bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022–10–02
35 papers selected by
Catalina Vasilescu, University of Helsinki
  1. Mitochondria-ER cooperation: NLRX1 detects mitochondrial protein import stress and promotes mitophagy through the ER protein RRBP1.
  2. Mitochondrial diseases mimicking autoimmune diseases of the CNS and good response to steroids initially.
  3. Dynamic features of human mitochondrial DNA maintenance and transcription.
  4. Differential requirements for mitochondrial electron transport chain components in the adult murine liver.
  5. Mitochondrial protein dysfunction in pathogenesis of neurological diseases.
  6. Mitochondrial pyruvate supports lymphoma proliferation by fueling a glutamate pyruvate transaminase 2-dependent glutaminolysis pathway.
  7. Understanding the molecular basis and pathogenesis of hereditary optic neuropathies: towards improved diagnosis and management.
  8. ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing.
  9. An LKB1-mitochondria axis controls TH17 effector function.
  10. Analysis of Mitochondrial Dynamics in Adult Drosophila Axons.
  11. Expert consensus on diagnosis and treatment of very long-chain acyl-CoA dehydrogenase deficiency.
  12. Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons.
  13. Clonal Imaging of Mitochondria in the Dissected Fly Wing.
  14. On the role of ubiquinone in the proton translocation mechanism of respiratory complex I.
  15. The neuropathologic findings in a case of progressive cavitating leukoencephalopathy due to NDUFV1 pathogenic variants.
  16. Live Imaging of Mitochondria in the Intact Fly Wing.
  17. Neurodegeneration-associated mitochondrial proteins, CHCHD2 and CHCHD10-what distinguishes the two?
  18. Kearns-Sayre syndrome case. Novel 5,9 kb mtDNA deletion.
  19. Promoting a new view of mitochondrial genome regulation.
  20. MFN2 mediates ER-mitochondrial coupling during ER stress through specialized stable contact sites.
  21. Recent advances in mitochondrial diseases: From molecular insights to therapeutic perspectives.
  22. Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3.
  23. Biallelic COX10 Mutations and PMP22 Deletion in a Family With Leigh Syndrome and Hereditary Neuropathy With Liability to Pressure Palsy.
  24. Control of mitochondrial dynamics and apoptotic pathways by peroxisomes.
  25. Eisosome protein Pil1 regulates mitochondrial morphology, mitophagy, and cell death in Saccharomyces cerevisiae.
  26. High-content phenotyping of Parkinson's disease patient stem cell-derived midbrain dopaminergic neurons using machine learning classification.
  27. A nomenclature consensus for nervous system organoids and assembloids.
  28. Inherited causes of combined vision and hearing loss: clinical features and molecular genetics.
  29. Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.
  30. Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.
  31. Databases and Tools to Investigate Protein-Metabolite Interactions.
  32. Histidine supplementation can escalate or rescue HARS deficiency in a Charcot Marie Tooth Disease model.
  33. Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers.
  34. GotEnzymes: an extensive database of enzyme parameter predictions.
  35. DNA Methylation Analysis Using Bisulfite Pyrosequencing.
  1. Autophagy. 2022 Sep 28.
    Mitochondria-ER cooperation: NLRX1 detects mitochondrial protein import stress and promotes mitophagy through the ER protein RRBP1.
    Samuel A Killackey, Yuntian Bi, Dana J Philpott, Damien Arnoult, Stephen E Girardin.
      Mitochondria rely on efficient protein import across their membranes for optimal function. We have shown that numerous mitochondrial stressors all converge on a common pathway disrupting this import efficiency. We identified a novel pathway involving NLRX1 and RRBP1 that responds to this import stress, resulting in LC3 lipidation, mitochondrial targeting and ultimate degradation. Furthermore, we demonstrated the relevance of this mitophagy axis in murine skeletal muscle following acute exercise. We propose that mitochondrial protein import stress is an underlying, common trigger for mitophagy, offering a novel avenue for therapeutic exploration and mechanistic insight.
    Keywords:  Autophagy; NLR; exercise; import; mitochondria; mitophagy; proteostasis
    DOI:  https://doi.org/10.1080/15548627.2022.2129763
  2. Eur J Paediatr Neurol. 2022 Sep 20. pii: S1090-3798(22)00138-6. [Epub ahead of print]41 27-35
    Mitochondrial diseases mimicking autoimmune diseases of the CNS and good response to steroids initially.
    Adela Della Marina, Annikki Bertolini, Andreas Wegener-Panzer, Marina Flotats-Bastardas, Tabea Reinhardt, Ines El Naggar, Felix Distelmaier, Astrid Blaschek, Ulrike Schara-Schmidt, Theresa Brunet, Matias Wagner, Dimitri Smirnov, Holger Prokisch, Saskia B Wortmann, Kevin Rostasy.
       INTRODUCTION: Neuroimmunological diseases such as autoimmune encephalitis (AE) or acquired demyelinating syndromes (ADS), can present with neurological symptoms and imaging features that are indistinguishable from mitochondrial diseases (MD) in particular at initial presentation.
    METHODS: Retrospective analysis of the clinical, laboratory and neuroimaging features of five patients who presented with signs of a neuroimmunological disease but all had pathological pathogenic variants in genes related to mitochondrial energy metabolism.
    RESULTS: Four patients presented with an acute neurological episode reminiscent of a possible AE and one patient with a suspected ADS at initial presentation. MRI findings were compatible with neuroimmunological diseases in all patients. In two children cerebrospinal fluid (CSF) studies revealed a mildly elevated cell count, two had elevated CSF lactate, none had oligoclonal bands (OCBs). All patients improved rapidly with intravenous steroids or immunoglobulins. Four patients had one or more relapses. Three patients showed worsening of their neurological symptoms with subsequent episodes and one patient died. Relapses in conjunction with new and progressive neurological symptoms, led to additional work-up which finally resulted in different genetic diagnosis of MD in all patients (MT-TL1, MT-ND5, APOA1-BP, HPDL, POLG).
    DISCUSSION: We would like to draw attention to a subset of patients with MD initially presenting with signs and symptoms mimicking neuroimmunological. Absence of CSF pleocytosis, elevated CSF lactate and progressive, relapsing course should trigger further (genetic) investigations in search of a MD even in patients with good response initially to immunomodulating therapies.
    Keywords:  Mimicry; Mitochondrial disease; Neuroinflammation; Treatment; Whole exome sequencing
    DOI:  https://doi.org/10.1016/j.ejpn.2022.09.003
  3. Front Cell Dev Biol. 2022 ;10 984245
    Dynamic features of human mitochondrial DNA maintenance and transcription.
