Genet. 2021 Aug 02. pii: ddab219. [Epub ahead of print]
    Linking genome variants to disease: Scalable approaches to test the functional impact of human mutations.
    Gregory M Findlay.
      The application of genomics to medicine has accelerated the discovery of mutations underlying disease and enhanced our knowledge of the molecular underpinnings of diverse pathologies. As the amount of human genetic material queried via sequencing has grown exponentially in recent years, so too has the number of rare variants observed. Despite progress, our ability to distinguish which rare variants have clinical significance remains limited. Over the last decade, however, powerful experimental approaches have emerged to characterise variant effects orders of magnitude faster than before. Fuelled by improved DNA synthesis and sequencing, and more recently by CRISPR/Cas9 genome editing, multiplex functional assays provide a means of generating variant effect data in wide-ranging experimental systems. Here, I review recent applications of multiplex assays that link human variants to disease phenotypes and describe emerging strategies that will enhance their clinical utility in coming years.
    DOI:  https://doi.org/10.1093/hmg/ddab219
  42. Int J Mol Sci. 2021 Jul 23. pii: 7875. [Epub ahead of print]22(15):
    Mutated CCDC51 Coding for a Mitochondrial Protein, MITOK Is a Candidate Gene Defect for Autosomal Recessive Rod-Cone Dystrophy.
    Christina Zeitz, Cécile Méjécase, Christelle Michiels, Christel Condroyer, Juliette Wohlschlegel, Marine Foussard, Aline Antonio, Vanessa Démontant, Lisa Emmenegger, Audrey Schalk, Marion Neuillé, Elise Orhan, Sébastien Augustin, Crystel Bonnet, Amrit Estivalet, Frédéric Blond, Steven Blanchard, Camille Andrieu, Sandra Chantot-Bastaraud, Thierry Léveillard, Saddek Mohand-Saïd, José-Alain Sahel, Isabelle Audo.
      The purpose of this work was to identify the gene defect underlying a relatively mild rod-cone dystrophy (RCD), lacking disease-causing variants in known genes implicated in inherited retinal disorders (IRD), and provide transcriptomic and immunolocalization data to highlight the best candidate. The DNA of the female patient originating from a consanguineous family revealed no large duplication or deletion, but several large homozygous regions. In one of these, a homozygous frameshift variant, c.244_246delins17 p.(Trp82Valfs*4); predicted to lead to a nonfunctional protein, was identified in CCDC51. CCDC51 encodes the mitochondrial coiled-coil domain containing 51 protein, also called MITOK. MITOK ablation causes mitochondrial dysfunction. Here we show for the first time that CCDC51/MITOK localizes in the retina and more specifically in the inner segments of the photoreceptors, well known to contain mitochondria. Mitochondrial proteins have previously been implicated in IRD, although usually in association with syndromic disease, unlike our present case. Together, our findings add another ultra-rare mutation implicated in non-syndromic IRD, whose pathogenic mechanism in the retina needs to be further elucidated.
    Keywords:  CCDC51; MITOK; candidate gene; inner segments; mitochondrial protein; retina; retinitis pigmentosa; rod-cone dystrophy
    DOI:  https://doi.org/10.3390/ijms22157875
  43. Cells. 2021 Jul 09. pii: 1737. [Epub ahead of print]10(7):
    The Role of Voltage-Dependent Anion Channel in Mitochondrial Dysfunction and Human Disease.
    Joyce T Varughese, Susan K Buchanan, Ashley S Pitt.
