bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023‒06‒11
47 papers selected by
Catalina Vasilescu
Helmholz Munich
  1. Defective mitochondrial import as a challenge for cellular protein homeostasis.
  2. Editorial: the role of mitochondrial endoplasmic reticulum contact sites in human health and disease.
  3. Mitochondrial networks through the lens of mathematics.
  4. A cytosolic surveillance mechanism activates the mitochondrial UPR.
  5. Ablation of Sam50 is associated with fragmentation and alterations in metabolism in human myotubes.
  6. Human mitochondrial ADP/ATP carrier SLC25A4 operates with a ping-pong kinetic mechanism.
  7. MICU1 deficiency alters mitochondrial morphology and cytochrome C release.
  8. Multimodal single-cell analysis of non-random heteroplasmy distribution in human retinal mitochondrial disease.
  9. Calcium and bicarbonate signaling pathways have pivotal, resonating roles in matching ATP production to demand.
  10. Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart.
  11. Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy.
  12. Case report: A rare variant m.4135T>C in the MT-ND1 gene leads to Leber hereditary optic neuropathy and altered respiratory chain supercomplexes.
  13. The acute effect of different NAD+ precursors included in the combined metabolic activators.
  14. FAM210A Regulates Mitochondrial Translation and Maintains Cardiac Mitochondrial Homeostasis.
  15. Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging.
  16. Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA.
  17. Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4.
  18. Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis.
  19. The multiple links between actin and mitochondria.
  20. Genetic deletion of skeletal muscle iPLA2γ results in mitochondrial dysfunction, muscle atrophy and alterations in whole-body energy metabolism.
  21. HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference.
  22. ATF4 regulates mitochondrial content, morphology, and function in differentiating skeletal muscle myotubes.
  23. LDLs take a shortcut to mitochondria.
  24. Mitophagy and long-term neuronal homeostasis.
  25. Eating your mitochondria-when too much of a good thing turns bad.
  26. Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.
  27. Oxidative phosphorylation in bone cells.
  28. DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data.
  29. PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy.
  30. Nicotinamide Riboside Activates SIRT5 Deacetylation.
  31. Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models.
  32. Expression and subcellular localization of mitochondrial docking protein, syntaphilin, in oligodendrocytes and CNS myelin sheath.
  33. Using light scattering to assess how phospholipid-protein interactions affect complex I functionality in liposomes.
  34. Megamitochondria plasticity: function transition from adaption to disease.
  35. Association of mitochondrial DNA variation with high myopia in a Han Chinese population.
  36. NMNAT2 supports vesicular glycolysis via NAD homeostasis to fuel fast axonal transport.
  37. SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.
  38. Creating Optimal Conditions for OPA1 isoforms by Western Blot in Muscle Tissue.
  39. The mTOR signaling pathway in cardiac aging.
  40. Roles of malate and aspartate in gluconeogenesis in various physiological and pathological states.
  41. Mitochondrial Protease Targeting Chimeras for Mitochondrial Matrix Protein Degradation.
  42. Dominant aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models.
  43. Nicotinamide adenine dinucleotide (NAD+)-dependent signaling in neurological disorders.
  44. Integrated multi-omics for rapid rare disease diagnosis on a national scale.
  45. Editorial: Mitochondrial disorders and cardiovascular diseases.
  46. The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila.
  47. Distinct longevity mechanisms across and within species and their association with aging.
  1. FEBS Lett. 2023 Jun 05.
    Defective mitochondrial import as a challenge for cellular protein homeostasis.
    Klaudia K Maruszczak, Selvaraj Ayyamperumal, Agnieszka Chacinska.
      Mitochondria are organelles indispensable for the correct functioning of eukaryotic cells. Their significance for cellular homeostasis is manifested by the existence of complex quality control pathways that monitor organellar fitness. Mitochondrial biogenesis relies on the efficient import of mitochondrial precursor proteins, a large majority of which are encoded by nuclear DNA and synthesized in the cytosol. This creates a demand for highly specialized import routes that comprise cytosolic factors and organellar translocases. The passage of newly encoded mitochondrial precursor proteins through the cytosol to the translocase of the outer mitochondrial membrane (TOM) is under tight surveillance. As a result of mitochondrial import defects, mitochondrial precursor proteins accumulate in the cytosol or clog the TOM complex, which in turn stimulates cellular stress responses to minimize the consequences of these challenges. These responses are critical for maintaining protein homeostasis under conditions of mitochondrial stress. The present review summarizes recent advances in the field of mitochondrial protein import quality control and discusses the role of this quality control within the network of cellular mechanisms that maintain the cellular homeostasis of proteins.
    Keywords:  cellular stress responses; mitochondria; mitochondrial dysfunction; mitochondrial quality control; protein aggregates; protein homeostasis
    DOI:  https://doi.org/10.1002/1873-3468.14677
  2. Front Mol Biosci. 2023 ;10 1223354
    Editorial: the role of mitochondrial endoplasmic reticulum contact sites in human health and disease.
    Prasanna Katti, Sharifa Love-Rutledge, Sandra A Murray, Antentor Hinton.
      
    Keywords:  MERCs; contact sites; disease; mitochondria; pathology
    DOI:  https://doi.org/10.3389/fmolb.2023.1223354
  3. Phys Biol. 2023 Jun 08.
    Mitochondrial networks through the lens of mathematics.
    Greyson Lewis, Wallace F Marshall.
      Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphological
space of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.
    Keywords:  graph theory; mitochondrial networks; persistent homology; planar graphs; scaling
    DOI:  https://doi.org/10.1088/1478-3975/acdcdb
  4. Nature. 2023 Jun 07.
    A cytosolic surveillance mechanism activates the mitochondrial UPR.
    F X Reymond Sutandy, Ines Gößner, Georg Tascher, Christian Münch.
      The mitochondrial unfolded protein response (UPRmt) is essential to safeguard mitochondria from proteotoxic damage by activating a dedicated transcriptional response in the nucleus to restore proteostasis1,2. Yet, it remains unclear how the information on mitochondria misfolding stress (MMS) is signalled to the nucleus as part of the human UPRmt (refs. 3,4). Here, we show that UPRmt signalling is driven by the release of two individual signals in the cytosol-mitochondrial reactive oxygen species (mtROS) and accumulation of mitochondrial protein precursors in the cytosol (c-mtProt). Combining proteomics and genetic approaches, we identified that MMS causes the release of mtROS into the cytosol. In parallel, MMS leads to mitochondrial protein import defects causing c-mtProt accumulation. Both signals integrate to activate the UPRmt; released mtROS oxidize the cytosolic HSP40 protein DNAJA1, which leads to enhanced recruitment of cytosolic HSP70 to c-mtProt. Consequently, HSP70 releases HSF1, which translocates to the nucleus and activates transcription of UPRmt genes. Together, we identify a highly controlled cytosolic surveillance mechanism that integrates independent mitochondrial stress signals to initiate the UPRmt. These observations reveal a link between mitochondrial and cytosolic proteostasis and provide molecular insight into UPRmt signalling in human cells.
    DOI:  https://doi.org/10.1038/s41586-023-06142-0
  5. bioRxiv. 2023 May 22. pii: 2023.05.20.541602. [Epub ahead of print]
    Ablation of Sam50 is associated with fragmentation and alterations in metabolism in human myotubes.
    Zer Vue, Chia Vang, Kit Neikirk, Edgar Garza-Lopez, Jian-Qiang Shao, Margaret Mungai, Larry Vang, Heather Beasley, Andrea G Marshall, Amber Crabtree, Dominique Stephens, Melanie McReynolds, Sandra A Murray, Prasanna Katti, Steven Damo, Jennifer A Gaddy, Antentor Hinton.
      The Sorting and Assembly Machinery (SAM) Complex functions in the assembly of β-barrel in the mitochondrial membrane. The SAM complex is made up of three subunits, Sam35, Sam37, and Sam50. While both Sam35 and Sam37 are peripheral membrane proteins that are not required for survival, Sam50 interacts with the MICOS complex to connect the inner and outer mitochondrial membranes and forms the mitochondrial intermembrane space bridging (MIB) complex. Specifically, Sam50 stabilizes the MIB complex for protein transport, respiratory chain complex assembly, and cristae integrity regulation. To structurally form and sustain the cristae, the MICOS complex assembles at the cristae junction and binds directly to Sam50. However, the role of Sam50 in overall mitochondrial structure and metabolism in skeletal muscle remains unclear. Here, we use SBF-SEM and Amira software perform 3D renderings of mitochondria and autophagosomes in human myotubes. Beyond this, Gas Chromatography-Mass Spectrometry-based metabolomics was utilized to interrogate differential changes of the metabolites in wild-type (WT) and Sam50 deficient myotubes. Ablation of Sam50 , revealed increases in ß-Alanine, propanoate, and phenylalanine, and tyrosine metabolism. Additionally, we observed that mitochondrial fragmentation and autophagosome formation was increased in Sam50 -deficient myotubes compared to control myotubes. Beyond this, the metabolomic analysis revealed an increase in amino acid metabolism and fatty acid metabolism. XF24 Seahorse Analyzer shows that oxidative capacity is further impaired upon ablation of Sam50 in both murine and human myotubes. Together, these data suggest Sam50 is critical for establishing and maintaining mitochondria, mitochondrial cristae structure, and mitochondrial metabolism.
    DOI:  https://doi.org/10.1101/2023.05.20.541602
  6. EMBO Rep. 2023 Jun 06. e57127
    Human mitochondrial ADP/ATP carrier SLC25A4 operates with a ping-pong kinetic mechanism.
