bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022‒11‒20
forty-two papers selected by
Catalina Vasilescu
Helmholz Munich
  1. Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.
  2. Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1.
  3. LUBAC and NF-κB trigger a nuclear response from mitochondria.
  4. Nonstop mRNAs generate a ground state of mitochondrial gene expression noise.
  5. A Case of a 23-Year-Old Male With Leber Hereditary Optic Neuropathy With a Rare Mutation.
  6. Mitochondrial DNA: Consensuses and Controversies.
  7. Self-Assembled Peptidyl Aggregates for the Fluorogenic Recognition of Mitochondrial DNA G-Quadruplexes.
  8. Mitochondrial Replacement Therapy: In Whose Interests?
  9. Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes.
  10. Unleashing a novel function of endonuclease G in mitochondrial genome instability.
  11. Elucidation of the Role of FAM210B in Mitochondrial Metabolism and Erythropoiesis.
  12. The interaction between E3 ubiquitin ligase Parkin and mitophagy receptor PHB2 links inner mitochondrial membrane ubiquitination to efficient mitophagy.
  13. Short communication: Acute hypoxia does not alter mitochondrial abundance in naked mole-rats.
  14. AAA+ proteases: the first line of defense against mitochondrial damage.
  15. Reply to: No Association between Rare TWNK Variants and Parkinson's Disease in European Cohorts.
  16. Phosphorylation of mammalian mitochondrial EF-Tu by Fyn and c-Src kinases.
  17. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.
  18. Analysis of mitochondrial dynamics and function in the retinal pigment epithelium by high-speed high-resolution live imaging.
  19. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.
  20. Cellular and computational models reveal environmental and metabolic interactions in MMUT-type methylmalonic aciduria.
  21. Alternative respiratory oxidases to study the animal electron transport chain.
  22. Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.
  23. Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.
  24. Bortezomib-induced neurotoxicity in human neurons is the consequence of nicotinamide adenine dinucleotide depletion.
  25. Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate.
  26. Mechanism and regulation of mitophagy in nonalcoholic fatty liver disease (NAFLD): A mini-review.
  27. Glaucomatous optic neuropathy: Mitochondrial dynamics, dysfunction and protection in retinal ganglion cells.
  28. Redox modulation of mitochondrial proteins in the neurotoxicant models of Parkinson's disease.
  29. Beneficial effects of SS-31 peptide on cardiac mitochondrial dysfunction in tafazzin knockdown mice.
  30. Glial TGFβ activity promotes neuron survival in peripheral nerves.
  31. Endogenous metabolism in endothelial and immune cells generates most of the tissue vitamin B3 (nicotinamide).
  32. Selection of red fluorescent protein for genetic labeling of mitochondria and intercellular transfer of viable mitochondria.
  33. Application of Machine Learning in Spatial Proteomics.
  34. The impact of TK2 deficiency syndrome and its treatment by nucleoside therapy on quality of life.
  35. Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.
  36. Mitochondrial dysfunction and intrinsic capacity: insights from a narrative review.
  37. Molecular diversity of astrocytes.
  38. Case report: Long-term follow-up of two patients with LHON caused by DNAJC30:c.152G>A pathogenic variant-case series.
  39. Quantification of Muscle Satellite Stem Cell Divisions by High-Content Analysis.
  40. Ciliary neurotrophic factor-mediated neuroprotection involves enhanced glycolysis and anabolism in degenerating mouse retinas.
  41. Organelle homeostasis: from cellular mechanisms to disease.
  42. A bioluminescent-based probe for in vivo non-invasive monitoring of nicotinamide riboside uptake reveals a link between metastasis and NAD+ metabolism.
  1. Proc Natl Acad Sci U S A. 2022 Nov 22. 119(47): e2210730119
    Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.
    Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Naotada Ishihara.
      Mitochondria have their own DNA (mtDNA), which encodes essential respiratory subunits. Under live imaging, mitochondrial nucleoids, composed of several copies of mtDNA and DNA-binding proteins, such as mitochondrial transcription factor A (TFAM), actively move inside mitochondria and change the morphology, in concert with mitochondrial membrane fission. Here we found the mitochondrial inner membrane-anchored AAA-ATPase protein ATAD3A mediates the nucleoid dynamics. Its ATPase domain exposed to the matrix binds directly to TFAM and mediates nucleoid trafficking along mitochondria by ATP hydrolysis. Nucleoid trafficking also required ATAD3A oligomerization via an interaction between the coiled-coil domains in intermembrane space. In ATAD3A deficiency, impaired nucleoid trafficking repressed the clustered and enlarged nucleoids observed in mitochondrial fission-deficient cells resulted in dispersed distribution of small nucleoids observed throughout the mitochondrial network, and this enhanced respiratory complex formation. Thus, mitochondrial fission and nucleoid trafficking cooperatively determine the size, number, and distribution of nucleoids in mitochondrial network, which should modulate respiratory complex formation.
    Keywords:  ATAD3A; Drp1; mitochondrial fission; mtDNA nucleoid; respiratory complex
    DOI:  https://doi.org/10.1073/pnas.2210730119
  2. Front Physiol. 2022 ;13 1004099
    Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1.
    Aditya Sen, Rachel T Cox.
      Mitochondria contain their own DNA, mitochondrial DNA, which encodes thirteen proteins. However, mitochondria require thousands of proteins encoded in the nucleus to carry out their many functions. Identifying the definitive mitochondrial proteome has been challenging as methods isolating mitochondrial proteins differ and different tissues and organisms may have specialized proteomes. Mitochondrial diseases arising from single gene mutations in nucleus encoded genes could affect the mitochondrial proteome, but deciphering which effects are due to loss of specific pathways or to accumulated general mitochondrial damage is difficult. To identify specific versus general effects, we have taken advantage of mutations in three Drosophila genes, clueless, Sod2, and Pink1, which are required for mitochondrial function through different pathways. We measured changes in each mutant's mitochondrial proteome using quantitative tandem mass tag mass spectrometry. Our analysis identified protein classes that are unique to each mutant and those shared between them, suggesting that some changes in the mitochondrial proteome are due to general mitochondrial damage whereas others are gene specific. For example, clueless mutants had the greatest number of less and more abundant mitochondrial proteins whereas loss of all three genes increased stress and metabolism proteins. This study is the first to directly compare in vivo steady state levels of mitochondrial proteins by examining loss of three pathways critical for mitochondrial function. These data could be useful to understand disease etiology, and how mutations in genes critical for mitochondrial function cause specific mitochondrial proteomic changes as opposed to changes due to generalized mitochondrial damage.
    Keywords:  Clueless; PINK1; SOD2; drosophila; mitochondria; mitochondrial proteome; respiratory chain complexes
    DOI:  https://doi.org/10.3389/fphys.2022.1004099
  3. EMBO J. 2022 Nov 18. e112920
    LUBAC and NF-κB trigger a nuclear response from mitochondria.
    Junsheng Chen, Thomas Simmen.
      Mitochondria are key signaling hubs for innate immune responses. In this issue, Wu et al (2022) report that remodeling of the outer mitochondrial membrane by the linear ubiquiting chain assembly complex (LUBAC) facilitates transport of activated NF-κB to the nucleus in response to TNF signaling.
    DOI:  https://doi.org/10.15252/embj.2022112920
  4. Sci Adv. 2022 Nov 16. 8(46): eabq5234
    Nonstop mRNAs generate a ground state of mitochondrial gene expression noise.
    Kah Ying Ng, Guleycan Lutfullahoglu Bal, Uwe Richter, Omid Safronov, Lars Paulin, Cory D Dunn, Ville O Paavilainen, Julie Richer, William G Newman, Robert W Taylor, Brendan J Battersby.
      A stop codon within the mRNA facilitates coordinated termination of protein synthesis, releasing the nascent polypeptide from the ribosome. This essential step in gene expression is impeded with transcripts lacking a stop codon, generating nonstop ribosome complexes. Here, we use deep sequencing to investigate sources of nonstop mRNAs generated from the human mitochondrial genome. We identify diverse types of nonstop mRNAs on mitochondrial ribosomes that are resistant to translation termination by canonical release factors. Failure to resolve these aberrations by the mitochondrial release factor in rescue (MTRFR) imparts a negative regulatory effect on protein synthesis that is associated with human disease. Our findings reveal a source of underlying noise in mitochondrial gene expression and the importance of responsive ribosome quality control mechanisms for cell fitness and human health.