      The voltage-dependent anion channel (VDAC) is a β-barrel membrane protein located in the outer mitochondrial membrane (OMM). VDAC has two conductance states: an open anion selective state, and a closed and slightly cation-selective state. VDAC conductance states play major roles in regulating permeability of ATP/ADP, regulation of calcium homeostasis, calcium flux within ER-mitochondria contact sites, and apoptotic signaling events. Three reported structures of VDAC provide information on the VDAC open state via X-ray crystallography and nuclear magnetic resonance (NMR). Together, these structures provide insight on how VDAC aids metabolite transport. The interaction partners of VDAC, together with the permeability of the pore, affect the molecular pathology of diseases including Parkinson's disease (PD), Friedreich's ataxia (FA), lupus, and cancer. To fully address the molecular role of VDAC in disease pathology, major questions must be answered on the structural conformers of VDAC. For example, further information is needed on the structure of the closed state, how binding partners or membrane potential could lead to the open/closed states, the function and mobility of the N-terminal α-helical domain of VDAC, and the physiological role of VDAC oligomers. This review covers our current understanding of the various states of VDAC, VDAC interaction partners, and the roles they play in mitochondrial regulation pertaining to human diseases.
    Keywords:  ATP transport; calcium homeostasis; disease; mitochondria-associated membranes; outer mitochondrial membrane; voltage-dependent anion channel (VDAC)
    DOI:  https://doi.org/10.3390/cells10071737
  44. Oxid Med Cell Longev. 2021 ;2021 4946711
    Targeting Mitochondrial Biogenesis with Polyphenol Compounds.
    Leila Chodari, Mutlu Dilsiz Aytemir, Parviz Vahedi, Mahdieh Alipour, Sepideh Zununi Vahed, Seyed Mahdi Hosseiniyan Khatibi, Elham Ahmadian, Mohammadreza Ardalan, Aziz Eftekhari.
      Appropriate mitochondrial physiology is an essential for health and survival. Cells have developed unique mechanisms to adapt to stress circumstances and changes in metabolic demands, by meditating mitochondrial function and number. In this context, sufficient mitochondrial biogenesis is necessary for efficient cell function and haemostasis, which is dependent on the regulation of ATP generation and maintenance of mitochondrial DNA (mtDNA). These procedures play a primary role in the processes of inflammation, aging, cancer, metabolic diseases, and neurodegeneration. Polyphenols have been considered as the main components of plants, fruits, and natural extracts with proven therapeutic effects during the time. These components regulate the intracellular pathways of mitochondrial biogenesis. Therefore, the current review is aimed at representing an updated review which determines the effects of different natural polyphenol compounds from various plant kingdoms on modulating signaling pathways of mitochondrial biogenesis that could be a promising alternative for the treatment of several disorders.
    DOI:  https://doi.org/10.1155/2021/4946711
  45. Sci Signal. 2021 Aug 03. pii: eabe0387. [Epub ahead of print]14(694):
    A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation.
    Orna Ernst, Jing Sun, Bin Lin, Balaji Banoth, Michael G Dorrington, Jonathan Liang, Benjamin Schwarz, Kaitlin A Stromberg, Samuel Katz, Sharat J Vayttaden, Clinton J Bradfield, Nadia Slepushkina, Christopher M Rice, Eugen Buehler, Jaspal S Khillan, Daniel W McVicar, Catharine M Bosio, Clare E Bryant, Fayyaz S Sutterwala, Scott E Martin, Madhu Lal-Nag, Iain D C Fraser.
      Noncanonical inflammasome activation by cytosolic lipopolysaccharide (LPS) is a critical component of the host response to Gram-negative bacteria. Cytosolic LPS recognition in macrophages is preceded by a Toll-like receptor (TLR) priming signal required to induce transcription of inflammasome components and facilitate the metabolic reprograming that fuels the inflammatory response. Using a genome-scale arrayed siRNA screen to find inflammasome regulators in mouse macrophages, we identified the mitochondrial enzyme nucleoside diphosphate kinase D (NDPK-D) as a regulator of both noncanonical and canonical inflammasomes. NDPK-D was required for both mitochondrial DNA synthesis and cardiolipin exposure on the mitochondrial surface in response to inflammasome priming signals mediated by TLRs, and macrophages deficient in NDPK-D had multiple defects in LPS-induced inflammasome activation. In addition, NDPK-D was required for the recruitment of TNF receptor-associated factor 6 (TRAF6) to mitochondria, which was critical for reactive oxygen species (ROS) production and the metabolic reprogramming that supported the TLR-induced gene program. NDPK-D knockout mice were protected from LPS-induced shock, consistent with decreased ROS production and attenuated glycolytic commitment during priming. Our findings suggest that, in response to microbial challenge, NDPK-D-dependent TRAF6 mitochondrial recruitment triggers an energetic fitness checkpoint required to engage and maintain the transcriptional program necessary for inflammasome activation.