    Camila Cimadamore-Werthein, Stephany Jaiquel Baron, Martin S King, Roger Springett, Edmund Rs Kunji.
      The mitochondrial ADP/ATP carrier (SLC25A4), also called the adenine nucleotide translocase, imports ADP into the mitochondrial matrix and exports ATP, which are key steps in oxidative phosphorylation. Historically, the carrier was thought to form a homodimer and to operate by a sequential kinetic mechanism, which involves the formation of a ternary complex with the two exchanged substrates bound simultaneously. However, recent structural and functional data have demonstrated that the mitochondrial ADP/ATP carrier works as a monomer and has a single substrate binding site, which cannot be reconciled with a sequential kinetic mechanism. Here, we study the kinetic properties of the human mitochondrial ADP/ATP carrier by using proteoliposomes and transport robotics. We show that the Km/Vmax ratio is constant for all of the measured internal concentrations. Thus, in contrast to earlier claims, we conclude that the carrier operates with a ping-pong kinetic mechanism in which substrate exchange across the membrane occurs consecutively rather than simultaneously. These data unite the kinetic and structural models, showing that the carrier operates with an alternating access mechanism.
    Keywords:  ADP/ATP translocase; SLC25; adenine nucleotide translocator; bioenergetics; mitochondrial carrier family
    DOI:  https://doi.org/10.15252/embr.202357127
  7. Cell Calcium. 2023 Jun 02. pii: S0143-4160(23)00077-5. [Epub ahead of print]113 102765
    MICU1 deficiency alters mitochondrial morphology and cytochrome C release.
    Benjamin Gottschalk, Roland Malli, Wolfgang F Graier.
      The mitochondrial inner boundary membrane harbors a protein called MICU1, which is sensitive to Ca2+ and binds to the MICOS components Mic60 and CHCHD2. Changes in the mitochondrial cristae junction structure and organization in MICU1-/- cells lead to increased cytochrome c release, membrane potential rearrangement, and changes in mitochondrial Ca2+ uptake dynamics. These findings shed new light on the multifaceted role of MICU1, highlighting its involvement not only as an interaction partner and regulator of the MCU complex but also as a crucial determinant of mitochondrial ultrastructure and, thus, an essential player in processes initiating apoptosis.
    Keywords:  Apoptosis; Ca(2+) signaling; Cristae junction; MICOS-complex; MICU1; Mitochondria
    DOI:  https://doi.org/10.1016/j.ceca.2023.102765
  8. JCI Insight. 2023 Jun 08. pii: e165937. [Epub ahead of print]
    Multimodal single-cell analysis of non-random heteroplasmy distribution in human retinal mitochondrial disease.
    Nathaniel K Mullin, Andrew P Voigt, Miles J Flamme-Wiese, Xiuying Liu, Megan J Riker, Katayoun Varzavand, Edwin M Stone, Budd A Tucker, Robert F Mullins.
      Variants within the high copy number mitochondrial genome (mtDNA) can disrupt organelle function and lead to severe multi-system disease. The wide range of manifestations observed in mitochondrial disease patients results from varying fractions of abnormal mtDNA molecules in different cells and tissues, a phenomenon termed heteroplasmy. However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. Here, we identify non-random distribution of a pathogenic mtDNA variant across a complex tissue using single-cell RNA sequencing, mitochondrial single-cell ATAC sequencing, and multimodal single-cell sequencing. We profile the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and healthy control donors. Utilizing the retina as a model for complex multi-lineage tissues, we found that the proportion of the pathogenic m.3243A>G allele was neither evenly nor randomly distributed across diverse cell types. All neuroectoderm-derived neural cells exhibited a high percentage of the mutant variant. However, a subset of mesoderm-derived lineage, namely the vasculature of the choroid, was near homoplasmic for the wildtype allele. Gene expression and chromatin accessibility profiles of cell types with high and low proportions of m.3243A>G implicate mTOR signaling in the cellular response to heteroplasmy. We further found by multimodal single-cell sequencing of retinal pigment epithelial cells that a high proportion of the pathogenic mtDNA variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings show the non-random nature of mitochondrial variant partitioning in human mitochondrial disease and underscore its implications for mitochondrial disease pathogenesis and treatment.
    Keywords:  Genetic diseases; Genetics; Mitochondria; Ophthalmology; Retinopathy
    DOI:  https://doi.org/10.1172/jci.insight.165937
  9. Elife. 2023 Jun 05. pii: e84204. [Epub ahead of print]12
    Calcium and bicarbonate signaling pathways have pivotal, resonating roles in matching ATP production to demand.
    Maura Greiser, Mariusz Karbowski, Aaron David Kaplan, Andrew Kyle Coleman, Nicolas Verhoeven, Carmen A Mannella, W Jonathan Lederer, Liron Boyman.
      Mitochondrial ATP production in cardiac ventricular myocytes must be continually adjusted to rapidly replenish the ATP consumed by the working heart. Two systems are known to be critical in this regulation: mitochondrial matrix Ca2+ ([Ca2+]m) and blood flow that is tuned by local ventricular myocyte metabolic signaling. However, these two regulatory systems do not fully account for the physiological range of ATP consumption observed. We report here on the identity, location, and signaling cascade of a third regulatory system -- CO2/bicarbonate. CO2 is generated in the mitochondrial matrix as a metabolic waste product of the oxidation of nutrients that powers ATP production. It is a lipid soluble gas that rapidly permeates the inner mitochondrial membrane (IMM) and produces bicarbonate (HCO3-) in a reaction accelerated by carbonic anhydrase (CA). The bicarbonate level is tracked physiologically by a bicarbonate-activated adenylyl cyclase, soluble adenylyl cyclase (sAC). Using structural Airyscan super-resolution imaging and functional measurements we find that sAC is primarily inside the mitochondria of ventricular myocytes where it generates cAMP when activated by HCO3-. Our data strongly suggest that ATP production in these mitochondria is regulated by this cAMP signaling cascade operating within the inter-membrane space (IMS) by activating local EPAC1 (Exchange Protein directly Activated by cAMP) which turns on Rap1 (Ras-related protein 1). Thus, mitochondrial ATP production is shown to be increased by bicarbonate-triggered sAC signaling through Rap1. Additional evidence is presented indicating that the cAMP signaling itself does not occur directly in the matrix. We also show that this third signaling process involving bicarbonate and sAC activates the cardiac mitochondrial ATP production machinery by working independently of, yet in conjunction with, [Ca2+]m-dependent ATP production to meet the energy needs of cellular activity in both health and disease. We propose that the bicarbonate and calcium signaling arms function in a resonant or complementary manner to match mitochondrial ATP production to the full range of energy consumption in cardiac ventricular myocytes in health and disease.
    Keywords:  biochemistry; chemical biology; molecular biophysics; rat; structural biology
    DOI:  https://doi.org/10.7554/eLife.84204
  10. bioRxiv. 2023 May 22. pii: 2023.05.22.541833. [Epub ahead of print]
    Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart.
    Chiemela Ohanele, Jessica N Peoples, Anja Karlstaedt, Joshua T Geiger, Ashley D Gayle, Nasab Ghazal, Fateemaa Sohani, Milton E Brown, Michael E Davis, George A Porter, Victor Faundez, Jennifer Q Kwong.
      The developing mammalian heart undergoes an important metabolic shift from glycolysis toward mitochondrial oxidation, such that oxidative phosphorylation defects may present with cardiac abnormalities. Here, we describe a new mechanistic link between mitochondria and cardiac morphogenesis, uncovered by studying mice with systemic loss of the mitochondrial citrate carrier SLC25A1. Slc25a1 null embryos displayed impaired growth, cardiac malformations, and aberrant mitochondrial function. Importantly, Slc25a1 haploinsufficient embryos, which are overtly indistinguishable from wild type, exhibited an increased frequency of these defects, suggesting Slc25a1 dose-dependent effects. Supporting clinical relevance, we found a near-significant association between ultrarare human pathogenic SLC25A1 variants and pediatric congenital heart disease. Mechanistically, SLC25A1 may link mitochondria to transcriptional regulation of metabolism through epigenetic control of PPARγ to promote metabolic remodeling in the developing heart. Collectively, this work positions SLC25A1 as a novel mitochondrial regulator of ventricular morphogenesis and cardiac metabolic maturation and suggests a role in congenital heart disease.
    DOI:  https://doi.org/10.1101/2023.05.22.541833
  11. Elife. 2023 Jun 05. pii: e82619. [Epub ahead of print]12
    Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy.
    Karthickeyan Chella Krishnan, Elie-Julien El Hachem, Mark P Keller, Sanjeet G Patel, Luke Carroll, Alexis Diaz Vegas, Isabela Gerdes Gyuricza, Christine Light, Yang Cao, Calvin Pan, Karolina Elżbieta Kaczor-Urbanowicz, Varun Shravah, Diana Anum, Matteo Pellegrini, Chi Fung Lee, Marcus M Seldin, Nadia A Rosenthal, Gary A Churchill, Alan D Attie, Benjamin Parker, David E James, Aldons J Lusis.