    Mansour Akbari, Hilde Loge Nilsen, Nicola Pietro Montaldo.
      Mitochondria are the primary sites for cellular energy production and are required for many essential cellular processes. Mitochondrial DNA (mtDNA) is a 16.6 kb circular DNA molecule that encodes only 13 gene products of the approximately 90 different proteins of the respiratory chain complexes and an estimated 1,200 mitochondrial proteins. MtDNA is, however, crucial for organismal development, normal function, and survival. MtDNA maintenance requires mitochondrially targeted nuclear DNA repair enzymes, a mtDNA replisome that is unique to mitochondria, and systems that control mitochondrial morphology and quality control. Here, we provide an overview of the current literature on mtDNA repair and transcription machineries and discuss how dynamic functional interactions between the components of these systems regulate mtDNA maintenance and transcription. A profound understanding of the molecular mechanisms that control mtDNA maintenance and transcription is important as loss of mtDNA integrity is implicated in normal process of aging, inflammation, and the etiology and pathogenesis of a number of diseases.
    Keywords:  DNA repair; base excision repair (BER); base excision repair (BER)glycosylases; mitochdrial damage; mitochondria; transcription
    DOI:  https://doi.org/10.3389/fcell.2022.984245
  4. Elife. 2022 Sep 26. pii: e80919. [Epub ahead of print]11
    Differential requirements for mitochondrial electron transport chain components in the adult murine liver.
    Nicholas P Lesner, Xun Wang, Zhenkang Chen, Anderson Frank, Cameron Menezes, Sara House, Spencer D Shelton, Andrew Lemoff, David G McFadden, Janaka Wanaspura, Ralph J DeBerardinis, Prashant Mishra.
      Mitochondrial electron transport chain (ETC) dysfunction due to mutations in the nuclear or mitochondrial genome is a common cause of metabolic disease in humans and displays striking tissue specificity depending on the affected gene. The mechanisms underlying tissue specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for basal respiration and maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function, redox and oxygen status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, impaired oxygen handling, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes use alternative electron donors to fuel the mitochondrial ETC.
    Keywords:  cell biology; genetics; genomics; mouse
    DOI:  https://doi.org/10.7554/eLife.80919
  5. Front Mol Neurosci. 2022 ;15 974480
    Mitochondrial protein dysfunction in pathogenesis of neurological diseases.
    Liang Wang, Ziyun Yang, Xiumei He, Shiming Pu, Cheng Yang, Qiong Wu, Zuping Zhou, Xiaobo Cen, Hongxia Zhao.
      Mitochondria are essential organelles for neuronal function and cell survival. Besides the well-known bioenergetics, additional mitochondrial roles in calcium signaling, lipid biogenesis, regulation of reactive oxygen species, and apoptosis are pivotal in diverse cellular processes. The mitochondrial proteome encompasses about 1,500 proteins encoded by both the nuclear DNA and the maternally inherited mitochondrial DNA. Mutations in the nuclear or mitochondrial genome, or combinations of both, can result in mitochondrial protein deficiencies and mitochondrial malfunction. Therefore, mitochondrial quality control by proteins involved in various surveillance mechanisms is critical for neuronal integrity and viability. Abnormal proteins involved in mitochondrial bioenergetics, dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance have been linked to the pathogenesis of a number of neurological diseases. The goal of this review is to give an overview of these pathways and to summarize the interconnections between mitochondrial protein dysfunction and neurological diseases.
    Keywords:  mitochondrial bioenergetics; mitochondrial dynamics; mitochondrial import machinery; mitochondrial proteins; mitophagy; mtDNA maintenance; neurological diseases; pathogenesis
    DOI:  https://doi.org/10.3389/fnmol.2022.974480
  6. Sci Adv. 2022 Sep 30. 8(39): eabq0117
    Mitochondrial pyruvate supports lymphoma proliferation by fueling a glutamate pyruvate transaminase 2-dependent glutaminolysis pathway.
    Peng Wei, Alex J Bott, Ahmad A Cluntun, Jeffrey T Morgan, Corey N Cunningham, John C Schell, Yeyun Ouyang, Scott B Ficarro, Jarrod A Marto, Nika N Danial, Ralph J DeBerardinis, Jared Rutter.
      The fate of pyruvate is a defining feature in many cell types. One major fate is mitochondrial entry via the mitochondrial pyruvate carrier (MPC). We found that diffuse large B cell lymphomas (DLBCLs) consume mitochondrial pyruvate via glutamate-pyruvate transaminase 2 to enable α-ketoglutarate production as part of glutaminolysis. This led us to discover that glutamine exceeds pyruvate as a carbon source for the tricarboxylic acid cycle in DLBCLs. As a result, MPC inhibition led to decreased glutaminolysis in DLBCLs, opposite to previous observations in other cell types. We also found that MPC inhibition or genetic depletion decreased DLBCL proliferation in an extracellular matrix (ECM)-like environment and xenografts, but not in a suspension environment. Moreover, the metabolic profile of DLBCL cells in ECM is markedly different from cells in a suspension environment. Thus, we conclude that the synergistic consumption and assimilation of glutamine and pyruvate enables DLBCL proliferation in an extracellular environment-dependent manner.
    DOI:  https://doi.org/10.1126/sciadv.abq0117
  7. Lancet Neurol. 2022 Sep 22. pii: S1474-4422(22)00174-0. [Epub ahead of print]
    Understanding the molecular basis and pathogenesis of hereditary optic neuropathies: towards improved diagnosis and management.
    Nancy J Newman, Patrick Yu-Wai-Man, Valérie Biousse, Valerio Carelli.
      Hereditary optic neuropathies result from defects in the human genome, both nuclear and mitochondrial. The two main and most recognised phenotypes are dominant optic atrophy and Leber hereditary optic neuropathy. Advances in modern molecular diagnosis have expanded our knowledge of genotypes and phenotypes of inherited disorders that affect the optic nerve, either alone or in combination, with various forms of neurological and systemic degeneration. A unifying feature in the pathophysiology of these disorders appears to involve mitochondrial dysfunction, suggesting that the retinal ganglion cells and their axons are especially susceptible to perturbations in mitochondrial homoeostasis. As we better understand the pathogenesis behind these genetic diseases, aetiologically targeted therapies are emerging and entering into clinical trials, including treatments aimed at halting the cascade of neurodegeneration, replacing or editing the defective genes or their protein products, and potentially regenerating damaged optic nerves, as well as preventing generational disease transmission.