    DOI:  https://doi.org/10.1126/sciadv.abq5234
  5. Cureus. 2022 Oct;14(10): e30198
    A Case of a 23-Year-Old Male With Leber Hereditary Optic Neuropathy With a Rare Mutation.
    Priyal Lnu, Vineet Sehgal, Lucky Bhalla Sehgal, Nihal Gulati, Saniya Kapila.
      Mitochondrial DNA (mtDNA) is responsible for encoding 13 subunits of the respiratory chain. These subunits are crucial in providing reducing equivalents for the energy-intensive intracellular processes. Leber hereditary optic neuropathy (LHON) is a mitochondrial illness that causes carcinogenesis due to oxidative stress and painless loss of central vision as a result of selective degradation of retinal ganglion cells as well as their axons. We present a case of a 23-year-old male patient who was diagnosed with subacute LHON. The mutation in our patient was found in a less commonly mutated exon sequence of MT-NDL4, which codes for NADH (nicotinamide adenine dinucleotide hydrogen, reduced) dehydrogenase subunit 4L. The MT-ND4L exon is located immediately upstream of the MTD4 exon on the human mtDNA. The take-home message is to always perform a comprehensive mitochondrial genome analysis for identifying rare mutations when LHON is suspected.
    Keywords:  blindness without neurological deficit; genetic eye diseases; leber hereditary optic neuropathy; mtdna disorder; mtdna mutation; rare genetic diseases; sudden loss of vision
    DOI:  https://doi.org/10.7759/cureus.30198
  6. DNA (Basel). 2022 Jun;2(2): 131-148
    Mitochondrial DNA: Consensuses and Controversies.
    Inna Shokolenko, Mikhail Alexeyev.
      In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.
    Keywords:  extramitochondrial mtDNA; mitochondrial theory of aging; mtDNA; mtDNA repair; mtDNA replication; mtDNA transcription
    DOI:  https://doi.org/10.3390/dna2020010
  7. Angew Chem Int Ed Engl. 2022 Nov 17.
    Self-Assembled Peptidyl Aggregates for the Fluorogenic Recognition of Mitochondrial DNA G-Quadruplexes.
    Anup Pandith, Yongyang Luo, Yul Jang, Jeehyeon Bae, Youngmi Kim.
      The selective monitoring of G-quadruplex structures (G4s) in living cells is important to elucidate their functions and reveal their value as diagnostic or therapeutic targets. Here we report a fluorogenic probe (CV2) able to selectively light-up parallel G4 DNA over antiparallel topologies. CV2 was constructed by conjugating the excimer-forming CV dye with a peptide sequence (l-Arg-l-Gly-glutaric acid) that specifically recognizes G4s. CV2 forms self-assembled, red excimer-emitting nanoaggregates in aqueous media, but specific binding to G4s triggers its disassembly into rigidified monomeric dyes, leading to a dramatic fluorescence enhancement. Moreover, selective permeation of CV2 stains G4s in mitochondria over the nucleus. CV2 was employed for tracking the folding and unfolding of G4s in living cells, and for monitoring mitochondrial DNA damage. These properties make CV2 appealing to investigate the possible roles of mtDNA G4s in diseases that involve mitochondrial dysfunction.
    Keywords:  Cyanovinylene; Excimer; Fluorescent probes; G-quadruplex; Self-assembly
    DOI:  https://doi.org/10.1002/anie.202215049
  8. J Law Med Ethics. 2022 ;50(3): 597-602
    Mitochondrial Replacement Therapy: In Whose Interests?
    Forough Noohi, Vardit Ravitsky, Bartha Maria Knoppers, Yann Joly.
      Mitochondrial replacement therapy (MRT), also called nuclear genome transfer and mitochondrial donation, is a new technique that can be used to prevent the transmission of mitochondrial DNA diseases. Apart from the United Kingdom, the first country to approve MRT in 2015, Australia became the second country with a clear regulatory path for the clinical applications of this technique in 2021. The rapidly evolving clinical landscape of MRT makes the elaboration and evaluation of the responsible use of this technology a pressing matter. As jurisdictions with less strict or non-existent reproductive laws are continuing to use MRT in the clinical context, the need to address the underlying ethical issues surrounding MRT's clinical translation is fundamental.
    Keywords:  Genetic Relatedness; MRT; Mitochondrial Replacement Therapy; Reproductive Autonomy
    DOI:  https://doi.org/10.1017/jme.2022.98
  9. J Cell Biol. 2023 Jan 02. pii: e202203019. [Epub ahead of print]222(1):
    Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes.
    Olesia Ignatenko, Satu Malinen, Sofiia Rybas, Helena Vihinen, Joni Nikkanen, Aleksander Kononov, Eija S Jokitalo, Gulayse Ince-Dunn, Anu Suomalainen.
      Astrocytes, often considered as secondary responders to neurodegeneration, are emerging as primary drivers of brain disease. Here we show that mitochondrial DNA depletion in astrocytes affects their primary cilium, the signaling organelle of a cell. The progressive oxidative phosphorylation deficiency in astrocytes induces FOXJ1 and RFX transcription factors, known as master regulators of motile ciliogenesis. Consequently, a robust gene expression program involving motile cilia components and multiciliated cell differentiation factors are induced. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. The data suggest that chronic activation of the mitochondrial integrated stress response (ISRmt) in astrocytes drives anabolic metabolism and promotes ciliary elongation. Collectively, our evidence indicates that an active signaling axis involving mitochondria and primary cilia exists and that ciliary signaling is part of ISRmt in astrocytes. We propose that metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.
    DOI:  https://doi.org/10.1083/jcb.202203019
  10. Elife. 2022 11 17. pii: e69916. [Epub ahead of print]11
    Unleashing a novel function of endonuclease G in mitochondrial genome instability.
    Sumedha Dahal, Humaira Siddiqua, Shivangi Sharma, Ravi K Babu, Diksha Rathore, Sheetal Sharma, Sathees C Raghavan.
      Having its genome makes the mitochondrion a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is a double-stranded closed circular molecule of about 16 kb coding for 37 genes. Mutations, including deletions in the mitochondrial genome, can culminate in different human diseases. Mapping the deletion junctions suggests that the breakpoints are generally seen at hotspots. '9-bp deletion' (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNA<sup>Lys</sup>, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with '9-bp deletion' when it is present on a plasmid or in the mitochondrial genome. Through a series of <i>in vitro</i> and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Therefore, we uncover a new role for Endonuclease G in generating mtDNA deletions, which depends on the formation of G4 DNA within the mitochondrial genome. In summary, we identify a novel property of Endonuclease G, besides its role in apoptosis and the recently described elimination of paternal mitochondria during fertilisation.
    Keywords:  E. coli; cell biology; genetics; genomics; human; rat
    DOI:  https://doi.org/10.7554/eLife.69916
  11. Mol Cell Biol. 2022 Nov 14. e0014322
    Elucidation of the Role of FAM210B in Mitochondrial Metabolism and Erythropoiesis.
    Chie Suzuki, Tohru Fujiwara, Hiroki Shima, Koya Ono, Kei Saito, Hiroki Kato, Koichi Onodera, Satoshi Ichikawa, Noriko Fukuhara, Yasushi Onishi, Hisayuki Yokoyama, Yukio Nakamura, Kazuhiko Igarashi, Hideo Harigae.