    DOI:  https://doi.org/10.1126/scisignal.abe0387
  46. Nat Commun. 2021 Aug 06. 12(1): 4773
    Impact of aging and exercise on skeletal muscle mitochondrial capacity, energy metabolism, and physical function.
    L Grevendonk, N J Connell, C McCrum, C E Fealy, L Bilet, Y M H Bruls, J Mevenkamp, V B Schrauwen-Hinderling, J A Jörgensen, E Moonen-Kornips, G Schaart, B Havekes, J de Vogel-van den Bosch, M C E Bragt, K Meijer, P Schrauwen, J Hoeks.
      The relationship between the age-associated decline in mitochondrial function and its effect on skeletal muscle physiology and function remain unclear. In the current study, we examined to what extent physical activity contributes to the decline in mitochondrial function and muscle health during aging and compared mitochondrial function in young and older adults, with similar habitual physical activity levels. We also studied exercise-trained older adults and physically impaired older adults. Aging was associated with a decline in mitochondrial capacity, exercise capacity and efficiency, gait stability, muscle function, and insulin sensitivity, even when maintaining an adequate daily physical activity level. Our data also suggest that a further increase in physical activity level, achieved through regular exercise training, can largely negate the effects of aging. Finally, mitochondrial capacity correlated with exercise efficiency and insulin sensitivity. Together, our data support a link between mitochondrial function and age-associated deterioration of skeletal muscle.
    DOI:  https://doi.org/10.1038/s41467-021-24956-2
  47. Int J Mol Sci. 2021 Jul 21. pii: 7809. [Epub ahead of print]22(15):
    Complexome Profiling: Assembly and Remodeling of Protein Complexes.
    Ilka Wittig, Pedro Felipe Malacarne.
      Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.
    Keywords:  assembly; complexome profiling; data repositories; mass spectrometry; protein complexes; protein–protein interaction; remodeling
    DOI:  https://doi.org/10.3390/ijms22157809
  48. EMBO Rep. 2021 Aug 02. e53086
    Alterations in mitochondrial morphology as a key driver of immunity and host defence.
    Mariana P Cervantes-Silva, Shannon L Cox, Annie M Curtis.
      Mitochondria are dynamic organelles whose architecture changes depending on the cell's energy requirements and other signalling events. These structural changes are collectively known as mitochondrial dynamics. Mitochondrial dynamics are crucial for cellular functions such as differentiation, energy production and cell death. Importantly, it has become clear in recent years that mitochondrial dynamics are a critical control point for immune cell function. Mitochondrial remodelling allows quiescent immune cells to rapidly change their metabolism and become activated, producing mediators, such as cytokines, chemokines and even metabolites to execute an effective immune response. The importance of mitochondrial dynamics in immunity is evident, as numerous pathogens have evolved mechanisms to manipulate host cell mitochondrial remodelling in order to promote their own survival. In this review, we comprehensively address the roles of mitochondrial dynamics in immune cell function, along with modulation of host cell mitochondrial morphology during viral and bacterial infections to facilitate either pathogen survival or host immunity. We also speculate on what the future may hold in terms of therapies targeting mitochondrial morphology for bacterial and viral control.
    Keywords:  bacteria; immune response; mitochondrial dynamics; therapy; virus
    DOI:  https://doi.org/10.15252/embr.202153086
  49. Cell Metab. 2021 Jul 27. pii: S1550-4131(21)00324-7. [Epub ahead of print]
    Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca2+ homeostasis with adipose tissue lipolysis.