      Mitochondria play an important role in both normal heart function and disease etiology. We report analysis of common genetic variations contributing to mitochondrial and heart functions using an integrative proteomics approach in a panel of inbred mouse strains called the Hybrid Mouse Diversity Panel (HMDP). We performed a whole heart proteome study in the HMDP (72 strains, n=2-3 mice) and retrieved 848 mitochondrial proteins (quantified in ≥50 strains). High-resolution association mapping on their relative abundance levels revealed three trans-acting genetic loci on chromosomes (chr) 7, 13 and 17 that regulate distinct classes of mitochondrial proteins as well as cardiac hypertrophy. DAVID enrichment analyses of genes regulated by each of the loci revealed that the chr13 locus was highly enriched for complex-I proteins (24 proteins, P=2.2E-61), the chr17 locus for mitochondrial ribonucleoprotein complex (17 proteins, P=3.1E-25) and the chr7 locus for ubiquinone biosynthesis (3 proteins, P=6.9E-05). Follow-up high resolution regional mapping identified NDUFS4, LRPPRC and COQ7 as the candidate genes for chr13, chr17 and chr7 loci, respectively, and both experimental and statistical analyses supported their causal roles. Furthermore, a large cohort of Diversity Outbred mice was used to corroborate Lrpprc gene as a driver of mitochondrial DNA (mtDNA)-encoded gene regulation, and to show that the chr17 locus is specific to heart. Variations in all three loci were associated with heart mass in at least one of two independent heart stress models, namely, isoproterenol-induced heart failure and diet-induced obesity. These findings suggest that common variations in certain mitochondrial proteins can act in trans to influence tissue-specific mitochondrial functions and contribute to heart hypertrophy, elucidating mechanisms that may underlie genetic susceptibility to heart failure in human populations.
    Keywords:  computational biology; genetic, association studies; genetics; genomics; heart failure; hypertrophy; metabolic syndrome; mitochondria; mouse; proteomics; systems biology
    DOI:  https://doi.org/10.7554/eLife.82619
  12. Front Genet. 2023 ;14 1182288
    Case report: A rare variant m.4135T>C in the MT-ND1 gene leads to Leber hereditary optic neuropathy and altered respiratory chain supercomplexes.
    Tereza Rákosníková, Silvie Kelifová, Hana Štufková, Kateřina Lokvencová, Petra Lišková, Bohdan Kousal, Tomáš Honzík, Hana Hansíková, Václav Martínek, Markéta Tesařová.
      Leber hereditary optic neuropathy is a primary mitochondrial disease characterized by acute visual loss due to the degeneration of retinal ganglion cells. In this study, we describe a patient carrying a rare missense heteroplasmic variant in MT-ND1, NC_012920.1:m.4135T>C (p.Tyr277His) manifesting with a typical bilateral painless decrease of the visual function, triggered by physical exercise or higher ambient temperature. Functional studies in muscle and fibroblasts show that amino acid substitution Tyr277 with His leads to only a negligibly decreased level of respiratory chain complex I (CI), but the formation of supercomplexes and the activity of the enzyme are disturbed noticeably. Our data indicate that although CI is successfully assembled in the patient's mitochondria, its function is hampered by the m.4135T>C variant, probably by stabilizing CI in its inactive form. We conclude that the m.4135T>C variant together with a combination of external factors is necessary to manifest the phenotype.
    Keywords:  complex I; mitochondria; mtDNA; optic neuropathy; supercomplexes
    DOI:  https://doi.org/10.3389/fgene.2023.1182288
  13. Free Radic Biol Med. 2023 Jun 02. pii: S0891-5849(23)00473-2. [Epub ahead of print]205 77-89
    The acute effect of different NAD+ precursors included in the combined metabolic activators.
    Xiangyu Li, Hong Yang, Han Jin, Hasan Turkez, Gurkan Ozturk, Hamdi Levent Doganay, Cheng Zhang, Jens Nielsen, Mathias Uhlén, Jan Borén, Adil Mardinoglu.
      NAD+ and glutathione precursors are currently used as metabolic modulators for improving the metabolic conditions associated with various human diseases, including non-alcoholic fatty liver disease, neurodegenerative diseases, mitochondrial myopathy, and age-induced diabetes. Here, we performed a one-day double blinded, placebo-controlled human clinical study to assess the safety and acute effects of six different Combined Metabolic Activators (CMAs) with 1 g of different NAD+ precursors based on global metabolomics analysis. Our integrative analysis showed that the NAD+ salvage pathway is the main source for boosting the NAD+ levels with the administration of CMAs without NAD+ precursors. We observed that incorporation of nicotinamide (Nam) in the CMAs can boost the NAD+ products, followed by niacin (NA), nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), but not flush free niacin (FFN). In addition, the NA administration led to a flushing reaction, accompanied by decreased phospholipids and increased bilirubin and bilirubin derivatives, which could be potentially risky. In conclusion, this study provided a plasma metabolomic landscape of different CMA formulations, and proposed that CMAs with Nam, NMN as well as NR can be administered for boosting NAD+ levels to improve altered metabolic conditions.
    Keywords:  Carnitine; Cysteine; Metabolomics; NAD(+) precursors; Serine; Systems medicine
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.05.032
  14. bioRxiv. 2023 May 22. pii: 2023.05.20.541585. [Epub ahead of print]
    FAM210A Regulates Mitochondrial Translation and Maintains Cardiac Mitochondrial Homeostasis.
    Jiangbin Wu, Kadiam C Venkata Subbaiah, Omar Hedaya, Si Chen, Joshua Munger, Wai Hong Wilson Tang, Chen Yan, Peng Yao.
      Aims: Mitochondria play a vital role in cellular metabolism and energetics and support normal cardiac function. Disrupted mitochondrial function and homeostasis cause a variety of heart diseases. Fam210a (family with sequence similarity 210 member A), a novel mitochondrial gene, is identified as a hub gene in mouse cardiac remodeling by multi-omics studies. Human FAM210A mutations are associated with sarcopenia. However, the physiological role and molecular function of FAM210A remain elusive in the heart. We aim to determine the biological role and molecular mechanism of FAM210A in regulating mitochondrial function and cardiac health in vivo .Methods and Results: Tamoxifen-induced αMHC MCM -driven conditional knockout of Fam210a in the mouse cardiomyocytes induced progressive dilated cardiomyopathy and heart failure, ultimately causing mortality. Fam210a deficient cardiomyocytes exhibit severe mitochondrial morphological disruption and functional decline accompanied by myofilament disarray at the late stage of cardiomyopathy. Furthermore, we observed increased mitochondrial reactive oxygen species production, disturbed mitochondrial membrane potential, and reduced respiratory activity in cardiomyocytes at the early stage before contractile dysfunction and heart failure. Multi-omics analyses indicate that FAM210A deficiency persistently activates integrated stress response (ISR), resulting in transcriptomic, translatomic, proteomic, and metabolomic reprogramming, ultimately leading to pathogenic progression of heart failure. Mechanistically, mitochondrial polysome profiling analysis shows that FAM210A loss of function compromises mitochondrial mRNA translation and leads to reduced mitochondrial encoded proteins, followed by disrupted proteostasis. We observed decreased FAM210A protein expression in human ischemic heart failure and mouse myocardial infarction tissue samples. To further corroborate FAM210A function in the heart, AAV9-mediated overexpression of FAM210A promotes mitochondrial-encoded protein expression, improves cardiac mitochondrial function, and partially rescues murine hearts from cardiac remodeling and damage in ischemia-induced heart failure.
    Conclusion: These results suggest that FAM210A is a mitochondrial translation regulator to maintain mitochondrial homeostasis and normal cardiomyocyte contractile function. This study also offers a new therapeutic target for treating ischemic heart disease.
    Translational Perspective: Mitochondrial homeostasis is critical for maintaining healthy cardiac function. Disruption of mitochondrial function causes severe cardiomyopathy and heart failure. In the present study, we show that FAM210A is a mitochondrial translation regulator required for maintaining cardiac mitochondrial homeostasis in vivo . Cardiomyocyte-specific FAM210A deficiency leads to mitochondrial dysfunction and spontaneous cardiomyopathy. Moreover, our results indicate that FAM210A is downregulated in human and mouse ischemic heart failure samples and overexpression of FAM210A protects hearts from myocardial infarction induced heart failure, suggesting that FAM210A mediated mitochondrial translation regulatory pathway can be a potential therapeutic target for ischemic heart disease.
    DOI:  https://doi.org/10.1101/2023.05.20.541585
  15. Nat Aging. 2023 Jun 05.
    Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging.
    Philip V Seegren, Logan R Harper, Taylor K Downs, Xiao-Yu Zhao, Shivapriya B Viswanathan, Marta E Stremska, Rachel J Olson, Joel Kennedy, Sarah E Ewald, Pankaj Kumar, Bimal N Desai.
      Mitochondrial dysfunction is linked to age-associated inflammation or inflammaging, but underlying mechanisms are not understood. Analyses of 700 human blood transcriptomes revealed clear signs of age-associated low-grade inflammation. Among changes in mitochondrial components, we found that the expression of mitochondrial calcium uniporter (MCU) and its regulatory subunit MICU1, genes central to mitochondrial Ca2+ (mCa2+) signaling, correlated inversely with age. Indeed, mCa2+ uptake capacity of mouse macrophages decreased significantly with age. We show that in both human and mouse macrophages, reduced mCa2+ uptake amplifies cytosolic Ca2+ oscillations and potentiates downstream nuclear factor kappa B activation, which is central to inflammation. Our findings pinpoint the mitochondrial calcium uniporter complex as a keystone molecular apparatus that links age-related changes in mitochondrial physiology to systemic macrophage-mediated age-associated inflammation. The findings raise the exciting possibility that restoring mCa2+ uptake capacity in tissue-resident macrophages may decrease inflammaging of specific organs and alleviate age-associated conditions such as neurodegenerative and cardiometabolic diseases.