      Mitochondria play essential and specific roles during erythroid differentiation. Recently, FAM210B, encoding a mitochondrial inner membrane protein, has been identified as a novel target of GATA-1, as well as an erythropoietin-inducible gene. While FAM210B protein is involved in regulate mitochondrial metabolism and heme biosynthesis, its detailed function remains unknown. Here, we generated both knockout and knockdown of endogenous FAM210B in human induced pluripotent stem-derived erythroid progenitor (HiDEP) cells using CRISPR/Cas9 methodology. Intriguingly, erythroid differentiation was more pronounced in the FAM210B-depleted cells, and this resulted in increased frequency of orthochromatic erythroblasts and decreased frequencies of basophilic/polychromatic erythroblasts. Comprehensive metabolite analysis and functional analysis indicated that oxygen consumption rates and the NAD (NAD+)/NADH ratio were significantly decreased, while lactate production was significantly increased in FAM210B deletion HiDEP cells, indicating involvement of FAM210B in mitochondrial energy metabolism in erythroblasts. Finally, we purified FAM210B-interacting protein from K562 cells that stably expressed His/biotin-tagged FAM210B. Mass spectrometry analysis of the His/biotin-purified material indicated interactions with multiple subunits of mitochondrial ATP synthases, such as subunit alpha (ATP5A) and beta (ATP5B). Our results suggested that FAM210B contributes prominently to erythroid differentiation by regulating mitochondrial energy metabolism. Our results provide insights into the pathophysiology of dysregulated hematopoiesis.
    Keywords:  FAM210B; erythroid differentiation; mitochondria; mitochondrial ATP synthase
    DOI:  https://doi.org/10.1128/mcb.00143-22
  12. J Biol Chem. 2022 Nov 12. pii: S0021-9258(22)01147-4. [Epub ahead of print] 102704
    The interaction between E3 ubiquitin ligase Parkin and mitophagy receptor PHB2 links inner mitochondrial membrane ubiquitination to efficient mitophagy.
    Shan Sun, Hongyu Hou, Guoqiang Ma, Qilian Ma, Ningning Li, Li Zhang, Chunsheng Dong, Mian Cao, Kin Yip Tam, Zheng Ying, Hongfeng Wang.
      The autophagic clearance of mitochondria has been defined as mitophagy, which is triggered by mitochondrial damage and serves as a major pathway for mitochondrial homeostasis and cellular quality control. PINK1 and Parkin-mediated mitophagy is the most extensively studied form of mitophagy, which has been linked to the pathogenesis of neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The current paradigm of this particular mitophagy pathway is that the ubiquitination of the outer mitochondrial membrane is the key step to enable the recognition of damaged mitochondria by the core autophagic component autophagosome. However, whether the inner mitochondrial membrane (IMM) is ubiquitinated by Parkin and its contribution to sufficient mitophagy remain unclear. Here, using molecular, cellular, and biochemical approaches, we report that prohibitin 2 (PHB2), an essential IMM receptor for mitophagy, is ubiquitinated by Parkin and thereby gains higher affinity to the autophagosome during mitophagy. Our findings suggest that Parkin directly binds to PHB2 through its RING1 domain and promotes K11- and K33-linked ubiquitination on K142/K200 sites of PHB2, thereby enhancing the interaction between PHB2 and MAP1LC3B/LC3B. Interestingly and importantly, our study allows us to propose a novel model in which IMM protein PHB2 serves as both a receptor and a ubiquitin-mediated base for autophagosome recruitment to ensure efficient mitophagy.
    Keywords:  MAP1LC3B/LC3B; PHB2; Parkin; mitophagy; ubiquitination
    DOI:  https://doi.org/10.1016/j.jbc.2022.102704
  13. Comp Biochem Physiol A Mol Integr Physiol. 2022 Nov 12. pii: S1095-6433(22)00201-X. [Epub ahead of print] 111343
    Short communication: Acute hypoxia does not alter mitochondrial abundance in naked mole-rats.
    Nathalie C Marks de Chabris, Soulene Sabir, Guy Perkins, Hang Cheng, Marc H Ellisman, Matthew E Pamenter.
      Hypoxia poses a significant energetic challenge and most species exhibit metabolic remodelling when exposed to prolonged hypoxia. One component of this remodelling is mitochondrial biogenesis/mitophagy, which alter mitochondrial abundance and helps to adjust metabolic throughput to match changes in energy demands in hypoxia. However, how acute hypoxia impacts mitochondrial abundance in hypoxia-tolerant species is poorly understood. To help address this gap, we exposed hypoxia-tolerant naked mole-rats to 3 h of normoxia or acute hypoxia (5% O2) and measured changes in mitochondrial abundance using two well-established markers: citrate synthase (CS) enzyme activity and mitochondrial DNA (mtDNA) abundance. We found that neither marker changed with hypoxia in brain, liver, or kidney, suggesting that mitochondrial biogenesis is not initiated during acute hypoxia in these tissues. Conversely in skeletal muscle, the ratio of CS activity to total protein decreased 50% with hypoxia. However, this change was likely driven by an increase in soluble protein density in hypoxia because CS activity was unchanged relative to wet tissue weight and the mtDNA copy number was unchanged. To confirm this, we examined skeletal muscle mitochondria using transmission electron microscopy and found no change in mitochondrial volume density. Taken together with previous studies of mitochondrial respiratory function, our present findings suggest that naked mole-rats primarily rely on tissue-specific functional remodelling of metabolic pathways and mitochondrial respiratory throughput, and not physical changes in mitochondrial number or volume, to adjust to short-term hypoxic exposure.
    Keywords:  Brain; Citrate synthase; Kidney; Liver; Mitochondrial DNA; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.cbpa.2022.111343
  14. PeerJ. 2022 ;10 e14350
    AAA+ proteases: the first line of defense against mitochondrial damage.
    Gautam Pareek.
      Mitochondria play essential cellular roles in Adenosine triphosphate (ATP) synthesis, calcium homeostasis, and metabolism, but these vital processes have potentially deadly side effects. The production of the reactive oxygen species (ROS) and the aggregation of misfolded mitochondrial proteins can lead to severe mitochondrial damage and even cell death. The accumulation of mitochondrial damage is strongly implicated in aging and several incurable diseases, including neurodegenerative disorders and cancer. To oppose this, metazoans utilize a variety of quality control strategies, including the degradation of the damaged mitochondrial proteins by the mitochondrial-resident proteases of the ATPase Associated with the diverse cellular Activities (AAA+) family. This mini-review focuses on the quality control mediated by the mitochondrial-resident proteases of the AAA+ family used to combat the accumulation of damaged mitochondria and on how the failure of this mitochondrial quality control contributes to diseases.
    Keywords:  AAA+ Protease; Mitochondria in neurological disorders; Mitochondrial Translation; Mitochondrial Unfolded Protein Response; Mitochondrial quality control
    DOI:  https://doi.org/10.7717/peerj.14350
  15. Mov Disord. 2022 11;37(11): 2319-2320
    Reply to: No Association between Rare TWNK Variants and Parkinson's Disease in European Cohorts.
    Marco Percetti, Edoardo Monfrini, Leonardo Caporali, Raffaella Minardi, Valerio Carelli, Enza Maria Valente, Alessio Di Fonzo.
      
    Keywords:  Parkinson's disease; TWNK; mtDNA; parkinsonism; twinkle
    DOI:  https://doi.org/10.1002/mds.29244
  16. Cell Signal. 2022 Nov 12. pii: S0898-6568(22)00286-8. [Epub ahead of print] 110524
    Phosphorylation of mammalian mitochondrial EF-Tu by Fyn and c-Src kinases.
    Emine C Koc, Caroline A Hunter, Hasan Koc.
      Src Family Kinases (SFKs) are tyrosine kinases known to regulate glucose and fatty acid metabolism as well as oxidative phosphorylation (OXPHOS) in mammalian mitochondria. We and others discovered the association of the SFK kinases Fyn and c-Src with mitochondrial translation components. This translational system is responsible for the synthesis of 13 mitochondrial (mt)-encoded subunits of the OXPHOS complexes and is, thus, essential for energy generation. Mitochondrial ribosomal proteins and various translation elongation factors including Tu (EF-Tumt) have been identified as possible Fyn and c-Src kinase targets. However, the phosphorylation of specific residues in EF-Tumt by these kinases and their roles in the regulation of protein synthesis are yet to be explored. In this study, we report the association of EF-Tumt with cSrc kinase and mapping of phosphorylated Tyr (pTyr) residues by these kinases. We determined that a specific Tyr residue in EF-Tumt at position 266 (EF-Tumt-Y266), located in a highly conserved c-Src consensus motif is one of the major phosphorylation sites. The potential role of EF-Tumt-Y266 phosphorylation in regulation of mitochondrial translation investigated by site-directed mutagenesis. Its phosphomimetic to Glu residue (EF-Tumt-E266) inhibited ternary complex (EF-Tumt•GTP•aatRNA) formation and translation in vitro. Our findings along with data mining analysis of the c-Src knock out (KO) mice proteome suggest that the SFKs have possible roles for regulation of mitochondrial protein synthesis and oxidative energy metabolism in animals.