    DOI:  https://doi.org/10.1016/S1474-4422(22)00174-0
  8. Nat Commun. 2022 Sep 30. 13(1): 5750
    ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing.
    Paula Clemente, Javier Calvo-Garrido, Sarah F Pearce, Florian A Schober, Megumi Shigematsu, Stefan J Siira, Isabelle Laine, Henrik Spåhr, Christian Steinmetzger, Katja Petzold, Yohei Kirino, Rolf Wibom, Oliver Rackham, Aleksandra Filipovska, Joanna Rorbach, Christoph Freyer, Anna Wredenberg.
      Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of processing has remained unsolved. Using Drosophila and mouse models, we demonstrate that non-canonical processing results in the formation of 3' phosphates, and that phosphatase activity by the carbon catabolite repressor 4 domain-containing family member ANGEL2 is required for their hydrolysis. Furthermore, our data suggest that members of the FAST kinase domain-containing protein family are responsible for these 3' phosphates. Our results therefore propose a mechanism for non-canonical RNA processing in metazoan mitochondria, by identifying the role of ANGEL2.
    DOI:  https://doi.org/10.1038/s41467-022-33368-9
  9. Nature. 2022 Sep 28.
    An LKB1-mitochondria axis controls TH17 effector function.
    Francesc Baixauli, Klara Piletic, Daniel J Puleston, Matteo Villa, Cameron S Field, Lea J Flachsmann, Andrea Quintana, Nisha Rana, Joy Edwards-Hicks, Mai Matsushita, Michal A Stanczak, Katarzyna M Grzes, Agnieszka M Kabat, Mario Fabri, George Caputa, Beth Kelly, Mauro Corrado, Yaarub Musa, Katarzyna J Duda, Gerhard Mittler, David O'Sullivan, Hiromi Sesaki, Thomas Jenuwein, Joerg M Buescher, Edward J Pearce, David E Sanin, Erika L Pearce.
      CD4+ T cell differentiation requires metabolic reprogramming to fulfil the bioenergetic demands of proliferation and effector function, and enforce specific transcriptional programmes1-3. Mitochondrial membrane dynamics sustains mitochondrial processes4, including respiration and tricarboxylic acid (TCA) cycle metabolism5, but whether mitochondrial membrane remodelling orchestrates CD4+ T cell differentiation remains unclear. Here we show that unlike other CD4+ T cell subsets, T helper 17 (TH17) cells have fused mitochondria with tight cristae. T cell-specific deletion of optic atrophy 1 (OPA1), which regulates inner mitochondrial membrane fusion and cristae morphology6, revealed that TH17 cells require OPA1 for its control of the TCA cycle, rather than respiration. OPA1 deletion amplifies glutamine oxidation, leading to impaired NADH/NAD+ balance and accumulation of TCA cycle metabolites and 2-hydroxyglutarate-a metabolite that influences the epigenetic landscape5,7. Our multi-omics approach revealed that the serine/threonine kinase liver-associated kinase B1 (LKB1) couples mitochondrial function to cytokine expression in TH17 cells by regulating TCA cycle metabolism and transcriptional remodelling. Mitochondrial membrane disruption activates LKB1, which restrains IL-17 expression. LKB1 deletion restores IL-17 expression in TH17 cells with disrupted mitochondrial membranes, rectifying aberrant TCA cycle glutamine flux, balancing NADH/NAD+ and preventing 2-hydroxyglutarate production from the promiscuous activity of the serine biosynthesis enzyme phosphoglycerate dehydrogenase (PHGDH). These findings identify OPA1 as a major determinant of TH17 cell function, and uncover LKB1 as a sensor linking mitochondrial cues to effector programmes in TH17 cells.
    DOI:  https://doi.org/10.1038/s41586-022-05264-1
  10. Cold Spring Harb Protoc. 2022 Sep 30.
    Analysis of Mitochondrial Dynamics in Adult Drosophila Axons.
    Daniel C Maddison, Francesca Mattedi, Alessio Vagnoni, Gaynor Ann Smith.
      Neuronal survival depends on the generation of ATP from an ever-changing mitochondrial network. This requires a fine balance between the constant degradation of damaged mitochondria, biogenesis of new mitochondria, movement along microtubules, dynamic processes, and adequate functional capacity to meet firing demands. The distribution of mitochondria needs to be tightly controlled throughout the entire neuron, including its projections. Axons in particular can be enormous structures compared to the size of the cell soma, and how mitochondria are maintained in these compartments is poorly defined. Mitochondrial dysfunction in neurons is associated with aging and neurodegenerative diseases, with the axon being preferentially vulnerable to destruction. Drosophila offer a unique way to study these organelles in fully differentiated adult neurons in vivo. Here, we briefly review the regulation of neuronal mitochondria in health, aging, and disease and introduce two methodological approaches to study mitochondrial dynamics and transport in axons using the Drosophila wing system.
    DOI:  https://doi.org/10.1101/pdb.top107819
  11. Zhejiang Da Xue Xue Bao Yi Xue Ban. 2022 Feb 25. 51(1): 122-128
    Expert consensus on diagnosis and treatment of very long-chain acyl-CoA dehydrogenase deficiency.
    Wenhui Lin.
      Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency is a metabolic disease of long chain fatty acid oxidation. The clinical manifestations are heterogeneous, mainly with heart, liver, skeletal muscle and brain damage, and the onset of which can be from newborn to adult. Cardiomyopathy type is more serious with high mortality. The liver failure type and myopathy type would be potentially lethal, but generally the prognosis is relatively good. Recurrent hypoglycemia, energy metabolism disorder, liver dysfunction, cardiomyopathy and serious arrhythmia are the main causes of death. Most patients can be identified through neonatal screening, and the prognosis is usually good in patients with early diagnosis and treatment. The purpose of this consensus is to standardize the diagnosis, treatment and management of VLCAD deficiency, so as to improve the prognosis of patients and reduce death and disability.
    Keywords:  Autosomal recessive disease; Expert consensus; Fatty acid β-oxidation; Neonatal screening; Very long-chain acyl-CoA dehydrogenase deficiency
    DOI:  https://doi.org/10.3724/zdxbyxb-2022-0107
  12. Sci Adv. 2022 Sep 30. 8(39): eabp8701
    Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons.