    DOI:  https://doi.org/10.1038/s43587-023-00436-8
  16. Nucleic Acids Res. 2023 Jun 09. pii: gkad502. [Epub ahead of print]
    Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA.
    Chaoxing Liu, Brandon H Le, Wenyan Xu, Ching-Hsin Yang, Yu Hsuan Chen, Linlin Zhao.
      Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.
    DOI:  https://doi.org/10.1093/nar/gkad502
  17. J Biol Chem. 2023 Jun 01. pii: S0021-9258(23)01905-1. [Epub ahead of print] 104877
    Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4.
    Marisa Miljkovic, Alexandra Seguin, Xuan Jia, James E Cox, Jonathan Leon Catrow, Hector Bergonia, John D Phillips, W Zac Stephens, Diane M Ward.
      Abcb10 is a mitochondrial membrane protein involved in hemoglobinization of red cells. Abcb10 topology and ATPase domain localization suggest it exports a substrate, likely biliverdin, out of mitochondria that is necessary for hemoglobinization. In this study we generated Abcb10 deletion cell lines in both mouse murine erythroleukemia (MEL) and human erythroid precursor human myelogenous leukemia (K562) cells to better understand the consequences of Abcb10 loss. Loss of Abcb10 resulted in an inability to hemoglobinize upon differentiation in both K562 and MEL cells with reduced heme and intermediate porphyrins and decreased levels of aminolevulinic acid synthase 2 activity. Metabolomic and transcriptional analyses revealed that Abcb10 loss gave rise to decreased cellular arginine levels, increased transcripts for cationic and neutral amino acid transporters with reduced levels of the citrulline to arginine converting enzymes argininosuccinate synthetase and argininosuccinate lyase. The reduced arginine levels in Abcb10 null cells gave rise to decreased proliferative capacity. Arginine supplementation improved both Abcb10 null proliferation and hemoglobinization upon differentiation. Abcb10 null cells showed increased phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2A), increased expression of nutrient sensing transcription factor ATF4 and downstream targets DNA damage inducible transcript 3 (Chop), ChaC glutathione specific gamma-glutamylcyclotransferase 1 (Chac1) and arginyl-tRNA synthetase 1 (Rars). These results suggest that when the Abcb10 substrate is trapped in the mitochondria, the nutrient sensing machinery is turned on remodeling transcription to block protein synthesis necessary for proliferation and hemoglobin biosynthesis in erythroid models.
    Keywords:  Arginine; differentiation; erythroid; metabolism; nutrient; transporter
    DOI:  https://doi.org/10.1016/j.jbc.2023.104877
  18. bioRxiv. 2023 May 26. pii: 2023.05.26.542250. [Epub ahead of print]
    Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis.
    Jyoti Tanwar, Kriti Ahuja, Akshay Sharma, Paras Sehgal, Gyan Ranjan, Farina Sultan, Anshu Priya, Manigandan Venkatesan, Vamsi K Yenamandra, Archana Singh, Muniswamy Madesh, Sridhar Sivasubbu, Rajender K Motiani.
      Mitochondria are versatile organelles that regulate several physiological functions. Many mitochondria-controlled processes are driven by mitochondrial Ca 2+ signaling. However, role of mitochondrial Ca 2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca 2+ uptake. In vitro gain and loss of function studies demonstrated that Mitochondrial Ca 2+ Uniporter (MCU) is crucial for melanogenesis while the MCU rheostats, MCUb and MICU1 negatively control melanogenesis. Zebrafish and mouse models showed that MCU plays a vital role in pigmentation in vivo . Mechanistically, MCU controls activation of transcription factor NFAT2 to induce expression of three keratins (keratin 5, 7 and 8), which we report as positive regulators of melanogenesis. Interestingly, keratin 5 in turn modulates mitochondrial Ca 2+ uptake thereby this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca 2+ signaling and melanogenesis. Mitoxantrone, an FDA approved drug that inhibits MCU, decreases physiological melanogenesis. Collectively, our data demonstrates a critical role for mitochondrial Ca 2+ signaling in vertebrate pigmentation and reveal the therapeutic potential of targeting MCU for clinical management of pigmentary disorders. Given the centrality of mitochondrial Ca 2+ signaling and keratin filaments in cellular physiology, this feedback loop may be functional in a variety of other pathophysiological conditions.Highlights: MCU complex mediated mitochondrial Ca 2+ uptake is a novel regulator of vertebrate pigmentation Keratin filaments bridge mitochondrial Ca 2+ signaling to melanosome biogenesis and maturation Transcription factor NFAT2 connects mitochondrial Ca 2+ dynamics to keratins expression MCU-NFAT2-Keratin 5 signaling module generates a negative feedback loop to maintain mitochondrial Ca 2+ homeostasis and to ensure optimal melanogenesis Inhibiting MCU with mitoxantrone, an FDA approved drug, leads to reduction in physiological pigmentation.
    DOI:  https://doi.org/10.1101/2023.05.26.542250
  19. Nat Rev Mol Cell Biol. 2023 Jun 05.
    The multiple links between actin and mitochondria.
    Tak Shun Fung, Rajarshi Chakrabarti, Henry N Higgs.
      Actin plays many well-known roles in cells, and understanding any specific role is often confounded by the overlap of multiple actin-based structures in space and time. Here, we review our rapidly expanding understanding of actin in mitochondrial biology, where actin plays multiple distinct roles, exemplifying the versatility of actin and its functions in cell biology. One well-studied role of actin in mitochondrial biology is its role in mitochondrial fission, where actin polymerization from the endoplasmic reticulum through the formin INF2 has been shown to stimulate two distinct steps. However, roles for actin during other types of mitochondrial fission, dependent on the Arp2/3 complex, have also been described. In addition, actin performs functions independent of mitochondrial fission. During mitochondrial dysfunction, two distinct phases of Arp2/3 complex-mediated actin polymerization can be triggered. First, within 5 min of dysfunction, rapid actin assembly around mitochondria serves to suppress mitochondrial shape changes and to stimulate glycolysis. At a later time point, at more than 1 h post-dysfunction, a second round of actin polymerization prepares mitochondria for mitophagy. Finally, actin can both stimulate and inhibit mitochondrial motility depending on the context. These motility effects can either be through the polymerization of actin itself or through myosin-based processes, with myosin 19 being an important mitochondrially attached myosin. Overall, distinct actin structures assemble in response to diverse stimuli to affect specific changes to mitochondria.
    DOI:  https://doi.org/10.1038/s41580-023-00613-y
  20. iScience. 2023 Jun 16. 26(6): 106895
    Genetic deletion of skeletal muscle iPLA2γ results in mitochondrial dysfunction, muscle atrophy and alterations in whole-body energy metabolism.
    Sung Ho Moon, Beverly Gibson Dilthey, Shaoping Guan, Harold F Sims, Sara K Pittman, Amy L Keith, Christopher M Jenkins, Conrad C Weihl, Richard W Gross.
      Skeletal muscle is the major site of glucose utilization in mammals integrating serum glucose clearance with mitochondrial respiration. To mechanistically elucidate the roles of iPLA2γ in skeletal muscle mitochondria, we generated a skeletal muscle-specific calcium-independent phospholipase A2γ knockout (SKMiPLA2γKO) mouse. Genetic ablation of skeletal muscle iPLA2γ resulted in pronounced muscle weakness, muscle atrophy, and increased blood lactate resulting from defects in mitochondrial function impairing metabolic processing of pyruvate and resultant bioenergetic inefficiency. Mitochondria from SKMiPLA2γKO mice were dysmorphic displaying marked changes in size, shape, and interfibrillar juxtaposition. Mitochondrial respirometry demonstrated a marked impairment in respiratory efficiency with decreases in the mass and function of oxidative phosphorylation complexes and cytochrome c. Further, a pronounced decrease in mitochondrial membrane potential and remodeling of cardiolipin molecular species were prominent. Collectively, these alterations prevented body weight gain during high-fat feeding through enhanced glucose disposal without efficient capture of chemical energy thereby altering whole-body bioenergetics.
    Keywords:  Cell biology; Cellular physiology; Physiology
    DOI:  https://doi.org/10.1016/j.isci.2023.106895
  21. PLoS Comput Biol. 2023 Jun 07. 19(6): e1011148
    HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference.
    Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett, Gabriel Renaud.
      Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011148
  22. Am J Physiol Cell Physiol. 2023 Jun 05.
    ATF4 regulates mitochondrial content, morphology, and function in differentiating skeletal muscle myotubes.
    Jonathan M Memme, Victoria C Sanfrancesco, David A Hood.
      Mitochondrial function is widely recognized as a major determinant of health, emphasizing the importance of understanding the mechanisms promoting mitochondrial quality in various tissues. Recently, the mitochondrial unfolded protein response (UPRmt) has come into focus as a modulator of mitochondrial homeostasis, particularly in stress conditions. In muscle, the necessity for ATF4 and its role in regulating mitochondrial quality control (MQC) has yet to be determined. We overexpressed (OE) and knocked down ATF4 in C2C12 myoblasts, differentiated them to myotubes for 5 days, and subjected them to acute (ACA) or chronic (CCA) contractile activity. ATF4 mediated myotube formation through the regulated expression of myogenic factors, mainly Myc and MyoD, and supressed mitochondrial biogenesis basally through PGC-1a. However, our data also show that ATF4 expression levels are directly related to mitochondrial fusion and dynamics, UPRmt activation, as well as lysosomal biogenesis and autophagy. Thus, ATF4 promoted enhanced mitochondrial networking, protein handling, and capacity for clearance of dysfunctional organelles under stress conditions, despite lower levels of mitophagy flux with OE. Indeed, we found that ATF4 promoted the formation of a smaller pool of high functioning mitochondria that are more responsive to contractile activity, have higher oxygen consumption rates and lower reactive oxygen species levels. These data provide evidence that ATF4 is both necessary and sufficient for mitochondrial quality control and adaptation during both differentiation and contractile activity, thus advancing the current understanding of ATF4 beyond its canonical functions, to include the regulation of mitochondrial morphology, lysosomal biogenesis and mitophagy in muscle cells.