    Keywords:  EF-Tu(mt) (TUFM); Fyn and c-Src kinases; Mitochondrial protein synthesis; SFKs; Translation; Tyr phosphorylation
    DOI:  https://doi.org/10.1016/j.cellsig.2022.110524
  17. EMBO J. 2022 Nov 18. e112006
    LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.
    Zhixiao Wu, Lena A Berlemann, Verian Bader, Dominik A Sehr, Eva Dawin, Alberto Covallero, Jens Meschede, Lena Angersbach, Cathrin Showkat, Jonas B Michaelis, Christian Münch, Bettina Rieger, Dmitry Namgaladze, Maria Georgina Herrera, Fabienne C Fiesel, Wolfdieter Springer, Marta Mendes, Jennifer Stepien, Katalin Barkovits, Katrin Marcus, Albert Sickmann, Gunnar Dittmar, Karin B Busch, Dietmar Riedel, Marisa Brini, Jörg Tatzelt, Tito Cali, Konstanze F Winklhofer.
      Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
    Keywords:  HOIP; NEMO; OTULIN; PINK1; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2022112006
  18. Front Cell Dev Biol. 2022 ;10 1044672
    Analysis of mitochondrial dynamics and function in the retinal pigment epithelium by high-speed high-resolution live imaging.
    Li Xuan Tan, Jianlong Li, Colin J Germer, Aparna Lakkaraju.
      Mitochondrial dysfunction is strongly implicated in neurodegenerative diseases including age-related macular degeneration (AMD), which causes irreversible blindness in over 50 million older adults worldwide. A key site of insult in AMD is the retinal pigment epithelium (RPE), a monolayer of postmitotic polarized cells that performs essential functions for photoreceptor health and vision. Recent studies from our group and others have identified several features of mitochondrial dysfunction in AMD including mitochondrial fragmentation and bioenergetic defects. While these studies provide valuable insight at fixed points in time, high-resolution, high-speed live imaging is essential for following mitochondrial injury in real time and identifying disease mechanisms. Here, we demonstrate the advantages of live imaging to investigate RPE mitochondrial dynamics in cell-based and mouse models. We show that mitochondria in the RPE form extensive networks that are destroyed by fixation and discuss important live imaging considerations that can interfere with accurate evaluation of mitochondrial integrity such as RPE differentiation status and acquisition parameters. Our data demonstrate that RPE mitochondria show localized heterogeneities in membrane potential and ATP production that could reflect focal changes in metabolism and oxidative stress. Contacts between the mitochondria and organelles such as the ER and lysosomes mediate calcium flux and mitochondrial fission. Live imaging of mouse RPE flatmounts revealed a striking loss of mitochondrial integrity in albino mouse RPE compared to pigmented mice that could have significant functional consequences for cellular metabolism. Our studies lay a framework to guide experimental design and selection of model systems for evaluating mitochondrial health and function in the RPE.
    Keywords:  RPE; live imaging; mitochondria; pigmented and albino mice; retina
    DOI:  https://doi.org/10.3389/fcell.2022.1044672
  19. BMC Bioinformatics. 2022 Nov 14. 23(1): 482
    Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.
    Michael J Cormier, Brent S Pedersen, Pinar Bayrak-Toydemir, Aaron R Quinlan.
      BACKGROUND: Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites.RESULTS: Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in "cryptic" splicing regions beyond canonical donor or acceptor splice sites.
    CONCLUSION: Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
    Keywords:  Alternative splicing; Genetic constraint; Genomic medicine; Genomics; Machine learning; Noncanonical cryptic splicing; Pathogenic interpretation; Purifying selection; Rare disease; Splicing
    DOI:  https://doi.org/10.1186/s12859-022-05041-x
  20. J Inherit Metab Dis. 2022 Nov 13.
    Cellular and computational models reveal environmental and metabolic interactions in MMUT-type methylmalonic aciduria.
    Charlotte Ramon, Florian Traversi, Céline Bürer, D Sean Froese, Jörg Stelling.
      MMUT-type methylmalonic aciduria is a rare inherited metabolic disease caused by the loss of function of the methylmalonyl-CoA mutase (MMUT) enzyme. Patients develop symptoms resembling those of primary mitochondrial disorders, but the underlying causes of mitochondrial dysfunction remain unclear. Here, we examined environmental and genetic interactions in MMUT deficiency using a combination of computational modeling and cellular models to decipher pathways interacting with MMUT. Immortalized fibroblast (hTERT BJ5ta) MMUT-KO (MUTKO) clones displayed a mild mitochondrial impairment in standard glucose-based medium, but they did not to show increased reliance on respiratory metabolism nor reduced growth or viability. Consistently, our modeling predicted MUTKO specific growth phenotypes only for lower extracellular glutamine concentrations. Indeed, two of three MMUT-deficient BJ5ta cell lines showed a reduced viability in glutamine-free medium. Further, growth on 183 different carbon and nitrogen substrates identified increased NADH (nicotinamide adenine dinucleotide) metabolism of BJ5ta and HEK293 MUTKO cells compared to controls on purine- and glutamine-based substrates. With this knowledge, our modeling predicted 13 reactions interacting with MMUT that potentiate an effect on growth, primarily those of secondary oxidation of propionyl-CoA, oxidative phosphorylation and oxygen diffusion. Of these, we validated 3-hydroxyisobutytyl-CoA hydrolase (HIBCH) in the secondary propionyl-CoA oxidation pathway. Altogether, these results suggest compensation for the loss of MMUT function by increasing anaplerosis through glutamine or by diverting flux away from MMUT through the secondary propionyl-CoA oxidation pathway, which may have therapeutic relevance.
    Keywords:  CRISPR-Cas9; Rare disease; constraint-based modeling; genetic interaction; metabolism; methylmalonic aciduria
    DOI:  https://doi.org/10.1002/jimd.12575
  21. Biochim Biophys Acta Bioenerg. 2022 Nov 14. pii: S0005-2728(22)00406-6. [Epub ahead of print] 148936
    Alternative respiratory oxidases to study the animal electron transport chain.
    Pablo Hernansanz-Agustín, José Antonio Enríquez.
      Oxidative phosphorylation is a common process to most organisms in which the main function is to generate an electrochemical gradient across the inner mitochondrial membrane (IMM) and to make energy available to the cell. However, plants, many fungi and some animals maintain non-energy conserving oxidases which serve as a bypass to coupled respiration. Namely, the alternative NADH:ubiquinone oxidoreductase NDI1, present in the complex I (CI)-lacking Saccharomyces cerevisiae, and the alternative oxidase, ubiquinol:oxygen oxidoreductase AOX, present in many organisms across different kingdoms. In the last few years, these alternative oxidases have been used to dissect previously indivisible processes in bioenergetics and have helped to discover, understand, and corroborate important processes in mitochondria. Here, we review how the use of alternative oxidases have contributed to the knowledge in CI stability, bioenergetics, redox biology, and the implications of their use in current and future research.
    Keywords:  AOX; Alternative oxidase; CoQ pool; Oxphos; ROS
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148936
  22. iScience. 2022 Nov 18. 25(11): 105410
    Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.
    Christine E Robbins, Bhumil Patel, Danielle L Sawyer, Barrie Wilkinson, Brian K Kennedy, Mark A McCormick.