    Alicia G Gómez-Valadés, Macarena Pozo, Luis Varela, Mehdi Boutagouga Boudjadja, Sara Ramírez, Iñigo Chivite, Elena Eyre, Roberta Haddad-Tóvolli, Arnaud Obri, Maria Milà-Guasch, Jordi Altirriba, Marc Schneeberger, Mónica Imbernón, Angela R Garcia-Rendueles, Pau Gama-Perez, Jonathan Rojo-Ruiz, Bence Rácz, Maria Teresa Alonso, Ramon Gomis, Antonio Zorzano, Giuseppe D'Agostino, Clara V Alvarez, Rubén Nogueiras, Pablo M Garcia-Roves, Tamas L Horvath, Marc Claret.
      Appropriate cristae remodeling is a determinant of mitochondrial function and bioenergetics and thus represents a crucial process for cellular metabolic adaptations. Here, we show that mitochondrial cristae architecture and expression of the master cristae-remodeling protein OPA1 in proopiomelanocortin (POMC) neurons, which are key metabolic sensors implicated in energy balance control, is affected by fluctuations in nutrient availability. Genetic inactivation of OPA1 in POMC neurons causes dramatic alterations in cristae topology, mitochondrial Ca2+ handling, reduction in alpha-melanocyte stimulating hormone (α-MSH) in target areas, hyperphagia, and attenuated white adipose tissue (WAT) lipolysis resulting in obesity. Pharmacological blockade of mitochondrial Ca2+ influx restores α-MSH and the lipolytic program, while improving the metabolic defects of mutant mice. Chemogenetic manipulation of POMC neurons confirms a role in lipolysis control. Our results unveil a novel axis that connects OPA1 in POMC neurons with mitochondrial cristae, Ca2+ homeostasis, and WAT lipolysis in the regulation of energy balance.
    Keywords:  OPA-1; POMC neurons; cristae; hypothalamus; lipolysis; mitochondria; obesity
    DOI:  https://doi.org/10.1016/j.cmet.2021.07.008
  50. Anal Biochem. 2021 Jul 29. pii: S0003-2697(21)00220-7. [Epub ahead of print] 114319
    Site-specific acetylation of adenine nucleotide translocase 1 at lysine 23 in human muscle.
    Jean Finlayson, Neusha Barakati, Paul R Langlais, Janet Funk, Rocio Zapata Bustos, Dawn K Coletta, Moulun Luo, Wayne T Willis, Lawrence J Mandarino.
      Evidence suggests acetylation of human adenine nucleotide translocase 1 (ANT1) at lysine 23 (Lys23) reduces binding of ADP. Lys23 contributes to the positive charge that facilitates this interaction. This study was undertaken to characterize ANT1 abundance and acetylation by a novel method using small amounts of human skeletal muscle biopsies. Lysates of whole muscle or mitochondria from the same tissue were prepared from needle biopsies of vastus lateralis muscle of healthy volunteers. Lysed proteins were resolved on gels, the section containing ANT1 (surrounding 30 Kd) was excised, digested with trypsin, spiked with labeled unacetylated and acetylated synthetic standard peptides and analyzed by mass spectrometry. Natural logarithm transformation of data linearized ion intensities over a 10-fold range of peptide mass. Coefficients of variation ranged from 7 to 30% for ANT1 abundance and Lys23 acetylation. In three volunteers, ANT1 content was 8.36 ± 0.33 nmoles/gram wet weight muscle and 0.64 ± 0.05 nmoles/mg mitochondria, so mitochondrial content was 13.3 ± 2.4 mg mitochondria per gram muscle. Acetylation of Lys23 averaged 14.3 ± 4.2% and 4.87 ± 1.84% in whole muscle and mitochondria, respectively. This assay makes it possible to assess effects of acetylation on the function of ANT1 in human muscle.
    Keywords:  Adenine nucleotide translocase; Lysine acetylation; Mitochondria; Proteomics; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.ab.2021.114319
  51. J Neurol Sci. 2021 Jul 27. pii: S0022-510X(21)00294-X. [Epub ahead of print]428 117600
    Expanding the phenotype of AFG3L2 mutations: Late-onset autosomal recessive spinocerebellar ataxia.