    Keywords:  ATF4; mitochondrial quality control; mitochondrial unfolded protein response; mitophagy and lysosomal biogenesis; skeletal muscle C2C12
    DOI:  https://doi.org/10.1152/ajpcell.00080.2023
  23. Nat Cell Biol. 2023 Jun 05.
    LDLs take a shortcut to mitochondria.
    Satoko Shinjo, Luca Scorrano.
      
    DOI:  https://doi.org/10.1038/s41556-023-01166-0
  24. J Cell Sci. 2023 Jun 01. pii: jcs260638. [Epub ahead of print]136(11):
    Mitophagy and long-term neuronal homeostasis.
    Maria Markaki, Dikaia Tsagkari, Nektarios Tavernarakis.
      Neurons are highly polarized, post-mitotic cells that are characterized by unique morphological diversity and complexity. As highly differentiated cells that need to survive throughout organismal lifespan, neurons face exceptional energy challenges in time and space. Therefore, neurons are heavily dependent on a healthy mitochondrial network for their proper function and maintenance under both physiological and stress conditions. Multiple quality control systems have evolved to fine-tune mitochondrial number and quality, thus preserving neuronal energy homeostasis. Here, we review the contribution of mitophagy, a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation, in maintaining nervous system homeostasis. In addition, we discuss recent evidence implicating defective or dysregulated mitophagy in the pathogenesis of neurodegenerative diseases.
    Keywords:  Autophagy; Energy homeostasis; Mitochondria; Mitophagy; Nervous system; Neurodegeneration; Neurodegenerative diseases; Neuron; Non-neuronal cells
    DOI:  https://doi.org/10.1242/jcs.260638
  25. EMBO J. 2023 Jun 05. e114542
    Eating your mitochondria-when too much of a good thing turns bad.
    Léa P Wilhelm, Ian G Ganley.
      How mitophagy is turned on to remove damaged or excess mitochondria from cells has been well-studied, but less is known about how the pathway is turned off to avoid "over-eating" of mitochondria under basal conditions. Three new studies now reveal the disease-associated FBXL4 protein as an important negative regulator of constitutive mitophagy, controlling the stability of mitophagy receptors BNIP3 and NIX.
    DOI:  https://doi.org/10.15252/embj.2023114542
  26. Cell Rep. 2023 Jun 07. pii: S2211-1247(23)00626-5. [Epub ahead of print]42(6): 112615
    Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.
    Angela Pelligra, Jessica Mrugala, Kerstin Griess, Philip Kirschner, Oliver Nortmann, Barbara Bartosinska, Andrea Köster, Natalia I Krupenko, Dominik Gebel, Philipp Westhoff, Bodo Steckel, Daniel Eberhard, Diran Herebian, Bengt-Frederik Belgardt, Jürgen Schrader, Andreas P M Weber, Sergey A Krupenko, Eckhard Lammert.
      Type 2 diabetes is characterized by insulin hypersecretion followed by reduced glucose-stimulated insulin secretion (GSIS). Here we show that acute stimulation of pancreatic islets with the insulin secretagogue dextrorphan (DXO) or glibenclamide enhances GSIS, whereas chronic treatment with high concentrations of these drugs reduces GSIS but protect islets from cell death. Bulk RNA sequencing of islets shows increased expression of genes for serine-linked mitochondrial one-carbon metabolism (OCM) after chronic, but not acute, stimulation. In chronically stimulated islets, more glucose is metabolized to serine than to citrate, and the mitochondrial ATP/ADP ratio decreases, whereas the NAPDH/NADP+ ratio increases. Activating transcription factor-4 (Atf4) is required and sufficient to activate serine-linked mitochondrial OCM genes in islets, with gain- and loss-of-function experiments showing that Atf4 reduces GSIS and is required, but not sufficient, for full DXO-mediated islet protection. In sum, we identify a reversible metabolic pathway that provides islet protection at the expense of secretory function.
    Keywords:  Activating transcription factor-4 (Atf4); CP: Metabolism; K(ATP) channel; beta cell exhaustion; beta cell survival; de novo serine synthesis; diabetes; mitochondria; one-carbon metabolism; pancreatic beta cell; pancreatic islets
    DOI:  https://doi.org/10.1016/j.celrep.2023.112615
  27. Bone Rep. 2023 Jun;18 101688
    Oxidative phosphorylation in bone cells.
    Elena Sabini, Lorenzo Arboit, Mohd Parvez Khan, Giulia Lanzolla, Ernestina Schipani.
      The role of energy metabolism in bone cells is an active field of investigation. Bone cells are metabolically very active and require high levels of energy in the form of adenosine triphosphate (ATP) to support their function. ATP is generated in the cytosol via glycolysis coupled with lactic acid fermentation and in the mitochondria via oxidative phosphorylation (OXPHOS). OXPHOS is the final convergent metabolic pathway for all oxidative steps of dietary nutrients catabolism. The formation of ATP is driven by an electrochemical gradient that forms across the mitochondrial inner membrane through to the activity of the electron transport chain (ETC) complexes and requires the presence of oxygen as the final electron acceptor. The current literature supports a model in which glycolysis is the main source of energy in undifferentiated mesenchymal progenitors and terminally differentiated osteoblasts, whereas OXPHOS appears relevant in an intermediate stage of differentiation of those cells. Conversely, osteoclasts progressively increase OXPHOS during differentiation until they become multinucleated and mitochondrial-rich terminal differentiated cells. Despite the abundance of mitochondria, mature osteoclasts are considered ATP-depleted, and the availability of ATP is a critical factor that regulates the low survival capacity of these cells, which rapidly undergo death by apoptosis. In addition to ATP, bioenergetic metabolism generates reactive oxygen species (ROS) and intermediate metabolites that regulate a variety of cellular functions, including epigenetics changes of genomic DNA and histones. This review will briefly discuss the role of OXPHOS and the cross-talks OXPHOS-glycolysis in the differentiation process of bone cells.
    Keywords:  Mitochondria; OXPHOS; Osteoblasts; Osteoclasts; Osteocytes
    DOI:  https://doi.org/10.1016/j.bonr.2023.101688
  28. Annu Rev Genomics Hum Genet. 2023 Jun 07.
    DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data.
    Julia Foreman, Daniel Perrett, Erica Mazaika, Sarah E Hunt, James S Ware, Helen V Firth.
      DECIPHER (Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources) shares candidate diagnostic variants and phenotypic data from patients with genetic disorders to facilitate research and improve the diagnosis, management, and therapy of rare diseases. The platform sits at the boundary between genomic research and the clinical community. DECIPHER aims to ensure that the most up-to-date data are made rapidly available within its interpretation interfaces to improve clinical care. Newly integrated cardiac case-control data that provide evidence of gene-disease associations and inform variant interpretation exemplify this mission. New research resources are presented in a format optimized for use by a broad range of professionals supporting the delivery of genomic medicine. The interfaces within DECIPHER integrate and contextualize variant and phenotypic data, helping to determine a robust clinico-molecular diagnosis for rare-disease patients, which combines both variant classification and clinical fit. DECIPHER supports discovery research, connecting individuals within the rare-disease community to pursue hypothesis-driven research. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 24 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-genom-102822-100509
  29. bioRxiv. 2023 May 18. pii: 2023.05.18.540420. [Epub ahead of print]
    PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy.
    Yao Wei Lu, Zhuomin Liang, Haipeng Guo, Tiago Fernandes, Ramon A Espinoza-Lewis, Tingting Wang, Kathryn Li, Xue Li, Gurinder Bir Singh, Yi Wang, Douglas Cowan, John D Mably, Caroline C Philpott, Hong Chen, Da-Zhi Wang.
      Alanyl-transfer RNA synthetase 2 (AARS2) is a nuclear encoded mitochondrial tRNA synthetase that is responsible for charging of tRNA-Ala with alanine during mitochondrial translation. Homozygous or compound heterozygous mutations in the Aars2 gene, including those affecting its splicing, are linked to infantile cardiomyopathy in humans. However, how Aars2 regulates heart development, and the underlying molecular mechanism of heart disease remains unknown. Here, we found that poly(rC) binding protein 1 (PCBP1) interacts with the Aars2 transcript to mediate its alternative splicing and is critical for the expression and function of Aars2. Cardiomyocyte-specific deletion of Pcbp1 in mice resulted in defects in heart development that are reminiscent of human congenital cardiac defects, including noncompaction cardiomyopathy and a disruption of the cardiomyocyte maturation trajectory. Loss of Pcbp1 led to an aberrant alternative splicing and a premature termination of Aars2 in cardiomyocytes. Additionally, Aars2 mutant mice with exon-16 skipping recapitulated heart developmental defects observed in Pcbp1 mutant mice. Mechanistically, we found dysregulated gene and protein expression of the oxidative phosphorylation pathway in both Pcbp1 and Aars2 mutant hearts; these date provide further evidence that the infantile hypertrophic cardiomyopathy associated with the disorder oxidative phosphorylation defect type 8 (COXPD8) is mediated by Aars2. Our study therefore identifies Pcbp1 and Aars2 as critical regulators of heart development and provides important molecular insights into the role of disruptions in metabolism on congenital heart defects.