      Deletion of genes encoding ribosomal proteins extends lifespan in yeast. This increases translation of the functionally conserved transcription factor Gcn4, and lifespan extension in these mutants is GCN4-dependent. Gcn4 is also translationally upregulated by uncharged tRNAs, as are its C aenorhabditis elegans and mammalian functional orthologs. Here, we show that cytosolic tRNA synthetase inhibitors upregulate Gcn4 translation and extend yeast lifespan in a Gcn4-dependent manner. This cytosolic tRNA synthetase inhibitor is also able to extend the lifespan of C. elegans in an atf-4-dependent manner. We show that mitochondrial tRNA synthetase inhibitors greatly extend the lifespan of C. elegans, and this depends on atf-4. This suggests that perturbations of both cytosolic and mitochondrial translation may act in part via the same downstream pathway. These findings establish GCN4 orthologs as conserved longevity factors and, as long-lived mice exhibit elevated ATF4, leave open the possibility that tRNA synthetase inhibitors could also extend lifespan in mammals.
    Keywords:  Biochemistry; Biological sciences; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105410
  23. iScience. 2022 Nov 18. 25(11): 105447
    Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.
    M A Neginskaya, S E Morris, E V Pavlov.
      An increase in permeability of the mitochondrial inner membrane, mitochondrial permeability transition (PT), is the central event responsible for cell death and tissue damage in conditions such as stroke and heart attack. PT is caused by the cyclosporin A (CSA)-dependent calcium-induced pore, the permeability transition pore (PTP). The molecular details of PTP are incompletely understood. We utilized holographic and fluorescent microscopy to assess the contribution of ATP synthase and adenine nucleotide translocator (ANT) toward PTP. In cells lacking either ATP synthase or ANT, we observed CSA-sensitive membrane depolarization, but not high-conductance PTP. In wild-type cells, calcium-induced CSA-sensitive depolarization preceded opening of PTP, which occurred only after nearly complete mitochondrial membrane depolarization. We propose that both ATP synthase and ANT are required for high-conductance PTP but not depolarization, which presumably occurs through activation of the low-conductance PT, which has a molecular nature that is different from both complexes.
    Keywords:  Cell biology; Functional aspects of cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105447
  24. Dis Model Mech. 2022 Nov 18. pii: dmm.049358. [Epub ahead of print]
    Bortezomib-induced neurotoxicity in human neurons is the consequence of nicotinamide adenine dinucleotide depletion.
    Andrew R Snavely, Keungjung Heo, Veselina Petrova, Tammy Szu-Yu Ho, Xuan Huang, Crystal Hermawan, Ruth Kagan, Tao Deng, Ilyas Singeç, Long Chen, Lee Barret, Clifford J Woolf.
      The proteosome inhibitor bortezomib has revolutionized the treatment of multiple hematologic malignancies, but in many cases its efficacy is limited by a dose-dependent peripheral neuropathy. We show that human induced pluripotent stem cell (hiPSC) derived motor neurons and sensory neurons provide a model system for the study of bortezomib-induced peripheral neuropathy with promising implications for furthering mechanistic understanding and developing treatments for preventing axonal damage. Human neurons in tissue culture display distal-to-proximal neurite degeneration when exposed to bortezomib. This process coincides with disruptions in mitochondrial function and energy homeostasis similar to those described in rodent models of bortezomib-induced neuropathy. Moreover, while the degenerative process is unaffected by inhibition of caspases, it is completely blocked by exogenous nicotinamide adenine dinucleotide (NAD+), a mediator of the SARM1-dependent axon degeneration pathway. We demonstrate that bortezomib-induced neurotoxicity in relevant human neurons proceeds through mitochondrial dysfunction and the NAD+ depletion mediated axon degeneration, raising the possibility that targeting these changes may provide effective therapeutics for the prevention of bortezomib-induced neuropathy and that modeling chemotherapy-induced neuropathy in human neurons has utility.
    Keywords:  CIPN; Neuropathy; Wallerian Degeneration
    DOI:  https://doi.org/10.1242/dmm.049358
  25. BMC Bioinformatics. 2022 Nov 16. 23(1): 490
    Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate.
    Thomas J Nicholas, Michael J Cormier, Aaron R Quinlan.
      BACKGROUND: Identification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of variants that are more likely to underlie a disease phenotype. Datasets reflecting population allele frequencies of different types of variants serve as powerful filtering tools, especially in the context of rare disease analysis. While such population-scale allele frequency datasets now exist for structural variants (SVs), it remains a challenge to match SV calls between multiple datasets, thereby complicating estimates of a putative SV's population allele frequency.RESULTS: We introduce SVAFotate, a software tool that enables the annotation of SVs with variant allele frequency and related information from existing SV datasets. As a result, VCF files annotated by SVAFotate offer a variety of metrics to aid in the stratification of SVs as common or rare in the broader human population.
    CONCLUSIONS: Here we demonstrate the use of SVAFotate in the classification of SVs with regards to their population frequency and illustrate how SVAFotate's annotations can be used to filter and prioritize SVs. Lastly, we detail how best to utilize these SV annotations in the analysis of genetic variation in studies of rare disease.
    Keywords:  Genome annotation; Population allele frequency; Structural variation
    DOI:  https://doi.org/10.1186/s12859-022-05008-y
  26. Life Sci. 2022 Nov 10. pii: S0024-3205(22)00862-1. [Epub ahead of print] 121162
    Mechanism and regulation of mitophagy in nonalcoholic fatty liver disease (NAFLD): A mini-review.
    Lihui Zhu, Xiao Wu, Rongrong Liao.
      Mitochondrial dysfunction has been hypothesized to play a central role in the pathobiology of nonalcoholic fatty liver disease (NAFLD). Thus, maintenance of mitochondria homeostasis and function is important for NAFLD treatment. Mitophagy, a process that selectively clears damaged or dysfunctional mitochondria through autophagic machinery, is beneficial for mitochondrial homeostasis. Notably, strategies that regulate mitophagy exert beneficial effects in preclinical experiments. Traditional Chinese medicine (TCM) is a natural product including active ingredients, extracts, and has great potential in the prevention and treatment of liver diseases. Given the importance of mitophagy, this review summarizes mitophagy-related pathways and the latest findings on the regulation of mitophagy in NAFLD. We also highlight the potential of TCM targeting mitophagy for the treatment of NAFLD.
    Keywords:  Autophagy; Fatty liver disease; Lipid; Metabolism; Traditional Chinese medicine
    DOI:  https://doi.org/10.1016/j.lfs.2022.121162
  27. Prog Retin Eye Res. 2022 Nov 15. pii: S1350-9462(22)00096-9. [Epub ahead of print] 101136
    Glaucomatous optic neuropathy: Mitochondrial dynamics, dysfunction and protection in retinal ganglion cells.
    Won-Kyu Ju, Guy A Perkins, Keun-Young Kim, Tonking Bastola, Woo-Young Choi, Soo-Ho Choi.
      Glaucoma is a leading cause of irreversible blindness worldwide and is characterized by a slow, progressive, and multifactorial degeneration of retinal ganglion cells (RGCs) and their axons, resulting in vision loss. Despite its high prevalence in individuals 60 years of age and older, the causing factors contributing to glaucoma progression are currently not well characterized. Intraocular pressure (IOP) is the only proven treatable risk factor. However, lowering IOP is insufficient for preventing disease progression. One of the significant interests in glaucoma pathogenesis is understanding the structural and functional impairment of mitochondria in RGCs and their axons and synapses. Glaucomatous risk factors such as IOP elevation, aging, genetic variation, neuroinflammation, neurotrophic factor deprivation, and vascular dysregulation, are potential inducers for mitochondrial dysfunction in glaucoma. Because oxidative phosphorylation stress-mediated mitochondrial dysfunction is associated with structural and functional impairment of mitochondria in glaucomatous RGCs, understanding the underlying mechanisms and relationship between structural and functional alterations in mitochondria would be beneficial to developing mitochondria-related neuroprotection in RGCs and their axons and synapses against glaucomatous neurodegeneration. Here, we review the current studies focusing on mitochondrial dynamics-based structural and functional alterations in the mitochondria of glaucomatous RGCs and therapeutic strategies to protect RGCs against glaucomatous neurodegeneration.
    Keywords:  Gene therapy; Glaucoma; Mitochondrial bioenergetics; Mitochondrial dynamics; Mitophagy; Retinal ganglion cell
    DOI:  https://doi.org/10.1016/j.preteyeres.2022.101136
  28. Antioxid Redox Signal. 2022 Nov 18.
    Redox modulation of mitochondrial proteins in the neurotoxicant models of Parkinson's disease.