    Enrico Zampese, David L Wokosin, Patricia Gonzalez-Rodriguez, Jaime N Guzman, Tatiana Tkatch, Jyothisri Kondapalli, William C Surmeier, Karis B D'Alessandro, Diego De Stefani, Rosario Rizzuto, Masamitsu Iino, Jeffery D Molkentin, Navdeep S Chandel, Paul T Schumacker, D James Surmeier.
      How do neurons match generation of adenosine triphosphate by mitochondria to the bioenergetic demands of regenerative activity? Although the subject of speculation, this coupling is still poorly understood, particularly in neurons that are tonically active. To help fill this gap, pacemaking substantia nigra dopaminergic neurons were studied using a combination of optical, electrophysiological, and molecular approaches. In these neurons, spike-activated calcium (Ca2+) entry through Cav1 channels triggered Ca2+ release from the endoplasmic reticulum, which stimulated mitochondrial oxidative phosphorylation through two complementary Ca2+-dependent mechanisms: one mediated by the mitochondrial uniporter and another by the malate-aspartate shuttle. Disrupting either mechanism impaired the ability of dopaminergic neurons to sustain spike activity. While this feedforward control helps dopaminergic neurons meet the bioenergetic demands associated with sustained spiking, it is also responsible for their elevated oxidant stress and possibly to their decline with aging and disease.
    DOI:  https://doi.org/10.1126/sciadv.abp8701
  13. Cold Spring Harb Protoc. 2022 Sep 30.
    Clonal Imaging of Mitochondria in the Dissected Fly Wing.
    Daniel C Maddison, Francesca Mattedi, Alessio Vagnoni, Gaynor Ann Smith.
      Mitochondria are essential for long-term neuronal function and survival. They are maintained in neurons, including long axonal stretches, through dynamic processes such as fission, fusion, biogenesis, and mitophagy. Here, we describe a protocol for the in-depth morphological analysis of individual mitochondria in axons in vivo. Most mitochondrial analysis of axons is currently performed in vitro with neurons in a developmental state. Therefore, an understanding of the axonal mitochondrial network during aging in fully differentiated neurons and the long-term consequence of gene knockout is often not developed. By using a clonal system paired with fluorescent genetically encoded markers in the Drosophila wing, we can visualize individual neurons (out of the whole bundle), including their long axons and the mitochondria that they contain, using confocal imaging. The clonal system also allows visualization of neurons with genetic perturbations that would otherwise be lethal if present in the whole organism, allowing investigators to bypass lethality. This protocol can further be adapted to measure the physiological and biochemical state of the mitochondria. Mitochondrial morphology and health in axons are tightly linked to aging, axon injury, and neurodegeneration; therefore, this method can be used to investigate mitochondrial dysfunction associated with novel genes or those linked to neurodegenerative disease and axonopathy.
    DOI:  https://doi.org/10.1101/pdb.prot108051
  14. FEBS Lett. 2022 Sep 30.
    On the role of ubiquinone in the proton translocation mechanism of respiratory complex I.
    Mårten Wikström, Amina Djurabekova, Vivek Sharma.
      Complex I converts oxidoreduction energy into a proton electrochemical gradient across the inner mitochondrial or bacterial cell membrane. This gradient is the primary source of energy for aerobic synthesis of ATP. Oxidation of reduced nicotinamide adenine dinucleotide (NADH) by ubiquinone (Q) yields NAD+ and ubiquinol (QH2 ), which is tightly coupled to translocation of four protons from the negatively to the positively charged side of the membrane. Electrons from NADH oxidation reach the iron-sulfur centre N2 positioned near the bottom of a tunnel that extends ca. 30Å from the membrane domain into the hydrophilic domain of the complex. The tunnel is occupied by ubiquinone, which can take a distal position near the N2 centre, or proximal positions closer to the membrane. Here, we review important structural, kinetic and thermodynamic properties of ubiquinone that define its role in complex I function. We suggest that this function exceeds that of a mere substrate or electron acceptor, and propose that ubiquinone may be the redox element of complex I coupling electron transfer to proton translocation.
    Keywords:  energy conservation; mitochondria; oxidative phosphorylation; proton pumping
    DOI:  https://doi.org/10.1002/1873-3468.14506
  15. Acta Neuropathol Commun. 2022 Sep 26. 10(1): 142
    The neuropathologic findings in a case of progressive cavitating leukoencephalopathy due to NDUFV1 pathogenic variants.
    Nicole Becker, Aditi Sharma, Matthew Gosse, Brooke Kubat, Kyle S Conway.
      Pathogenic variants in the NDUFV1 gene, which codes for complex I of the mitochondrial respiratory chain, have been associated with a variety of clinical phenotypes, including a progressive cavitating leukoencephalopathy. The neuropathology of NDUFV1-associated leukoencephalopathy is not well-described. We present a report of a 24-year-old female with two pathogenic variants in the NDUFV1 gene, together with antemortem skeletal muscle biopsy and postmortem neuropathologic examination. Autopsy neuropathology showed a cavitating leukoencephalopathy with extensive white matter involvement, regions of active demyelination, and sparing of the subcortical U-fibers. Muscle biopsy showed subtle but distinct histologic abnormalities by light microscopy, and ultrastructural analysis demonstrated mitochondrial abnormalities including abnormal subsarcolemmal mitochondrial accumulation, electron-dense inclusions, and enlarged mitochondria with abnormal cristae. Our report is the first comprehensive description of the neuropathology in a patient with compound heterozygous variants in the NDUFV1 gene and progressive cavitating leukoencephalopathy. This case is evidence of pathogenicity of one NDUFV1 variant (c.565 T > C, p.S189P), which has not been previously described as pathogenic. These findings, in combination with the ultrastructural abnormalities in the mitochondria by electron microscopy, support the mitochondrial nature of the pathology. Together, this case highlights the link between mitochondrial abnormalities and demyelinating processes in the central nervous system (CNS).
    Keywords:  Complex I; Demyelination; Mitochondrial leukoencephalopathy; Progressive cavitating leukoencephalopathy
    DOI:  https://doi.org/10.1186/s40478-022-01445-1
  16. Cold Spring Harb Protoc. 2022 Sep 30.
    Live Imaging of Mitochondria in the Intact Fly Wing.
    Francesca Mattedi, Daniel C Maddison, Gaynor Ann Smith, Alessio Vagnoni.