    DOI:  https://doi.org/10.1101/2023.05.18.540420
  30. FEBS J. 2023 Jun 08.
    Nicotinamide Riboside Activates SIRT5 Deacetylation.
    Alyson M Curry, Stacia Rymarchyk, Noah B Herrington, Dickson Donu, Glen E Kellogg, Yana Cen.
      Human sirtuins play important roles in various cellular events including DNA repair, gene silencing, mitochondrial biogenesis, insulin secretion as well as apoptosis. They regulate a wide array of protein and enzyme targets through their NAD+ -dependent deacetylase activities. Sirtuins are also thought to mediate the beneficial effects of low-calorie intake to extend longevity in diverse organisms from yeast to mammals. Small molecules mimicking calorie restriction to stimulate sirtuin activity are attractive therapeutics against age-related disorders such as cardiovascular diseases, diabetes and neurodegeneration. Little is known about one of the mitochondrial sirtuins, SIRT5. SIRT5 has emerged as a critical player in maintaining cardiac health and neuronal viability upon stress, and functions as a tumor suppressor in a context-specific manner. Much has been debated about whether SIRT5 has evolved away from being a deacetylase because of its weak catalytic activity, especially in the in vitro testing. We have, for the first time, identified a SIRT5-selective allosteric activator, nicotinamide riboside (NR). It can increase SIRT5 catalytic efficiency with different synthetic peptide substrates. The mechanism of action was further explored using a combination of molecular biology and biochemical strategies. Based on the existing structural biology information, the NR binding site was also mapped out. These activators are powerful chemical probes for the elucidation of cellular regulations and biological functions of SIRT5. The knowledge gained in the current study can be used to guide the design and synthesis of more potent, isotype-selective SIRT5 activators, and to develop them into therapeutics for metabolic disorders and age-related diseases.
    Keywords:  NR; allosteric; sirtuin
    DOI:  https://doi.org/10.1111/febs.16887
  31. Front Neurosci. 2023 ;17 1182874
    Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models.
    Elizabeth Kalotay, Matthias Klugmann, Gary D Housley, Dominik Fröhlich.
      Protein synthesis is a fundamental process that underpins almost every aspect of cellular functioning. Intriguingly, despite their common function, recessive mutations in aminoacyl-tRNA synthetases (ARSs), the family of enzymes that pair tRNA molecules with amino acids prior to translation on the ribosome, cause a diverse range of multi-system disorders that affect specific groups of tissues. Neurological development is impaired in most ARS-associated disorders. In addition to central nervous system defects, diseases caused by recessive mutations in cytosolic ARSs commonly affect the liver and lungs. Patients with biallelic mutations in mitochondrial ARSs often present with encephalopathies, with variable involvement of peripheral systems. Many of these disorders cause severe disability, and as understanding of their pathogenesis is currently limited, there are no effective treatments available. To address this, accurate in vivo models for most of the recessive ARS diseases are urgently needed. Here, we discuss approaches that have been taken to model recessive ARS diseases in vivo, highlighting some of the challenges that have arisen in this process, as well as key results obtained from these models. Further development and refinement of animal models is essential to facilitate a better understanding of the pathophysiology underlying recessive ARS diseases, and ultimately to enable development and testing of effective therapies.
    Keywords:  ARS1; ARS2; aminoacyl-tRNA synthetases; animal models; cytosolic ARS; mitochondrial ARS; recessive ARS mutations
    DOI:  https://doi.org/10.3389/fnins.2023.1182874
  32. Glia. 2023 Jun 05.
    Expression and subcellular localization of mitochondrial docking protein, syntaphilin, in oligodendrocytes and CNS myelin sheath.
    Diane S Nakamura, Jean-David M Gothié, Samantha F Kornfeld, Rashmi Kothary, Timothy E Kennedy.
      Oligodendrocytes produce lipid-rich myelin sheaths that provide metabolic support to the underlying axon and facilitate saltatory conduction. Oligodendrocyte mitochondria supply the bulk of energy and carbon-chain backbones required for lipid synthesis. The sparsity of mitochondria in the myelin sheath suggests that tight regulation of mitochondrial trafficking is crucial for their efficient distribution in the cell. In particular, retention of mitochondria at axoglial junctions would support local lipid synthesis and membrane remodeling during myelination. How mitochondrial docking in oligodendrocytes is regulated is not known. Our findings indicate that syntaphilin (SNPH), a mitochondrial docking protein that has been characterized in neurons, is expressed by oligodendrocyte precursor cells (OPCs) and mature oligodendrocytes in vitro and present in the myelin sheath in vivo. We have previously reported that bath application of netrin-1 promotes the elaboration of myelin basic protein-positive membranes, and that localized presentation of a netrin-1 coated microbead results in rapid accumulation of mitochondria at the site of oligodendrocyte-bead adhesion. Here we show that netrin-1 increases the redistribution of SNPH to oligodendrocyte processes during the expansion of myelin basic protein-positive membranes and that SNPH clusters at the oligodendrocyte plasma membrane at sites of adhesion with netrin-1-coated beads where mitochondria are retained. These findings suggest roles for SNPH in oligodendrocytes regulating netrin-1-mediated mitochondrial docking and myelin membrane expansion.
    Keywords:  docking; mitochondria; myelin; netrin; oligodendrocyte; syntaphilin; trafficking
    DOI:  https://doi.org/10.1002/glia.24425
  33. RSC Chem Biol. 2023 Jun 07. 4(6): 386-398
    Using light scattering to assess how phospholipid-protein interactions affect complex I functionality in liposomes.
    Jana Eisermann, John J Wright, James D E T Wilton-Ely, Judy Hirst, Maxie M Roessler.
      Complex I is an essential membrane protein in respiration, oxidising NADH and reducing ubiquinone to contribute to the proton-motive force that powers ATP synthesis. Liposomes provide an attractive platform to investigate complex I in a phospholipid membrane with the native hydrophobic ubiquinone substrate and proton transport across the membrane, but without convoluting contributions from other proteins present in the native mitochondrial inner membrane. Here, we use dynamic and electrophoretic light scattering techniques (DLS and ELS) to show how physical parameters, in particular the zeta potential (ζ-potential), correlate strongly with the biochemical functionality of complex I-containing proteoliposomes. We find that cardiolipin plays a crucial role in the reconstitution and functioning of complex I and that, as a highly charged lipid, it acts as a sensitive reporter on the biochemical competence of proteoliposomes in ELS measurements. We show that the change in ζ-potential between liposomes and proteoliposomes correlates linearly with protein retention and catalytic oxidoreduction activity of complex I. These correlations are dependent on the presence of cardiolipin, but are otherwise independent of the liposome lipid composition. Moreover, changes in the ζ-potential are sensitive to the proton motive force established upon proton pumping by complex I, thereby constituting a complementary technique to established biochemical assays. ELS measurements may thus serve as a more widely useful tool to investigate membrane proteins in lipid systems, especially those that contain charged lipids.
    DOI:  https://doi.org/10.1039/d2cb00158f
  34. Mitochondrion. 2023 Jun 03. pii: S1567-7249(23)00053-3. [Epub ahead of print]
    Megamitochondria plasticity: function transition from adaption to disease.
    Yuxing Shang, Zhanghui Li, Peiyang Cai, Wuhao Li, Ye Xu, Yangjing Zhao, Sheng Xia, Qixiang Shao, Hui Wang.
      As the cell's energy factory and metabolic hub, mitochondria are critical for ATP synthesis to maintain cellular function. Mitochondria are highly dynamic organelles that continuously undergo fusion and fission to alter their size, shape, and position, with mitochondrial fusion and fission being interdependent to maintain the balance of mitochondrial morphological changes. However, in response to metabolic and functional damage, mitochondria can grow in size, resulting in a form of abnormal mitochondrial morphology known as megamitochondria. Megamitochondria are characterized by their considerably larger size, pale matrix, and marginal cristae structure and have been observed in various human diseases. In energy-intensive cells like hepatocytes or cardiomyocytes, the pathological process can lead to the growth of megamitochondria, which can further cause metabolic disorders, cell damage and aggravates the progression of the disease. Nonetheless, megamitochondria can also form in response to short-term environmental stimulation as a compensatory mechanism to support cell survival. However, extended stimulation can reverse the benefits of megamitochondria leading to adverse effects. In this review, we will focus on the findings of the different roles of megamitochondria, and their link to disease development to identify promising clinical therapeutic targets.
    Keywords:  Megamitochondria; Mitochondria dynamics; Mitochondria morphology
    DOI:  https://doi.org/10.1016/j.mito.2023.06.001
  35. Mol Genet Genomics. 2023 Jun 05.
    Association of mitochondrial DNA variation with high myopia in a Han Chinese population.