    Alika Sarkar, Mohd Sami Ur Rasheed, Mahendra Pratap Singh.
      SIGNIFICANCE: Mitochondrial proteins regulate the oxidative phosphorylation, cellular metabolism and free radical generation. Redox modulation alters the mitochondrial proteins and instigates the damage to dopaminergic neurons. Toxicants contribute to Parkinson's disease (PD) pathogenesis in conjunction with aging and genetic factors. While oxidative modulation of a number of mitochondrial proteins is linked to xenobiotic exposure, little is known about its role in the toxicant-induced PD. Understanding the role of redox modulation of mitochondrial proteins in complex cellular events leading to neurodegeneration is highly relevant.RECENT ADVANCES: Many toxicants are shown to inhibit complex I or III and elicit free radical production that alters the redox status of mitochondrial proteins. Implication of redox modulation of the mitochondrial proteins makes them a target to comprehend the underlying mechanism of toxicant-induced PD.
    CRITICAL ISSUES: Owing to multi-factorial etiology, exploration of onset and progression and treatment outcomes need a comprehensive approach. The article explains about a few mitochondrial proteins, which undergo redox changes along with the promising strategies, which help to alleviate the toxicant-induced redox imbalance leading to neurodegeneration.
    FUTURE DIRECTIONS: Although mitochondrial proteins are linked to PD, their role in toxicant-induced Parkinsonism is not yet completely known. Preservation of antioxidant defense machinery could alleviate the redox modulation of mitochondrial proteins. Targeted antioxidant delivery, use of metal chelators and activation of nuclear factor erythroid 2-related factor 2 and combinational therapy that encounters multiple free radicals, could ameliorate the redox modulation of mitochondrial proteins and thereby PD progression.
    DOI:  https://doi.org/10.1089/ars.2022.0106
  29. Sci Rep. 2022 Nov 18. 12(1): 19847
    Beneficial effects of SS-31 peptide on cardiac mitochondrial dysfunction in tafazzin knockdown mice.
    Silvia Russo, Domenico De Rasmo, Anna Signorile, Angela Corcelli, Simona Lobasso.
      Barth Syndrome (BTHS), a genetic disease associated with early-onset cardioskeletal myopathy, is caused by loss-of-function mutations of the TAFAZZIN gene, which is responsible for remodeling the mitochondrial phospholipid cardiolipin (CL). Deregulation of CL biosynthesis and maturation in BTHS mitochondria result in a dramatically increased monolysocardiolipin (MLCL)/CL ratio associated with bioenergetic dysfunction. One of the most promising therapeutic approaches for BTHS includes the mitochondria-targeted tetrapeptide SS-31, which interacts with CL. Here, we used TAFAZZIN knockdown (TazKD) mice to investigate for the first time whether in vivo administration of SS-31 could affect phospholipid profiles and mitochondrial dysfunction. The CL fingerprinting of TazKD cardiac mitochondria obtained by MALDI-TOF/MS revealed the typical lipid changes associated with BTHS. TazKD mitochondria showed lower respiratory rates in state 3 and 4 together with a decreased in maximal respiratory rates. Treatment of TazKD mice with SS-31 improved mitochondrial respiratory capacity and promoted supercomplex organization, without affecting the MLCL/CL ratio. We hypothesize that SS-31 exerts its effect by influencing the function of the respiratory chain rather than affecting CL directly. In conclusion, our results indicate that SS-31 have beneficial effects on improving cardiac mitochondrial dysfunction in a BTHS animal model, suggesting the peptide as future pharmacologic agent for therapy.
    DOI:  https://doi.org/10.1038/s41598-022-24231-4
  30. J Cell Biol. 2023 Jan 02. pii: e202111053. [Epub ahead of print]222(1):
    Glial TGFβ activity promotes neuron survival in peripheral nerves.
    Alexandria P Lassetter, Megan M Corty, Romina Barria, Amy E Sheehan, Jo Q Hill, Sue A Aicher, A Nicole Fox, Marc R Freeman.
      Maintaining long, energetically demanding axons throughout the life of an animal is a major challenge for the nervous system. Specialized glia ensheathe axons and support their function and integrity throughout life, but glial support mechanisms remain poorly defined. Here, we identified a collection of secreted and transmembrane molecules required in glia for long-term axon survival in vivo. We showed that the majority of components of the TGFβ superfamily are required in glia for sensory neuron maintenance but not glial ensheathment of axons. In the absence of glial TGFβ signaling, neurons undergo age-dependent degeneration that can be rescued either by genetic blockade of Wallerian degeneration or caspase-dependent death. Blockade of glial TGFβ signaling results in increased ATP in glia that can be mimicked by enhancing glial mitochondrial biogenesis or suppressing glial monocarboxylate transporter function. We propose that glial TGFβ signaling supports axon survival and suppresses neurodegeneration through promoting glial metabolic support of neurons.
    DOI:  https://doi.org/10.1083/jcb.202111053
  31. iScience. 2022 Nov 18. 25(11): 105431
    Endogenous metabolism in endothelial and immune cells generates most of the tissue vitamin B3 (nicotinamide).
    Julianna D Zeidler, Claudia C S Chini, Karina S Kanamori, Sonu Kashyap, Jair M Espindola-Netto, Katie Thompson, Gina Warner, Fernanda S Cabral, Thais R Peclat, Lilian Sales Gomez, Sierra A Lopez, Miles K Wandersee, Renee A Schoon, Kimberly Reid, Keir Menzies, Felipe Beckedorff, Joel M Reid, Sebastian Brachs, Ralph G Meyer, Mirella L Meyer-Ficca, Eduardo Nunes Chini.
      In mammals, nicotinamide (NAM) is the primary NAD precursor available in circulation, a signaling molecule, and a precursor for methyl-nicotinamide (M-NAM) synthesis. However, our knowledge about how the body regulates tissue NAM levels is still limited. Here we demonstrate that dietary vitamin B3 partially regulates plasma NAM and NAM-derived metabolites, but not their tissue levels. We found that NAD de novo synthesis from tryptophan contributes to plasma and tissue NAM, likely by providing substrates for NAD-degrading enzymes. We also demonstrate that tissue NAM is mainly generated by endogenous metabolism and that the NADase CD38 is the main enzyme that produces tissue NAM. Tissue-specific CD38-floxed mice revealed that CD38 activity on endothelial and immune cells is the major contributor to tissue steady-state levels of NAM in tissues like spleen and heart. Our findings uncover the presence of different pools of NAM in the body and a central role for CD38 in regulating tissue NAM levels.
    Keywords:  Biochemistry; Biological sciences; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105431
  32. Sci Rep. 2022 Nov 18. 12(1): 19841
    Selection of red fluorescent protein for genetic labeling of mitochondria and intercellular transfer of viable mitochondria.
    Isamu Taiko, Chika Takano, Masayuki Nomoto, Shingo Hayashida, Kazunori Kanemaru, Toshio Miki.
      The phenomenon of intercellular mitochondrial transfer has attracted great attention in various fields of research, including stem cell biology. Elucidating the mechanism of mitochondrial transfer from healthy stem cells to cells with mitochondrial dysfunction may lead to the development of novel stem cell therapies to treat mitochondrial diseases, among other advances. To visually evaluate and analyze the mitochondrial transfer process, dual fluorescent labeling systems are often used to distinguish the mitochondria of donor and recipient cells. Although enhanced green fluorescent protein (EGFP) has been well-characterized for labeling mitochondria, other colors of fluorescent protein have been less extensively evaluated in the context of mitochondrial transfer. Here, we generated different lentiviral vectors with mitochondria-targeted red fluorescent proteins (RFPs), including DsRed, mCherry (both from Discosoma sp.) Kusabira orange (mKOκ, from Verrillofungia concinna), and TurboRFP (from Entacmaea quadricolor). Among these proteins, mitochondria-targeted DsRed and its variant mCherry often generated bright aggregates in the lysosome while other proteins did not. We further validated that TurboRFP-labeled mitochondria were successfully transferred from amniotic epithelial cells, one of the candidates for donor stem cells, to mitochondria-damaged recipient cells without losing the membrane potential. Our study provides new insight into the genetic labeling of mitochondria with red fluorescent proteins, which may be utilized to analyze the mechanism of intercellular mitochondrial transfer.