    Han-Lin Chiang, Jong-Ling Fuh, Yu-Shuen Tsai, Bing-Wen Soong, Yi-Chu Liao, Yi-Chung Lee.
      The AFG3L2 gene encodes AFG3-like protein 2, which is a subunit of human mitochondrial ATPases associated with various cellular protease activities (m-AAA). The clinical spectrum of AFG3L2 mutations is broad. Dominant AFG3L2 mutations can cause autosomal dominant spinocerebellar ataxia type 28 (SCA28), whereas biallelic AFG3L2 mutations may lead to spastic ataxia 5 (SPAX5). However, the role of AFG3L2 mutations in autosomal recessive spinocerebellar ataxia (SCAR) remains elusive. The aim of this study is to delineate the clinical features and spectrum of AFG3L2 mutations in a Taiwanese cohort with cerebellar ataxia. Mutational analyses of AFG3L2 were carried out by targeted resequencing in a cohort of 133 unrelated patients with molecularly undetermined cerebellar ataxia. We identified one single patient carrying compound heterozygous mutations in AFG3L2, p.[R632*];[V723M] (c.[1894C > T];[2167G > A]). The patient has suffered from apparently sporadic and slowly progressive cerebellar ataxia, ptosis, and ophthalmoparesis since age 55 years. These findings expand the clinical spectrum of AFG3L2 mutations and suggest a new subtype of late-onset SCAR caused by biallelic AFG3L2 mutations.
    Keywords:  AFG3L2; Autosomal recessive cerebellar ataxia; SCA28; SCAR; SPAX5; Spinocerebellar ataxia
    DOI:  https://doi.org/10.1016/j.jns.2021.117600
  52. Front Physiol. 2021 ;12 638352
    Mammalian Target of Rapamycin Signaling Pathway Regulates Mitochondrial Quality Control of Brown Adipocytes in Mice.
    Bahetiyaer Huwatibieke, Wenzhen Yin, Lingchao Liu, Yuxin Jin, Xinxin Xiang, Jingyan Han, Weizhen Zhang, Yin Li.
      The mammalian target of rapamycin (mTOR) is an important protein kinase that senses changes in extracellular and intracellular energy levels and plays a key role in regulating energy metabolism. Brown adipose tissue, which can be converted to white adipose tissue, contains a large number of mitochondria and regulates energy expenditure through thermogenesis. Because obesity is a process of fat accumulation due to chronic excessive energy intake, we attempted to determine whether the mTOR signaling pathway can affect the mitochondrial quality control of brown adipocytes through sensing energy status, thereby regulating brown/white adipocyte transformation. In the present study, through activation or inhibition of mTOR signaling, we detected mitochondrial biogenesis, dynamics, and autophagy-related markers in brown adipocytes. We found that activation of mTOR signaling downregulated the expression of mitochondrial biogenesis, dynamics, and autophagy-relevant markers and inhibited the mitochondrial quality control of brown adipocytes, indicating a phenotypic transformation of brown to white adipocytes. In contrast, inhibition of mTOR signaling upregulated the expression of mitochondrial biogenesis, dynamics, and mitophagy-relevant markers and strengthened mitochondrial quality control, suggesting an inhibition of the phenotypic transformation of brown to white adipocytes. In conclusion, the mTOR signaling pathway plays an important role in modulating the transformation of adipocytes by regulating mitochondrial quality control.
    Keywords:  brown adipose tissue; mammalian target of rapamycin; mitochondria; obesity; white adipose tissue
    DOI:  https://doi.org/10.3389/fphys.2021.638352
  53. Br J Anaesth. 2021 Jul 28. pii: S0007-0912(21)00393-7. [Epub ahead of print]
    Selective mitochondrial antioxidant MitoTEMPO reduces renal dysfunction and systemic inflammation in experimental sepsis.
    Nishkantha Arulkumaran, Sean J Pollen, Robert Tidswell, Charlotte Gaupp, Vera B M Peters, Giacomo Stanzani, Timothy A C Snow, Michael R Duchen, Mervyn Singer.