    Myopia Associated Genetics and Intervention Consortium
      High myopia (HM), which is characterized by oxidative stress, is one of the leading causes of visual impairment and blindness across the world. Family and population genetic studies have uncovered nuclear-genome variants in proteins functioned in the mitochondria. However, whether mitochondrial DNA mutations are involved in HM remains unexplored. Here, we performed the first large-scale whole-mitochondrial genome study in 9613 HM cases and 9606 control subjects of Han Chinese ancestry for identifying HM-associated mitochondrial variants. The single-variant association analysis identified nine novel genetic variants associated with HM reaching the entire mitochondrial wide significance level, including rs370378529 in ND2 with an odds ratio (OR) of 5.25. Interestingly, eight out of nine variants were predominantly located in related sub-haplogroups, i.e. m.5261G > A in B4b1c, m.12280A > G in G2a4, m.7912G > A in D4a3b, m.94G > A in D4e1, m.14857 T > C in D4e3, m.14280A > G in D5a2, m.16272A > G in G2a4, m.8718A > G in M71 and F1a3, indicating that the sub-haplogroup background can increase the susceptible risk for high myopia. The polygenic risk score analysis of the target and validation cohorts indicated a high accuracy for predicting HM with mtDNA variants (AUC = 0.641). Cumulatively, our findings highlight the critical roles of mitochondrial variants in untangling the genetic etiology of HM.
    Keywords:  Haplogroup; High myopia; Mitochondrial genomics; Oxidative phosphorylation; Susceptibility
    DOI:  https://doi.org/10.1007/s00438-023-02036-y
  36. Res Sq. 2023 May 19. pii: rs.3.rs-2859584. [Epub ahead of print]
    NMNAT2 supports vesicular glycolysis via NAD homeostasis to fuel fast axonal transport.
    Sen Yang, Zhen-Xian Niou, Andrea Enriquez, Jacob LaMar, Jui-Yen Huang, Karen Ling, Paymaan Jafar-Nejad, Jonathan Gilley, Michael P Coleman, Jason M Tennessen, Vidhya Rangaraju, Hui-Chen Lu.
      Background Bioenergetic maladaptations and axonopathy are often found in the early stages of neurodegeneration. Nicotinamide adenine dinucleotide (NAD), an essential cofactor for energy metabolism, is mainly synthesized by Nicotinamide mononucleotide adenylyl transferase 2 (NMNAT2) in CNS neurons. NMNAT2 mRNA levels are reduced in the brains of Alzheimer's, Parkinson's, and Huntington's disease. Here we addressed whether NMNAT2 is required for axonal health of cortical glutamatergic neurons, whose long-projecting axons are often vulnerable in neurodegenerative conditions. We also tested if NMNAT2 maintains axonal health by ensuring axonal ATP levels for axonal transport, critical for axonal function. Methods We generated mouse and cultured neuron models to determine the impact of NMNAT2 loss from cortical glutamatergic neurons on axonal transport, energetic metabolism, and morphological integrity. In addition, we determined if exogenous NAD supplementation or inhibiting a NAD hydrolase, sterile alpha and TIR motif-containing protein 1 (SARM1), prevented axonal deficits caused by NMNAT2 loss. This study used a combination of genetics, molecular biology, immunohistochemistry, biochemistry, fluorescent time-lapse imaging, live imaging with optical sensors, and anti-sense oligos. Results We provide in vivo evidence that NMNAT2 in glutamatergic neurons is required for axonal survival. Using in vivo and in vitro studies, we demonstrate that NMNAT2 maintains the NAD-redox potential to provide "on-board" ATP via glycolysis to vesicular cargos in distal axons. Exogenous NAD + supplementation to NMNAT2 KO neurons restores glycolysis and resumes fast axonal transport. Finally, we demonstrate both in vitro and in vivo that reducing the activity of SARM1, an NAD degradation enzyme, can reduce axonal transport deficits and suppress axon degeneration in NMNAT2 KO neurons. Conclusion NMNAT2 ensures axonal health by maintaining NAD redox potential in distal axons to ensure efficient vesicular glycolysis required for fast axonal transport.
    DOI:  https://doi.org/10.21203/rs.3.rs-2859584/v1
  37. BMC Genomics. 2023 Jun 06. 24(1): 305
    SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.
    Renee Salz, Nuno Saraiva-Agostinho, Emil Vorsteveld, Caspar I van der Made, Simone Kersten, Merel Stemerdink, Jamie Allen, Pieter-Jan Volders, Sarah E Hunt, Alexander Hoischen, Peter A C 't Hoen.
      Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are not predicted to be pathogenic using the reference transcript annotation. In further support of SUsPECT's utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.
    Keywords:  Computational pipeline; Immune response; Medical diagnostics; Primary immunodeficiencies; Rare diseases; Variant effect prediction
    DOI:  https://doi.org/10.1186/s12864-023-09391-5
  38. bioRxiv. 2023 May 22. pii: 2023.05.20.541601. [Epub ahead of print]
    Creating Optimal Conditions for OPA1 isoforms by Western Blot in Muscle Tissue.
    Dominique C Stephens, Amber Crabtree, Heather K Beasley, Edgar Garza-Lopez, Margaret Mungai, Kit Neikirk, Larry Vang, Zer Vue, Neng Vue, Andrea G Marshall, Kyrin Turner, Jianqiang Shao, Sandra Murray, Jennifer A Gaddy, Celestine Wanjalla, Jamaine Davis, Steven Damo, Antentor O Hinton.
      OPA1 is a dynamin-related GTPase that modulates various mitochondrial functions and is involved in mitochondrial morphology. There are eight different isoforms of OPA1 in humans that are expressed as short or long-form isoforms. These isoforms contribute to OPA1's ability to control mitochondrial functions. However, isolating OPA1 isoforms through western blot has been a difficult task. To address this issue, we outline an optimized western blot protocol to isolate different isoforms of OPA1 on the basis of different antibodies. This protocol can be used to study changes in mitochondrial structure and function.Tweetable Abstract: Western blot protocol optimization to visualize OPA1 isoforms.
    Highlights: Protocol for isolating OPA1 isoforms in skeletal muscle tissueSteps for running isolated skeletal muscle cells from muscle tissue on a gelHow to collect samples in preparation for western blottingDetection of OPA1 isoforms.
    Key Resources Table:
    Method Summary: Samples for western blot analysis are isolated from lysed cells, loaded onto a gel, and ran using optimized conditions to better isolate OPA1 isoforms. Samples are transferred to a membrane to for incubation and protein detection using OPA1 antibodies.
    DOI:  https://doi.org/10.1101/2023.05.20.541601
  39. J Cardiovasc Aging. 2023 ;pii: 24. [Epub ahead of print]3(3):
    The mTOR signaling pathway in cardiac aging.
    Dao-Fu Dai, Ping Kang, Hua Bai.
      The mammalian target of rapamycin (mTOR) is one of the most important signaling pathways that regulate nutrient sensing, cell growth, metabolism, and aging. The mTOR pathway, particularly mTOR complex 1 (mTORC1), has been shown to control aging, lifespan, and healthspan through the regulation of protein synthesis, autophagy, mitochondrial function, and metabolic health. The mTOR pathway also plays critical roles in the heart, from cardiac development, growth and maturation, and maintenance of cardiac homeostasis. Hyperactivation of mTORC1 signaling is well documented in aging and many age-related pathologies, including age-related cardiac dysfunction and heart failure. Suppression of mTORC1 by calorie restriction or rapamycin not only extends lifespan but also restores youthful phenotypes in the heart. In this article, we review model organisms of cardiac aging and highlight recent advances in the impact of the mTORC1 pathway on organismal and cardiac aging, particularly in Drosophila and mice. We focus on the downstream signaling pathways S6 kinase and 4EBP1, which regulates protein synthesis, as well as ULK1 and its related pathway that regulates autophagy. The interaction with mTOR complex 2 (mTORC2) and its potential role in cardiac aging are also discussed.
    Keywords:  aging; caloric restriction; cardiac aging; heart failure; mTOR; rapamycin
    DOI:  https://doi.org/10.20517/jca.2023.10
  40. Metabolism. 2023 Jun 05. pii: S0026-0495(23)00218-4. [Epub ahead of print] 155614
    Roles of malate and aspartate in gluconeogenesis in various physiological and pathological states.
    Milan Holeček.
      Gluconeogenesis, a pathway for glucose synthesis from non-carbohydrate substances, begins with the synthesis of oxaloacetate (OA) from pyruvate and intermediates of citric acid cycle in hepatocyte mitochondria. The traditional view is that OA does not cross the mitochondrial membrane and must be shuttled to the cytosol, where most enzymes involved in gluconeogenesis are compartmentalized, in the form of malate. Thus, the possibility of transporting OA in the form of aspartate has been ignored. In the article is shown that malate supply to the cytosol increases only when fatty acid oxidation in the liver is activated, such as during starvation or untreated diabetes. Alternatively, aspartate synthesized from OA by mitochondrial aspartate aminotransferase (AST) is transported to the cytosol in exchange for glutamate via the aspartate-glutamate carrier 2 (AGC2). If the main substrate for gluconeogenesis is an amino acid, aspartate is converted to OA via urea cycle, therefore, ammonia detoxification and gluconeogenesis are simultaneously activated. If the main substrate is lactate, OA is synthesized by cytosolic AST, glutamate is transported to the mitochondria through AGC2, and nitrogen is not lost. It is concluded that, compared to malate, aspartate is a more suitable form of OA transport from the mitochondria for gluconeogenesis.
    Keywords:  AGC2; Citrin; Mitochondrial carriers; Oxaloacetate; Urea cycle
    DOI:  https://doi.org/10.1016/j.metabol.2023.155614
  41. J Am Chem Soc. 2023 Jun 05.
    Mitochondrial Protease Targeting Chimeras for Mitochondrial Matrix Protein Degradation.