    DOI:  https://doi.org/10.1038/s41598-022-24297-0
  33. J Chem Inf Model. 2022 Nov 15.
    Application of Machine Learning in Spatial Proteomics.
    Minjie Mou, Ziqi Pan, Mingkun Lu, Huaicheng Sun, Yunxia Wang, Yongchao Luo, Feng Zhu.
      Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
    Keywords:  analytical tools; cell biology; data resources; deep learning; imaging; machine learning; mass spectrometry; protein subcellular localization; spatial proteomics
    DOI:  https://doi.org/10.1021/acs.jcim.2c01161
  34. Mitochondrion. 2022 Oct 29. pii: S1567-7249(22)00089-7. [Epub ahead of print]68 1-9
    The impact of TK2 deficiency syndrome and its treatment by nucleoside therapy on quality of life.
    Dagmar Amtmann, Arnold R Gammaitoni, Bradley S Galer, Rana Salem, Mark P Jensen.
      TK2d is an ultrarare autosomal recessive mitochondrial DNA depletion syndrome. Nucleoside therapy improves or stabilizes disease across key outcomes including survival, ambulation, and requirement for mechanical ventilation. However, little is known about the effects of nucleoside therapy treatment of TK2d from the patient's perspective. This study sought to address this knowledge gap. Participants with TK2d and/or their parents/caregivers completed online surveys with standardized health measures and interviews. During interviews, participants rated and described TK2d's impact on 13 quality of life domains, changes since starting nucleoside therapy, and if they would recommend nucleoside therapy. Twenty-five individuals participated (17 adults with TK2d, 4 parent-participant pairs, 4 parents of children with TK2d). Adult participants with TK2d had clinically meaningfully worse scores than the general population on global physical and mental health, physical function, pain interference, fatigue, anxiety, and social function. Children's mobility and pain interference were significantly worse than the general pediatric population. Physical domains most affected by TK2d were: mobility (84%), fatigue (60%), respiratory function (56%), and hospitalizations (55%). Psychosocial domains most affected were: impact on family members (39%), mood (36%), and social life (28%). Most (77%) treated patients reported improvement; whereas, 67% in the untreated group reported worsening. All participants would recommend nucleoside therapy. In summary, TK2d has significant negative impacts on most areas of life and function. Measures of fatigue, sleep, swallowing/eating, speaking, and mood, should be considered as outcomes in clinical trials and research studies. Nucleoside therapy appears to provide meaningful improvements across many health domains affected by TK2d. SYNOPSIS: The consequences of having TK2d are devastating for both those with the disorder and their families; however, nucleoside therapy appears to provide meaningful improvements across many health domains affected by TK2d.
    Keywords:  Mitochondrial disease; Nucleoside therapy; Quality of life; Thymidine kinase 2 deficiency; Treatment effects
    DOI:  https://doi.org/10.1016/j.mito.2022.10.003
  35. Cell Metab. 2022 Nov 08. pii: S1550-4131(22)00489-2. [Epub ahead of print]
    Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.
    Goda Snieckute, Aitana Victoria Genzor, Anna Constance Vind, Laura Ryder, Mark Stoneley, Sébastien Chamois, René Dreos, Cathrine Nordgaard, Frederike Sass, Melanie Blasius, Aida Rodríguez López, Sólveig Hlín Brynjólfsdóttir, Kasper Langebjerg Andersen, Anne E Willis, Lisa B Frankel, Steen Seier Poulsen, David Gatfield, Zachary Gerhart-Hines, Christoffer Clemmensen, Simon Bekker-Jensen.
      Impairment of translation can lead to collisions of ribosomes, which constitute an activation platform for several ribosomal stress-surveillance pathways. Among these is the ribotoxic stress response (RSR), where ribosomal sensing by the MAP3K ZAKα leads to activation of p38 and JNK kinases. Despite these insights, the physiological ramifications of ribosomal impairment and downstream RSR signaling remain elusive. Here, we show that stalling of ribosomes is sufficient to activate ZAKα. In response to amino acid deprivation and full nutrient starvation, RSR impacts on the ensuing metabolic responses in cells, nematodes, and mice. The RSR-regulated responses in these model systems include regulation of AMPK and mTOR signaling, survival under starvation conditions, stress hormone production, and regulation of blood sugar control. In addition, ZAK-/- male mice present a lean phenotype. Our work highlights impaired ribosomes as metabolic signals and demonstrates a role for RSR signaling in metabolic regulation.
    Keywords:  AMPK; FGF21; ZAK-alpha; amino acid starvation; mTOR; metabolic regulation; mouse models; ribosome collision; ribotoxic stress response
    DOI:  https://doi.org/10.1016/j.cmet.2022.10.011
  36. J Gerontol A Biol Sci Med Sci. 2022 Nov 13. pii: glac227. [Epub ahead of print]
    Mitochondrial dysfunction and intrinsic capacity: insights from a narrative review.
    Jaqueline Aragoni da Silva, Yves Rolland, Laurent O Martinez, Philipe de Souto Barreto.
      Mitochondrial dysfunction occurs during aging and may play a role, by distinct mechanisms, in the loss of intrinsic capacity (IC), operationalized through five domains: locomotion, psychological, cognition, vitality/nutrition, and sensory (hearing, vision). The objective of this review is to provide an overview of the associations between mitochondrial function and IC domains. This study is a narrative review of original investigations (any study design) on the relationship of mitochondrial function in humans with locomotion (e.g., gait speed), psychological (e.g., depressive symptoms), cognition (e.g., global cognitive function), vitality (e.g., handgrip strength), and/or sensory (hearing and vision acuity) domains. The IC domains were considered from the perspective of the Integrated Care for Older People (ICOPE), according to the World Health Organization guidelines. The results show that there is still limited evidence regarding the associations between mitochondrial function and IC domains. Most studies were cross-sectional and involved small samples. The tissues/cells most often investigated in the original studies were skeletal muscle and peripheral blood mononuclear cells. The available evidence, although limited, indicates that mitochondrial function, in particular the mitochondrial DNA copy number, is associated with all IC domains. The evidence is more robust for locomotion and less abundant for hearing. In conclusion, this review supports the notion that mitochondrial function is correlated with IC domains by distinct mechanisms. Future studies are needed to confirm whether mitochondria play a role in maintaining optimal function and preventing/delaying the onset of disability during aging, which could ultimately contribute to healthy aging.
    Keywords:  cognitive function; depression; handgrip strength; mitochondria; mobility
    DOI:  https://doi.org/10.1093/gerona/glac227
  37. Science. 2022 11 04. 378(6619): 475-476
    Molecular diversity of astrocytes.
    Katherine T Baldwin.
      The tissue environment influences astrocyte form and function in health and disease.
    DOI:  https://doi.org/10.1126/science.ade9249
  38. Front Neurol. 2022 ;13 1003046
    Case report: Long-term follow-up of two patients with LHON caused by DNAJC30:c.152G>A pathogenic variant-case series.
    Sanja Petrovic Pajic, Martina Jarc-Vidmar, Ana Fakin, Maja Sustar Habjan, Jelka Brecelj, Marija Volk, Ales Maver, Borut Peterlin, Marko Hawlina.