      BACKGROUND: Excess mitochondrial reactive oxygen species (mROS) in sepsis is associated with organ failure, in part by generating inflammation through the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome. We determined the impact of a mitochondrial-targeted antioxidant (MitoTEMPO) on mitochondrial dysfunction in renal proximal tubular epithelial cells, peritoneal immune cell function ex vivo, and organ dysfunction in a rat model of sepsis.METHODS: The effects of MitoTEMPO were assessed ex vivo using adenosine triphosphate and lipopolysaccharide-stimulated rat peritoneal immune cells and fresh rat kidney slices exposed to serum from septic rats. We assessed mROS production and phagocytotic capacity (flow cytometry), mitochondrial functionality (multiphoton imaging, respirometry), and NLRP3 inflammasome activation in cell culture. The effect of MitoTEMPO on organ dysfunction was evaluated in a rat model of faecal peritonitis.
    RESULTS: MitoTEMPO decreased septic serum-induced mROS (P<0.001) and maintained normal reduced nicotinamide adenine dinucleotide redox state (P=0.02) and mitochondrial membrane potential (P<0.001) in renal proximal tubular epithelial cells ex vivo. In lipopolysaccharide-stimulated peritoneal immune cells, MitoTEMPO abrogated the increase in mROS (P=0.006) and interleukin-1β (IL-1β) (P=0.03) without affecting non-mitochondrial oxygen consumption or the phagocytotic-induced respiratory burst (P>0.05). In vivo, compared with untreated septic animals, MitoTEMPO reduced systemic IL-1β (P=0.01), reduced renal oxidative stress as determined by urine isoprostane levels (P=0.04), and ameliorated renal dysfunction (reduced serum urea (P<0.001) and creatinine (P=0.05).
    CONCLUSIONS: Reduction of mROS by a mitochondria-targeted antioxidant reduced IL-1β, and protected mitochondrial, cellular, and organ functionality after septic insults.
    Keywords:  NLRP3 inflammasome; acute kidney injury; animal model; macrophage; mitochondria; reactive oxygen species; sepsis
    DOI:  https://doi.org/10.1016/j.bja.2021.05.036
  54. Genome Biol. 2021 Aug 05. 22(1): 219
    Specific splice junction detection in single cells with SICILIAN.
    Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic, Julia Salzman.
      Precise splice junction calls are currently unavailable in scRNA-seq pipelines such as the 10x Chromium platform but are critical for understanding single-cell biology. Here, we introduce SICILIAN, a new method that assigns statistical confidence to splice junctions from a spliced aligner to improve precision. SICILIAN is a general method that can be applied to bulk or single-cell data, but has particular utility for single-cell analysis due to that data's unique challenges and opportunities for discovery. SICILIAN's precise splice detection achieves high accuracy on simulated data, improves concordance between matched single-cell and bulk datasets, and increases agreement between biological replicates. SICILIAN detects unannotated splicing in single cells, enabling the discovery of novel splicing regulation through single-cell analysis workflows.
    DOI:  https://doi.org/10.1186/s13059-021-02434-8
  55. Sci Data. 2021 Aug 05. 8(1): 205
    ACO2 clinicobiological dataset with extensive phenotype ontology annotation.
    Khadidja Guehlouz, Thomas Foulonneau, Patrizia Amati-Bonneau, Majida Charif, Estelle Colin, Céline Bris, Valérie Desquiret-Dumas, Dan Milea, Philippe Gohier, Vincent Procaccio, Dominique Bonneau, Johan T den Dunnen, Guy Lenaers, Pascal Reynier, Marc Ferré.