      Detailed mechanisms governing the transport of mitochondria in neurons have recently emerged, although it is still poorly understood how the regulation of transport is coordinated in space and time within the physiological context of an organism. Here, we provide a protocol to study the intracellular dynamics of mitochondria in the wing neurons of adult Drosophila in situ. The mounting and imaging procedures that we describe are suitable for use on most microscopes, and they can be easily implemented in any laboratory. Our noninvasive mounting procedures, combined with the translucency of the wing cuticle in adult animals, makes the wing nervous system accessible to advanced microscopy studies in a physiological environment. Combining the powerful genetics of Drosophila with time-lapse live imaging, users of this protocol will be able to analyze mitochondrial dynamics over time in a subset of sensory neurons in the wing. These cells extend long axons with a stereotypical plus-end-out microtubule orientation that represents a unique model to understand the logic of neuronal cargo transport, including the mitochondria. Finally, the neurons in this tissue respond to mechanical and chemical stimulation of the sensory organs of the wing, opening up the possibility of coupling the study of mitochondrial dynamics with the modulation of neuronal activity in aging Drosophila We anticipate that the unique characteristics of this in vivo system will contribute to the discovery of novel mechanisms that regulate mitochondrial dynamics within an organismal context with relevant implications for the pathogenesis of age-dependent neurological disorders.
    DOI:  https://doi.org/10.1101/pdb.prot108052
  17. Front Cell Dev Biol. 2022 ;10 996061
    Neurodegeneration-associated mitochondrial proteins, CHCHD2 and CHCHD10-what distinguishes the two?
    Aya Ikeda, Yuzuru Imai, Nobutaka Hattori.
      Coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) and Coiled-coil-helix-coiled-coil-helix domain containing 10 (CHCHD10) are mitochondrial proteins that are thought to be genes which duplicated during evolution and are the causative genes for Parkinson's disease and amyotrophic lateral sclerosis/frontotemporal lobe dementia, respectively. CHCHD2 forms a heterodimer with CHCHD10 and a homodimer with itself, both of which work together within the mitochondria. Various pathogenic and disease-risk variants have been identified; however, how these mutations cause neurodegeneration in specific diseases remains a mystery. This review focuses on important new findings published since 2019 and discusses avenues to solve this mystery.
    Keywords:  amyothophic lateral sclerosis; dopaminergic (DA) neuron; genetics; mitochondria; motor neurons; parkinson's disease
    DOI:  https://doi.org/10.3389/fcell.2022.996061
  18. Mol Genet Genomic Med. 2022 Oct 01. e2059
    Kearns-Sayre syndrome case. Novel 5,9 kb mtDNA deletion.
    Kristina Grigalionienė, Birutė Burnytė, Danutė Balkelienė, Laima Ambrozaitytė, Algirdas Utkus.
       BACKGROUND: Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder characterized by onset before 20 years of age and a typical clinical triad: progressive external ophthalmoplegia, pigmentary retinopathy and cardiac conduction anomalies. In most cases KSS is caused by spontaneous heteroplasmic single large-scale mitochondrial DNA (mtDNA) deletions. Long-range polymerase chain reaction (LR-PCR), next generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) are the most widely applied methods for the identification of mtDNA deletions. Here, we report the case of 20-year-old male who presented with classic Kearns-Sayre syndrome, confirmed by novel 5,9 kb mtDNA deletion.
    METHODS AND RESULTS: LR-PCR and MLPA methods were applied to identify the mitochondrial DNA deletion for the patient, but the results were conflicting. Molecular analysis using primer walking and Sanger sequencing identified a novel 5888 base pairs mtDNA deletion (NC_012920.1:m.6069_11956del) with CAAC nucleotides repeat sequence at the breakpoints.
    CONCLUSION: Our study enriched the mtDNA variation spectrum associated with KSS and demonstrated the importance of choosing relevant molecular genetic methods.
    Keywords:  KSS; Kearns-Sayre syndrome; mitochondrial disorder; single large-scale mitochondrial DNA deletion syndromes
    DOI:  https://doi.org/10.1002/mgg3.2059
  19. Nat Rev Genet. 2022 Sep 27.
    Promoting a new view of mitochondrial genome regulation.
    Dorothy Clyde.
      
    DOI:  https://doi.org/10.1038/s41576-022-00536-y
  20. Front Cell Dev Biol. 2022 ;10 918691
    MFN2 mediates ER-mitochondrial coupling during ER stress through specialized stable contact sites.
    Benjamin Gottschalk, Zhanat Koshenov, Olaf A Bachkoenig, René Rost, Roland Malli, Wolfgang F Graier.
      Endoplasmic reticulum (ER) functions critically depend on a suitable ATP supply to fuel ER chaperons and protein trafficking. A disruption of the ability of the ER to traffic and fold proteins leads to ER stress and the unfolded protein response (UPR). Using structured illumination super-resolution microscopy, we revealed increased stability and lifetime of mitochondrial associated ER membranes (MAM) during ER stress. The consequent increase of basal mitochondrial Ca2+ leads to increased TCA cycle activity and enhanced mitochondrial membrane potential, OXPHOS, and ATP generation during ER stress. Subsequently, OXPHOS derived ATP trafficking towards the ER was increased. We found that the increased lifetime and stability of MAMs during ER stress depended on the mitochondrial fusion protein Mitofusin2 (MFN2). Knockdown of MFN2 blunted mitochondrial Ca2+ effect during ER stress, switched mitochondrial F1FO-ATPase activity into reverse mode, and strongly reduced the ATP supply for the ER during ER stress. These findings suggest a critical role of MFN2-dependent MAM stability and lifetime during ER stress to compensate UPR by strengthening ER ATP supply by the mitochondria.
    Keywords:  ER stress; mitochondria; mitochondria-associated membranes (MAM); mitochondrial Ca2+; mitofusin 2
    DOI:  https://doi.org/10.3389/fcell.2022.918691
  21. Saudi Pharm J. 2022 Aug;30(8): 1065-1078
    Recent advances in mitochondrial diseases: From molecular insights to therapeutic perspectives.
    Ahmad M Aldossary, Essam A Tawfik, Mohammed N Alomary, Samar A Alsudir, Ahmed J Alfahad, Abdullah A Alshehri, Fahad A Almughem, Rean Y Mohammed, Mai M Alzaydi.