      Background: We present the disease course and long-term follow-up of two patients who were phenotypically diagnosed with atypical Leber Hereditary Optic Neuropathy (LHON) 14 and 12 years ago, respectively, whereby whole exome sequencing revealed recently described recessive DNAJC30:c.152G>A 152 A>G (p.Tyr51Cys) homozygous pathogenic variant with significant spontaneous visual acuity recovery in one.Case presentation: Two presented unrelated males with atypical LHON with sequential visual acuity (VA) loss were followed for many years. Both patients had negative family history. At the presentation at ages 17 (Case 1) and 18 years (Case 2), both had reduced visual acuity (Snellen): (Case 1) right eye (RE):CF 3m, left eye (LE):0.6, (Case 2) RE:0.2, LE:0.15; and color vision (Ishihara): (Case 1) 1/15 and 13/15; (Case 2) 2/15 and 3/15. Both had hyperemic optic disks (PNO) and central scotoma in their visual fields. Electrophysiology in the acute phase showed reduced and delayed visually evoked potentials (VEP) P100 in both patients, with reduced N95 amplitude in Case 2, and initially normal N95 amplitude in Case 1. Fluorescein angiography showed no early leakage with some late pooling at optic disks. Extensive clinical workout, including brain magnetic resonance imaging (MRI), aquaporin 4 (Aq4), and anti-myelin oligodendrocyte protein (anti-MOG) antibodies, was negative. Intravenous corticosteroids did not improve vision. Both experienced further deterioration several months after the onset accompanied by thinning of the peripapillary retinal nerve fiber layer (RNFL). Genetic testing for typical LHON pathogenic variants and whole mitochondrial DNA (mtDNA) sequencing was negative. 1 year after the onset, modest VA improvement began in Case 2 and continued over the next 3 years. VA improved bilaterally to 0.7, color vision 15/15, and islands of vision appeared within the visual field scotoma. VEP P100 peak time shortened, and amplitude increased, despite further RNFL thinning on optical coherent tomography (OCT). The patient's visual function remained stable during the entire 12-year follow-up period. Case 1 experienced modest VA improvement to 0.1 with some improvement in the visual field seven years after the disease onset, remaining stable during the entire 14-year follow-up period. VEP P100 wave remained undetectable.
    Conclusions: Presented are two autosomal recessive LHON (arLHON, OMIM:619382) cases with the same DNAJC30:c.152G>A pathogenic variant and different degrees of spontaneous visual recovery despite progressive RNFL thinning during a long-term follow-up. This mutation should be screened in every atypical LHON patient.
    Keywords:  152 A>G (p.Tyr51Cys) pathogenic variant; DNAJC30:c.152G>A gene; arLHON; color vision improvement; perimetry improvement; recessive optic neuropathy; visual acuity improvement
    DOI:  https://doi.org/10.3389/fneur.2022.1003046
  39. Methods Mol Biol. 2023 ;2587 537-553
    Quantification of Muscle Satellite Stem Cell Divisions by High-Content Analysis.
    William Chen, Theodore J Perkins, Michael A Rudnicki.
      High-content screening is commonly performed on 2D cultured cells, which is high throughput but has low biological relevance. In contrast, single myofiber culture assay preserves the satellite cell niche between the basal lamina and sarcolemma and consequently has high biological relevance but is low throughput. We describe here a high-content screening method that utilizes single myofiber culture that addresses the caveats of both techniques. Our method utilizes the transgenic reporter allele Myf5-Cre:R26R-eYFP to differentiate stem and committed cells within a dividing couplet that can be quantified by high-content throughput immunodetection and bioinformatic analysis.
    Keywords:  Asymmetric self-renewal; High-content screening; Muscle satellite stem cell; Myofiber culture; Niche; Symmetric division
    DOI:  https://doi.org/10.1007/978-1-0716-2772-3_29
  40. Nat Commun. 2022 Nov 17. 13(1): 7037
    Ciliary neurotrophic factor-mediated neuroprotection involves enhanced glycolysis and anabolism in degenerating mouse retinas.
    Kun Do Rhee, Yanjie Wang, Johanna Ten Hoeve, Linsey Stiles, Thao Thi Thu Nguyen, Xiangmei Zhang, Laurent Vergnes, Karen Reue, Orian Shirihai, Dean Bok, Xian-Jie Yang.
      Ciliary neurotrophic factor (CNTF) acts as a potent neuroprotective cytokine in multiple models of retinal degeneration. To understand mechanisms underlying its broad neuroprotective effects, we have investigated the influence of CNTF on metabolism in a mouse model of photoreceptor degeneration. CNTF treatment improves the morphology of photoreceptor mitochondria, but also leads to reduced oxygen consumption and suppressed respiratory chain activities. Molecular analyses show elevated glycolytic pathway gene transcripts and active enzymes. Metabolomics analyses detect significantly higher levels of ATP and the energy currency phosphocreatine, elevated glycolytic pathway metabolites, increased TCA cycle metabolites, lipid biosynthetic pathway intermediates, nucleotides, and amino acids. Moreover, CNTF treatment restores the key antioxidant glutathione to the wild type level. Therefore, CNTF significantly impacts the metabolic status of degenerating retinas by promoting aerobic glycolysis and augmenting anabolic activities. These findings reveal cellular mechanisms underlying enhanced neuronal viability and suggest potential therapies for treating retinal degeneration.
    DOI:  https://doi.org/10.1038/s41467-022-34443-x
  41. FEBS J. 2022 Nov;289(22): 6822-6831
    Organelle homeostasis: from cellular mechanisms to disease.
    Emma Burbridge, Colin Adrain.
      The major criterion that distinguishes eukaryotes from prokaryotes is the presence of organelles in the former. Organelles provide a compartment in which biochemical processes are corralled within bespoke biophysical conditions and act as storage depots, powerhouses, waste storage/recycling units and innate immune signalling hubs. A key challenge faced by organelles is to define, and then retain, their identity; this is mediated by complex proteostasis mechanisms including the import of an organelle-specific proteome, the exclusion of non-organellar proteins and the removal of misfolded proteins via dedicated quality control mechanisms. This Special Issue on Organelle Homeostasis provides an engaging, eclectic, yet integrative, perspective on organelle homeostasis in a range of organelles including those from the secretory and endocytic pathways, mitochondria, the autophagy-lysosomal pathway and the nucleus and its sub-compartments. Some lesser-known organelles including migrasomes (organelles that are released by migrating cells) and GOMED (a Golgi-specific form of autophagy) are also introduced. In the spirit of the principles of organelle biology, we hope you find the reviews in this Issue both encapsulating and captivating, and we thank the authors for their excellent contributions.
    Keywords:  endoplasmic reticulum; mitochondria; nucleus; organelle homeostasis; quality control
    DOI:  https://doi.org/10.1111/febs.16667
  42. Biosens Bioelectron. 2022 Oct 29. pii: S0956-5663(22)00866-1. [Epub ahead of print]220 114826
    A bioluminescent-based probe for in vivo non-invasive monitoring of nicotinamide riboside uptake reveals a link between metastasis and NAD+ metabolism.
    Tamara Maric, Arkadiy Bazhin, Pavlo Khodakivskyi, Georgy Mikhaylov, Ekaterina Solodnikova, Aleksey Yevtodiyenko, Greta Maria Paola Giordano Attianese, George Coukos, Melita Irving, Magali Joffraud, Carles Cantó, Elena Goun.
      Nicotinamide riboside (NR) is a form of vitamin B3 and is one of the most studied compounds for the restoration of cellular NAD+ levels demonstrating clinical potential in many metabolic and age-related disorders. Despite its wide commercial availability as a powerful nutraceutical, our understanding of NR uptake by different cells and tissues is greatly limited by the lack of noninvasive in vivo imaging tools limiting its clinical translation. Here, we report the development and validation of a bioluminescent NR uptake probe (BiNR) for non-invasive longitudinal imaging of NR uptake both in vitro and in vivo. In addition, we optimized an assay that allows monitoring of NR flux without the need to transfect cells with the luciferase gene, enabling the use of the BiNR probe in clinical samples, as demonstrated with human T cells. Lastly, we used BiNR to investigate the role of NR uptake in cancer prevalence and metastases formation in triple negative breast cancer (TNBC) animal model. Our results demonstrate that NR supplementation results in a significant increase in cancer prevalence and metastases of TNBC to the brain. These results outline the important role of powerful nutraceuticals like NR in cancer metabolism and the need to personalize their use in certain patient populations.
    Keywords:  Brain metastases; Cancer prevalence; Human T cells; In vivo noninvasive bioluminescent imaging; NR supplementation; Nicotinamide riboside (NR) uptake
    DOI:  https://doi.org/10.1016/j.bios.2022.114826
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