      Pathogenic variants of the aconitase 2 gene (ACO2) are responsible for a broad clinical spectrum involving optic nerve degeneration, ranging from isolated optic neuropathy with recessive or dominant inheritance, to complex neurodegenerative syndromes with recessive transmission. We created the first public locus-specific database (LSDB) dedicated to ACO2 within the "Global Variome shared LOVD" using exclusively the Human Phenotype Ontology (HPO), a standard vocabulary for describing phenotypic abnormalities. All the variants and clinical cases listed in the literature were incorporated into the database, from which we produced a dataset. We followed a rational and comprehensive approach based on the HPO thesaurus, demonstrating that ACO2 patients should not be classified separately between isolated and syndromic cases. Our data highlight that certain syndromic patients do not have optic neuropathy and provide support for the classification of the recurrent pathogenic variants c.220C>G and c.336C>G as likely pathogenic. Overall, our data records demonstrate that the clinical spectrum of ACO2 should be considered as a continuum of symptoms and refines the classification of some common variants.
    DOI:  https://doi.org/10.1038/s41597-021-00984-x
  56. Ann Neurol. 2021 Aug 02.
    Synergistic deoxynucleoside and gene therapies for thymidine kinase 2 deficiency.
    Carlos Lopez-Gomez, Maria J Sanchez-Quintero, Eung Jeon Lee, Gulio Kleiner, Saba Tadesse, Jun Xie, Hasan Orhan Akman, Guangping Gao, Michio Hirano.
      OBJECTIVE: Autosomal recessive human thymidine kinase 2 (TK2) mutations cause TK2 deficiency, which typically manifests as a progressive and fatal mitochondrial myopathy in infants and children. Treatment with pyrimidine deoxynucleosides deoxycytidine and thymidine ameliorates mitochondrial defects and extends the lifespan of Tk2 knock-in mouse (Tk2KI ) and compassionate use deoxynucleoside therapy in TK2 deficient patients have shown promising indications of efficacy. To augment therapy for Tk2 deficiency, we assessed gene therapy alone and in combination with deoxynucleoside therapy in Tk2KI mice.METHODS: We generated pAAVsc CB6 PI vectors containing human TK2 cDNA (TK2). AAV-TK2 was administered to Tk2KI , which were serially assessed for weight, motor functions, and survival as well as biochemical functions in tissues. AAV-TK2 treated mice were further treated with deoxynucleosides.
    RESULTS: AAV9 delivery of human TK2 cDNA to Tk2KI mice efficiently rescued Tk2 activity in all the tissues tested except kidney, delayed disease onset, and increased lifespan. Sequential treatment of Tk2KI mice with AAV9 first followed by AAV2 at different ages allowed us to reduce the viral dose while further prolonging the lifespan. Furthermore, addition of deoxycytidine and deoxythymidine supplementation to AAV9 + AAV2 treated Tk2KI mice dramatically improved mtDNA copy numbers in liver and kidney, animal growth, and lifespan.
    INTERPRETATION: Our data indicate that AAV-TK2 gene therapy as well as combination deoxynucleoside and gene therapies is more effective in Tk2KI mice than pharmacological alone. Thus, combination of gene therapy with substrate enhancement is promising therapeutic approach for TK2 deficiency and potentially other metabolic disorders. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/ana.26185
  57. Front Pediatr. 2021 ;9 663752
    The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health.
    Audrey C Woerner, Renata C Gallagher, Jerry Vockley, Aashish N Adhikari.
      Newborn screening (NBS) is a population-based program with a goal of reducing the burden of disease for conditions with significant clinical impact on neonates. Screening tests were originally developed and implemented one at a time, but newer methods have allowed the use of multiplex technologies to expand additions more rapidly to standard panels. Recent improvements in next-generation sequencing are also evolving rapidly from first focusing on individual genes, then panels, and finally all genes as encompassed by whole exome and genome sequencing. The intersection of these two technologies brings the revolutionary possibility of identifying all genetic disorders in newborns, allowing implementation of therapies at the optimum time regardless of symptoms. This article reviews the history of newborn screening and early studies examining the use of whole genome and exome sequencing as a screening tool. Lessons learned from these studies are discussed, along with technical, ethical, and societal challenges to broad implementation.
    Keywords:  newborn screening; next-generation sequencing; recommended uniform screening panel; whole exome sequencing; whole genome sequencing
    DOI:  https://doi.org/10.3389/fped.2021.663752
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