    Dachi Wang, Wenxi Wang, Le Fang, Lubin Qi, Yuchao Zhang, Jie Liu, Yuxin Liang, Hongwei Yang, Mengjie Wang, Xiaojian Wei, Ruibin Jiang, Yuan Liu, Wei Zhou, Xiaohong Fang.
      Targeted protein degradation (TPD) is an emerging technique for protein regulation. Currently, all TPD developed in eukaryotic cells relies on either ubiquitin-proteasome or lysosomal systems, thus are powerless against target proteins in membrane organelles lacking proteasomes and lysosomes, such as mitochondria. Here, we developed a mitochondrial protease targeting chimera (MtPTAC) to address this issue. MtPTAC is a bifunctional small molecule that can bind to mitochondrial caseinolytic protease P (ClpP) at one end and target protein at the other. Mechanistically, MtPTAC activates the hydrolase activity of ClpP while simultaneously bringing target proteins into proximity with ClpP. Taking mitochondrial RNA polymerase (POLRMT) as a model protein, we have demonstrated the powerful proteolytic ability and antitumor application prospects of MtPTAC, both in vivo and in vitro. This is the first modularly designed TPD that can specifically hydrolyze target proteins inside mitochondria.
    DOI:  https://doi.org/10.1021/jacs.3c03756
  42. Front Neurosci. 2023 ;17 1182845
    Dominant aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models.
    Elizabeth Kalotay, Matthias Klugmann, Gary D Housley, Dominik Fröhlich.
      Aminoacyl-tRNA synthetases (ARSs) play an essential role in protein synthesis, being responsible for ligating tRNA molecules to their corresponding amino acids in a reaction known as 'tRNA aminoacylation'. Separate ARSs carry out the aminoacylation reaction in the cytosol and in mitochondria, and mutations in almost all ARS genes cause pathophysiology most evident in the nervous system. Dominant mutations in multiple cytosolic ARSs have been linked to forms of peripheral neuropathy including Charcot-Marie-Tooth disease, distal hereditary motor neuropathy, and spinal muscular atrophy. This review provides an overview of approaches that have been employed to model each of these diseases in vivo, followed by a discussion of the existing animal models of dominant ARS disorders and key mechanistic insights that they have provided. In summary, ARS disease models have demonstrated that loss of canonical ARS function alone cannot fully account for the observed disease phenotypes, and that pathogenic ARS variants cause developmental defects within the peripheral nervous system, despite a typically later onset of disease in humans. In addition, aberrant interactions between mutant ARSs and other proteins have been shown to contribute to the disease phenotypes. These findings provide a strong foundation for future research into this group of diseases, providing methodological guidance for studies on ARS disorders that currently lack in vivo models, as well as identifying candidate therapeutic targets.
    Keywords:  ARS1; CMT; Charcot-Marie-Tooth disease; aminoacyl-tRNA synthetases; animal models; dominant mutations; peripheral neuropathy
    DOI:  https://doi.org/10.3389/fnins.2023.1182845
  43. Antioxid Redox Signal. 2023 Jun 08.
    Nicotinamide adenine dinucleotide (NAD+)-dependent signaling in neurological disorders.
    Mariana Bresque, Daniel Esteve, Mariana Pehar, Marcelo R Vargas.
      SIGNIFICANCE: Nicotinamide adenine dinucleotide (NAD+) participates in redox reactions and NAD+-dependent signaling processes, which couples the enzymatic degradation of NAD+ to post-translational modifications of proteins or the production of second messengers. Cellular NAD+ levels are dynamically controlled by synthesis and degradation, and dysregulation of this balance has been associated with acute and chronic neuronal dysfunction.RECENT ADVANCES: A decline in NAD+ has been observed during normal aging and since aging is the primary risk factor for many neurological disorders; NAD+ metabolism has become a promising therapeutic target and prolific research field in recent years.
    CRITICAL ISSUES: In many neurological disorders, either as a primary feature or as consequence of the pathological process, neuronal damage is accompanied by dysregulated mitochondrial homeostasis, oxidative stress or metabolic reprograming. Modulating NAD+ availability appears to have a protective effect against such changes observed in acute neuronal damage and age-related neurological disorders. Such beneficial effects could be, at least in part, due to the activation of NAD+-dependent signaling processes.
    FUTURE DIRECTIONS: While in many instances the protective effect has been ascribed to the activation of sirtuins; approaches that directly test the role of sirtuins or that target the NAD+ pool in a cell type-specific manner may be able to provide further mechanistic insight. Likewise, these approaches may afford greater efficacy to strategies aimed at harnessing the therapeutic potential of NAD+-dependent signaling in neurological disorders.
    DOI:  https://doi.org/10.1089/ars.2023.0241
  44. Nat Med. 2023 Jun 08.
    Integrated multi-omics for rapid rare disease diagnosis on a national scale.
    Sebastian Lunke, Sophie E Bouffler, Chirag V Patel, Sarah A Sandaradura, Meredith Wilson, Jason Pinner, Matthew F Hunter, Christopher P Barnett, Mathew Wallis, Benjamin Kamien, Tiong Y Tan, Mary-Louise Freckmann, Belinda Chong, Dean Phelan, David Francis, Karin S Kassahn, Thuong Ha, Song Gao, Peer Arts, Matilda R Jackson, Hamish S Scott, Stefanie Eggers, Simone Rowley, Kirsten Boggs, Ana Rakonjac, Gemma R Brett, Michelle G de Silva, Amanda Springer, Michelle Ward, Kirsty Stallard, Cas Simons, Thomas Conway, Andreas Halman, Nicole J Van Bergen, Tim Sikora, Liana N Semcesen, David A Stroud, Alison G Compton, David R Thorburn, Katrina M Bell, Simon Sadedin, Kathryn N North, John Christodoulou, Zornitza Stark.
      Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
    DOI:  https://doi.org/10.1038/s41591-023-02401-9
  45. Front Physiol. 2023 ;14 1179922
    Editorial: Mitochondrial disorders and cardiovascular diseases.
    Quanjiang Zhang, Qiuxia Li, Wenjuan Xing.
      
    Keywords:  calcium; cardiovascular diseases; mitochondrial dynamics; mitochondrial dysfunction; mtROS
    DOI:  https://doi.org/10.3389/fphys.2023.1179922
  46. J Cell Sci. 2023 Jun 05. pii: jcs.260717. [Epub ahead of print]
    The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila.
    Nicanor González-Morales, Océane Marescal, Szilárd Szikora, Anja Katzemich, Tuana Correia-Mesquita, Péter Bíró, Miklos Erdelyi, József Mihály, Frieder Schöck.
      Myofibrils are long intracellular cables specific to muscles, composed mainly of actin and myosin filaments. The actin and myosin filaments are organized into repeated units called sarcomeres, which form the myofibrils. Muscle contraction is achieved by the simultaneous shortening of sarcomeres, which requires all sarcomeres to be the same size. Muscles have a variety of ways to ensure sarcomere homogeneity. We previously showed that the controlled oligomerization of Zasp proteins sets the diameter of the myofibril. Here we looked for Zasp-binding proteins at the Z-disc to identify additional proteins coordinating myofibril growth and assembly. We found that the E1 subunit of the oxoglutarate dehydrogenase complex localizes to both the Z-disc and the mitochondria, and is recruited to the Z-disc by Zasp52. The three subunits of the oxoglutarate dehydrogenase complex are required for myofibril formation. Using super-resolution microscopy, we revealed the overall organization of the complex at the Z-disc. Metabolomics identified an amino acid imbalance affecting protein synthesis as a possible cause of myofibril defects, which is supported by OGDH-dependent localization of ribosomes at the Z-disc.
    Keywords:  Drosophila; Muscle; Myofibril; Ogdh; Zasp; tca cycle
    DOI:  https://doi.org/10.1242/jcs.260717
  47. Cell. 2023 May 26. pii: S0092-8674(23)00476-2. [Epub ahead of print]
    Distinct longevity mechanisms across and within species and their association with aging.
    Alexander Tyshkovskiy, Siming Ma, Anastasia V Shindyapina, Stanislav Tikhonov, Sang-Goo Lee, Perinur Bozaykut, José P Castro, Andrei Seluanov, Nicholas J Schork, Vera Gorbunova, Sergey E Dmitriev, Richard A Miller, Vadim N Gladyshev.
      Lifespan varies within and across species, but the general principles of its control remain unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species, identifying longevity signatures and examining their relationship with transcriptomic biomarkers of aging and established lifespan-extending interventions. An integrative analysis uncovered shared longevity mechanisms within and across species, including downregulated Igf1 and upregulated mitochondrial translation genes, and unique features, such as distinct regulation of the innate immune response and cellular respiration. Signatures of long-lived species were positively correlated with age-related changes and enriched for evolutionarily ancient essential genes, involved in proteolysis and PI3K-Akt signaling. Conversely, lifespan-extending interventions counteracted aging patterns and affected younger, mutable genes enriched for energy metabolism. The identified biomarkers revealed longevity interventions, including KU0063794, which extended mouse lifespan and healthspan. Overall, this study uncovers universal and distinct strategies of lifespan regulation within and across species and provides tools for discovering longevity interventions.
    Keywords:  Igf1, KU0063794; aging; bowhead whale; gene expression; lifespan extension; longevity; longevity signatures; mSALT; naked mole rat
    DOI:  https://doi.org/10.1016/j.cell.2023.05.002
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