      Mitochondria are double-membraned cytoplasmic organelles that are responsible for the production of energy in eukaryotic cells. The process is completed through oxidative phosphorylation (OXPHOS) by the respiratory chain (RC) in mitochondria. Thousands of mitochondria may be present in each cell, depending on the function of that cell. Primary mitochondria disorder (PMD) is a clinically heterogeneous disease associated with germline mutations in mitochondrial DNA (mtDNA) and/or nuclear DNA (nDNA) genes, and impairs mitochondrial structure and function. Mitochondrial dysfunction can be detected in early childhood and may be severe, progressive and often multi-systemic, involving a wide range of organs. Understanding epigenetic factors and pathways mutations can help pave the way for developing an effective cure. However, the lack of information about the disease (including age of onset, symptoms, clinical phenotype, morbidity and mortality), the limits of current preclinical models and the wide range of phenotypic presentations hamper the development of effective medicines. Although new therapeutic approaches have been introduced with encouraging preclinical and clinical outcomes, there is no definitive cure for PMD. This review highlights recent advances, particularly in children, in terms of etiology, pathophysiology, clinical diagnosis, molecular pathways and epigenetic alterations. Current therapeutic approaches, future advances and proposed new therapeutic plans will also be discussed.
    Keywords:  Epigenetic alterations; Fetal gene therapy; Gene editing; Mitochondrial diseases; Nanomedicine
    DOI:  https://doi.org/10.1016/j.jsps.2022.05.011
  22. Cell Rep. 2022 Sep 27. pii: S2211-1247(22)01249-9. [Epub ahead of print]40(13): 111408
    Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3.
    Ryan R Cupo, Alexandrea N Rizo, Gabriel A Braun, Eric Tse, Edward Chuang, Kushol Gupta, Daniel R Southworth, James Shorter.
      The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). How Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. These advances illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.
    Keywords:  AAA+ proteins, protein aggregation; CP: Cell biology; chaperone; disaggregase; mitochondria; mitochondrial disorders; therapeutics
    DOI:  https://doi.org/10.1016/j.celrep.2022.111408
  23. Neurol Genet. 2022 Oct;8(5): e200030
    Biallelic COX10 Mutations and PMP22 Deletion in a Family With Leigh Syndrome and Hereditary Neuropathy With Liability to Pressure Palsy.
    Yasuko Kuroha, Takanobu Ishiguro, Mari Tada, Norikazu Hara, Kei Murayama, Izumi Kawachi, Kensaku Kasuga, Akinori Miyashita, Arika Hasegawa, Tetsuya Takahashi, Nae Matsubara, Osamu Onodera, Akiyoshi Kakita, Ryoko Koike, Takeshi Ikeuchi.
       Objectives: Leigh syndrome is a progressive encephalopathy characterized by symmetrical lesions in brain. This study aimed to investigate the clinicopathologic and genetic characteristics of a family with Leigh syndrome and hereditary neuropathy with liability to pressure palsy (HNPP).
    Methods: Data from a Japanese family's clinical features, MRIs, muscle biopsy, and an autopsy were analyzed. A whole-exome sequence was performed, as well as real-time PCR analysis to determine copy number variations and Western blot analyses.
    Results: The proband and her 2 siblings developed spastic paraplegia and mental retardation during childhood. The proband and her sister had peripheral neuropathy, whereas their father developed compression neuropathy. Leigh encephalopathy was diagnosed neuropathologically. Brain MRI revealed changes in cerebral white matter as well as multiple lesions in the brainstem and cerebellum. Muscle biopsy revealed type 2 fiber uniformity and decreased staining of cytochrome c oxidase. The COX10 missense mutation was identified through whole-exome sequence. A 1.4-Mb genomic deletion extending from intron 5 of COX10 to PMP22 was detected.
    Discussion: These findings suggest that in this family, Leigh syndrome is associated with a mitochondrial respiratory chain complex IV deficiency caused by biallelic COX10 mutations coexisting with HNPP caused by heterozygous PMP22 deletion.
    DOI:  https://doi.org/10.1212/NXG.0000000000200030
  24. Front Cell Dev Biol. 2022 ;10 938177
    Control of mitochondrial dynamics and apoptotic pathways by peroxisomes.
    Chenxing Jiang, Tomohiko Okazaki.
      Peroxisomes are organelles containing different enzymes that catalyze various metabolic pathways such as β-oxidation of very long-chain fatty acids and synthesis of plasmalogens. Peroxisome biogenesis is controlled by a family of proteins called peroxins, which are required for peroxisomal membrane formation, matrix protein transport, and division. Mutations of peroxins cause metabolic disorders called peroxisomal biogenesis disorders, among which Zellweger syndrome (ZS) is the most severe. Although patients with ZS exhibit severe pathology in multiple organs such as the liver, kidney, brain, muscle, and bone, the pathogenesis remains largely unknown. Recent findings indicate that peroxisomes regulate intrinsic apoptotic pathways and upstream fission-fusion processes, disruption of which causes multiple organ dysfunctions reminiscent of ZS. In this review, we summarize recent findings about peroxisome-mediated regulation of mitochondrial morphology and its possible relationship with the pathogenesis of ZS.
    Keywords:  Zellweger syndrome; apoptosis; fission-fusion; mitochondria; organelle interaction; peroxisomes; tethering
    DOI:  https://doi.org/10.3389/fcell.2022.938177
  25. J Biol Chem. 2022 Sep 23. pii: S0021-9258(22)00976-0. [Epub ahead of print] 102533
    Eisosome protein Pil1 regulates mitochondrial morphology, mitophagy, and cell death in Saccharomyces cerevisiae.
    Amita Pal, Arunkumar Paripati, Pallavi Deolal, Arpan Chatterjee, Pushpa Rani Prasad, Priyanka Adla, Naresh Babu V Sepuri.
      Mitochondrial morphology and dynamics maintain mitochondrial integrity by regulating its size, shape, distribution, and connectivity, thereby modulating various cellular processes. Several studies have established a functional link between mitochondrial dynamics, mitophagy, and cell death, but further investigation is needed to identify specific proteins involved in mitochondrial dynamics. Any alteration in the integrity of the mitochondria has severe ramifications that include disorders like cancer and neurodegeneration. In this study, we used budding yeast as a model organism and found that Pil1, the major component of the eisosome complex, also localizes to the periphery of mitochondria. Interestingly, the absence of Pil1 causes the branched tubular morphology of mitochondria to be abnormally fused or aggregated, whereas its overexpression leads to mitochondrial fragmentation. Most importantly, pil1Δ cells are defective in mitophagy and bulk autophagy, resulting in elevated levels of ROS and protein aggregates. In addition, we show that pil1Δ cells are more prone to cell death. Yeast two-hybrid analysis and co-immunoprecipitations show the interaction of Pil1 with two major proteins in mitochondrial fission, Fis1 and Dnm1. Additionally, our data suggest that the role of Pil1 in maintaining mitochondrial shape is dependent on Fis1 and Dnm1, but it functions independently in mitophagy and cell death pathways. Together, our data suggest that Pil1, an eisosome protein, is a novel regulator of mitochondrial morphology, mitophagy, and cell death.
    Keywords:  Saccharomyces cerevisiae; autophagy; cell death; mitochondria; mitophagy; protein aggregation; reactive oxygen species (ROS)
    DOI:  https://doi.org/10.1016/j.jbc.2022.102533
  26. Stem Cell Reports. 2022 Sep 12. pii: S2213-6711(22)00423-4. [Epub ahead of print]
    High-content phenotyping of Parkinson's disease patient stem cell-derived midbrain dopaminergic neurons using machine learning classification.
    Aurore Vuidel, Loïc Cousin, Beatrice Weykopf, Simone Haupt, Zahra Hanifehlou, Nicolas Wiest-Daesslé, Michaela Segschneider, Joohyun Lee, Yong-Jun Kwon, Michael Peitz, Arnaud Ogier, Laurent Brino, Oliver Brüstle, Peter Sommer, Johannes H Wilbertz.
      Combining multiple Parkinson's disease (PD) relevant cellular phenotypes might increase the accuracy of midbrain dopaminergic neuron (mDAN) in vitro models. We differentiated patient-derived induced pluripotent stem cells (iPSCs) with a LRRK2 G2019S mutation, isogenic control, and genetically unrelated iPSCs into mDANs. Using automated fluorescence microscopy in 384-well-plate format, we identified elevated levels of α-synuclein (αSyn) and serine 129 phosphorylation, reduced dendritic complexity, and mitochondrial dysfunction. Next, we measured additional image-based phenotypes and used machine learning (ML) to accurately classify mDANs according to their genotype. Additionally, we show that chemical compound treatments, targeting LRRK2 kinase activity or αSyn levels, are detectable when using ML classification based on multiple image-based phenotypes. We validated our approach using a second isogenic patient-derived SNCA gene triplication mDAN model which overexpresses αSyn. This phenotyping and classification strategy improves the practical exploitability of mDANs for disease modeling and the identification of novel LRRK2-associated drug targets.
    Keywords:  LRRK2; Parkinson's disease; SNCA; disease modeling; iPSC; machine learning
    DOI:  https://doi.org/10.1016/j.stemcr.2022.09.001
  27. Nature. 2022 09;609(7929): 907-910
    A nomenclature consensus for nervous system organoids and assembloids.
    Sergiu P Pașca, Paola Arlotta, Helen S Bateup, J Gray Camp, Silvia Cappello, Fred H Gage, Jürgen A Knoblich, Arnold R Kriegstein, Madeline A Lancaster, Guo-Li Ming, Alysson R Muotri, In-Hyun Park, Orly Reiner, Hongjun Song, Lorenz Studer, Sally Temple, Giuseppe Testa, Barbara Treutlein, Flora M Vaccarino.
      Self-organizing three-dimensional cellular models derived from human pluripotent stem cells or primary tissue have great potential to provide insights into how the human nervous system develops, what makes it unique and how disorders of the nervous system arise, progress and could be treated. Here, to facilitate progress and improve communication with the scientific community and the public, we clarify and provide a basic framework for the nomenclature of human multicellular models of nervous system development and disease, including organoids, assembloids and transplants.
    DOI:  https://doi.org/10.1038/s41586-022-05219-6
  28. Br J Ophthalmol. 2022 Sep 26. pii: bjophthalmol-2022-321790. [Epub ahead of print]
    Inherited causes of combined vision and hearing loss: clinical features and molecular genetics.
    Thales Antonio Cabral de Guimaraes, Elizabeth Arram, Ahmed F Shakarchi, Michalis Georgiou, Michel Michaelides.
      Combined vision and hearing loss, also known as dual sensory impairment, can occur in several genetic conditions, including ciliopathies such as Usher and Bardet-Biedl syndrome, mitochondrial DNA disorders and systemic diseases, such as CHARGE, Stickler, Waardenburg, Alport and Alstrom syndrome. The retinal phenotype may point to the diagnosis of such disorders. Herein, we aim to provide a comprehensive review of the molecular genetics and clinical features of the most common non-chromosomal inherited disorders to cause dual sensory impairment.
    Keywords:  dystrophy; genetics; imaging; macula; retina
    DOI:  https://doi.org/10.1136/bjo-2022-321790
  29. Nat Methods. 2022 Sep 29.
    Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.
    Trang Le, Casper F Winsnes, Ulrika Axelsson, Hao Xu, Jayasankar Mohanakrishnan Kaimal, Diana Mahdessian, Shubin Dai, Ilya S Makarov, Vladislav Ostankovich, Yang Xu, Eric Benhamou, Christof Henkel, Roman A Solovyev, Nikola Banić, Vito Bošnjak, Ana Bošnjak, Andrija Miličević, Wei Ouyang, Emma Lundberg.
      While spatial proteomics by fluorescence imaging has quickly become an essential discovery tool for researchers, fast and scalable methods to classify and embed single-cell protein distributions in such images are lacking. Here, we present the design and analysis of the results from the competition Human Protein Atlas - Single-Cell Classification hosted on the Kaggle platform. This represents a crowd-sourced competition to develop machine learning models trained on limited annotations to label single-cell protein patterns in fluorescent images. The particular challenges of this competition include class imbalance, weak labels and multi-label classification, prompting competitors to apply a wide range of approaches in their solutions. The winning models serve as the first subcellular omics tools that can annotate single-cell locations, extract single-cell features and capture cellular dynamics.
    DOI:  https://doi.org/10.1038/s41592-022-01606-z
  30. Nat Genet. 2022 Sep 29.
    Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.
    Karthik A Jagadeesh, Kushal K Dey, Daniel T Montoro, Rahul Mohan, Steven Gazal, Jesse M Engreitz, Ramnik J Xavier, Alkes L Price, Aviv Regev.
      Genome-wide association studies provide a powerful means of identifying loci and genes contributing to disease, but in many cases, the related cell types/states through which genes confer disease risk remain unknown. Deciphering such relationships is important for identifying pathogenic processes and developing therapeutics. In the present study, we introduce sc-linker, a framework for integrating single-cell RNA-sequencing, epigenomic SNP-to-gene maps and genome-wide association study summary statistics to infer the underlying cell types and processes by which genetic variants influence disease. The inferred disease enrichments recapitulated known biology and highlighted notable cell-disease relationships, including γ-aminobutyric acid-ergic neurons in major depressive disorder, a disease-dependent M-cell program in ulcerative colitis and a disease-specific complement cascade process in multiple sclerosis. In autoimmune disease, both healthy and disease-dependent immune cell-type programs were associated, whereas only disease-dependent epithelial cell programs were prominent, suggesting a role in disease response rather than initiation. Our framework provides a powerful approach for identifying the cell types and cellular processes by which genetic variants influence disease.
    DOI:  https://doi.org/10.1038/s41588-022-01187-9
  31. Methods Mol Biol. 2023 ;2554 231-249
    Databases and Tools to Investigate Protein-Metabolite Interactions.
    Leonardo Perez de Souza, Alisdair R Fernie.
      Protein-metabolite interactions (PMIs) are directly responsible for the regulation of numerous processes. From the direct regulation of enzymes to complex developmental processes intermediated by hormones, PMIs are central to understanding the molecular mechanisms of important physiological phenomena. Still, proving such interactions experimentally has proven an arduous task. We discuss here some of the current technologies contributing to expand our knowledge on PMIs, with particular emphasis on platforms and databases to explore the highly heterogenous nature of characterized PMIs, which is likely to be an essential resource on the development of new computational approaches to predict and validate interactions based on large-scale PMI screenings.
    Keywords:  Metabolomics; Metabolomics web resources; Protein-metabolite databases; Protein-metabolite interactions; Proteomics
    DOI:  https://doi.org/10.1007/978-1-0716-2624-5_14
  32. Hum Mol Genet. 2022 Sep 26. pii: ddac239. [Epub ahead of print]
    Histidine supplementation can escalate or rescue HARS deficiency in a Charcot Marie Tooth Disease model.
    Yi Qiu, Rosan Kenana, Aruun Beharry, Sarah D P Wilhelm, Sung Yuan Hsu, Victoria M Siu, Martin Duennwald, Ilka U Heinemann.
      Aminoacyl-tRNA synthetases (ARSs) are essential enzymes responsible for charging amino acids onto cognate tRNAs during protein synthesis. In histidyl-tRNA synthetase (HARS), autosomal dominant mutations V133F, V155G, Y330C, S356N in the HARS catalytic domain cause Charcot Marie Tooth Disease Type 2 W (CMT2W), while RNA-binding domain mutation Y454S causes recessive Usher Syndrome Type IIIB (USH3B). In a yeast model, all human HARS variants complemented a genomic deletion of the yeast ortholog hts1 at high expression levels. CMT2W associated mutations, but not Y454S, resulted in reduced growth. We show mistranslation of histidine to glutamine and threonine in V155G and S356N but not Y330C mutants in yeast. Mistranslating V155G and S356N mutants lead to accumulation of insoluble proteins, which was rescued by histidine. Mutants V133F and Y330C showed the most significant growth defect and decreased HARS abundance in cells. Here, histidine supplementation led to insoluble protein aggregation and further reduced viability, indicating histidine toxicity associated with these mutants. V133F proteins displayed reduced thermal stability in vitro, which was rescued by tRNA. Our data will inform future treatment options for HARS patients, where histidine supplementation may either have a toxic or compensating effect depending on the nature of the causative HARS variant.
    DOI:  https://doi.org/10.1093/hmg/ddac239
  33. Methods Mol Biol. 2023 ;2577 55-64
    Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers.
    Shinjiro Hino, Tetsuya Sato, Mitsuyoshi Nakao.
      Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the most widely used method for analyzing genome-wide DNA-protein interactions. Because there is considerable variation in the modes and strengths of DNA-protein interactions, chromatin immunoprecipitation (ChIP) protocols have been diversified and optimized for different needs. Here, we describe protocols for detecting histone modifications and modifiers using various crosslinking and immunoprecipitation conditions. We provide a complete ChIP-seq workflow covering sample preparation, immunoprecipitation, next-generation sequencing (NGS) library preparation, and data analyses.
    Keywords:  Dual crosslink; Histone; Immunoprecipitation; Next-generation sequencing
    DOI:  https://doi.org/10.1007/978-1-0716-2724-2_4
  34. Nucleic Acids Res. 2022 Sep 28. pii: gkac831. [Epub ahead of print]
    GotEnzymes: an extensive database of enzyme parameter predictions.
    Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen.
      Enzyme parameters are essential for quantitatively understanding, modelling, and engineering cells. However, experimental measurements cover only a small fraction of known enzyme-compound pairs in model organisms, much less in other organisms. Artificial intelligence (AI) techniques have accelerated the pace of exploring enzyme properties by predicting these in a high-throughput manner. Here, we present GotEnzymes, an extensive database with enzyme parameter predictions by AI approaches, which is publicly available at https://metabolicatlas.org/gotenzymes for interactive web exploration and programmatic access. The first release of this data resource contains predicted turnover numbers of over 25.7 million enzyme-compound pairs across 8099 organisms. We believe that GotEnzymes, with the readily-predicted enzyme parameters, would bring a speed boost to biological research covering both experimental and computational fields that involve working with candidate enzymes.
    DOI:  https://doi.org/10.1093/nar/gkac831
  35. Methods Mol Biol. 2023 ;2577 3-20
    DNA Methylation Analysis Using Bisulfite Pyrosequencing.
    Ken Higashimoto, Satoshi Hara, Hidenobu Soejima.
      Pyrosequencing is a DNA sequencing-by-synthesis technique that can quantitatively detect single-nucleotide polymorphisms (SNPs). With pyrosequencing, the level of DNA methylation can be calculated according to the ratio of artificial cytosine/thymine SNPs produced by bisulfite conversion at each CpG site. This analysis method provides a reproducible and accurate measurement of methylation levels at CpG sites near sequencing primers with high quantitative resolution. DNA methylation plays an important role in mammalian development and cellular physiology; alterations in DNA methylation patterns have been implicated in several common diseases as well as cancers and imprinting disorders. Evaluating DNA methylation levels via pyrosequencing is useful for identifying biomarkers that could help with the diagnosis, prognosis, treatment selection, and onset risk assessment for several diseases. We describe the principles of pyrosequencing and detail a bisulfite pyrosequencing protocol based on our experience and the PyroMark Q24 User Manual.
    Keywords:  Biomarker detection; Bisulfite conversion; CpG site; DNA methylation; Primer design; Pyrosequencing technology; SNPs
    DOI:  https://doi.org/10.1007/978-1-0716-2724-2_1
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