bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–07–30
fifty-five papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mitochondrial defects leading to arrested spermatogenesis and ferroptosis in the PARL deficient mouse model of Leigh Syndrome.
  2. Complex II Biology in Aging, Health, and Disease.
  3. Purification of functional mouse skeletal muscle mitochondria using Percoll density gradient centrifugation.
  4. Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD+ precursor nicotinamide riboside.
  5. A Novel ENU-Induced Mfn2 Mutation Causes Motor Deficits in Mice without Causing Peripheral Neuropathy.
  6. Promotion of mitochondrial fragmentation suppresses the formation of mitochondrial spherical compartmentation in PINK1B9Drosophila melanogaster.
  7. Gene Editing Technologies Targeting TFAM and Its Relation to Mitochondrial Diseases.
  8. Mitochondrial Magnesium is the cationic rheostat for MCU-mediated mitochondrial Ca2+ uptake.
  9. Mitochondrial proteostasis mediated by CRL5 Ozz and Alix maintains skeletal muscle function.
  10. Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's.
  11. Biosynthesis, Deficiency, and Supplementation of Coenzyme Q.
  12. Mitochondrial DNA methylation and mitochondria-related epigenetics in neurodegeneration.
  13. Assembly of mitochondrial succinate dehydrogenase in human health and disease.
  14. Loss of the mitochondrial citrate carrier, Slc25a1/CIC disrupts embryogenesis via 2-Hydroxyglutarate.
  15. PGAM5 is an MFN2 phosphatase that plays an essential role in the regulation of mitochondrial dynamics.
  16. Hyper-ubiquitylation of DNA helicase RECQL4 by E3 ligase MITOL prevents mitochondrial entry and potentiates mitophagy.
  17. COPI-regulated mitochondria-ER contact site formation maintains axonal integrity.
  18. Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins.
  19. Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling.
  20. Coenzyme Q 4 is a functional substitute for coenzyme Q 10 and can be targeted to the mitochondria.
  21. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I.
  22. A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types.
  23. FUS Unveiled in Mitochondrial DNA Repair and Targeted Ligase-1 Expression Rescues Repair-Defects in FUS-Linked Neurodegeneration.
  24. A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer.
  25. Understanding the Molecular Basis of the Multiple Mitochondrial Dysfunctions Syndrome 2: The Disease-Causing His96Arg Mutation of BOLA3.
  26. The Role of Mitochondrial Dynamics and Mitotic Fission in Regulating the Cell Cycle in Cancer and Pulmonary Arterial Hypertension: Implications for Dynamin-Related Protein 1 and Mitofusin2 in Hyperproliferative Diseases.
  27. Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface.
  28. Pathophysiological mechanisms of complications associated with propionic acidemia.
  29. Repression of ferroptotic cell death by mitochondrial calcium signaling.
  30. Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane.
  31. UBQLN2 and HSP70 participate in Parkin-mediated mitophagy by facilitating outer mitochondrial membrane rupture.
  32. Mitochondrial dysfunction: roles in skeletal muscle atrophy.
  33. Current advances of Mitochondrial dysfunction and cardiovascular disease and promising therapeutic strategies.
  34. Human IP3 receptor triple knockout stem cells remain pluripotent despite altered mitochondrial metabolism.
  35. Mitochondrial Proteome Changes in Rett Syndrome.
  36. Exercise, mitochondrial dysfunction and inflammasomes in skeletal muscle.
  37. Red Blood Cell Metabolism In Vivo and In Vitro.
  38. Applications of artificial intelligence in clinical laboratory genomics.
  39. Visualization of automatically combined disease maps and pathway diagrams for rare diseases.
  40. Impaired BCAA catabolism in adipose tissues promotes age-associated metabolic derangement.
  41. The AAA+ protein Msp1 selects substrates by recognizing a hydrophobic mismatch between the substrate transmembrane domain and the lipid bilayer.
  42. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans.
  43. Molecular Understanding of ER-MT Communication Dysfunction during Neurodegeneration.
  44. Single Cell Transcriptomic Analysis in a Mouse Model of Barth Syndrome Reveals Cell-Specific Alterations in Gene Expression and Intercellular Communication.
  45. OPA1 deficiency impacts oxidative metabolism in cycling cells: a translational approach for degenerative diseases.
  46. The lncRNA HOXA11os regulates mitochondrial function in myeloid cells to maintain intestinal homeostasis.
  47. Riboflavin 1 Transporter Deficiency: Novel SLC52A1 Variants and Expansion of the Phenotypic Spectrum.
  48. Lipoylation is dependent on the ferredoxin FDX1 and dispensable under hypoxia in human cells.
  49. An evaluation of clinical presentation and genetic testing approaches for patients with neuromuscular disorders.
  50. Choosing Variant Interpretation Tools for Clinical Applications: Context Matters.
  51. Oral enzyme therapy for maple syrup urine disease (MSUD) suppresses plasma leucine levels in intermediate MSUD mice and healthy non-human primates.
  52. RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors.
  53. New Insights on the Uptake and Trafficking of Coenzyme Q.
  54. Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines.
  55. Inborn Errors of Purine Salvage and Catabolism.
  1. Elife. 2023 Jul 28. pii: e84710. [Epub ahead of print]12
    Mitochondrial defects leading to arrested spermatogenesis and ferroptosis in the PARL deficient mouse model of Leigh Syndrome.
    Enrico Radaelli, Charles-Antoine Assenmacher, Jillian Verrelle, Esha Banerjee, Florence Manero, Salim Khiati, Anais Girona, Guillermo Lopez-Lluch, Placido Navas, Marco Spinazzi.
      Impaired spermatogenesis and male infertility are common manifestations of mitochondrial diseases, but the underlying mechanisms are unclear. Here we show that mice deficient for the mitochondrial intra-membrane rhomboid protease PARL, a recently reported model of Leigh syndrome, develop early testicular atrophy caused by a complete arrest of spermatogenesis at meiotic prophase I, followed by germ cell death independently of neurodegeneration. Genetic modifications of PINK1, PGAM5, and TTC19, three major substrates of PARL with important roles in mitochondrial homeostasis, do not reproduce or modify this severe phenotype. PARL deficiency in spermatocytes leads to severe abnormalities in mitochondrial structure associated with prominent electron transfer chain defects, alterations in Coenzyme Q (CoQ) biosynthesis, and metabolic rewiring. These mitochondrial defects are associated with a germ-cell specific decrease in GPX4 expression committing arrested spermatocytes to ferroptosis, a regulated cell death modality characterized by uncontrolled lipid peroxidation. Thus, mitochondrial defects, such as those induced by depletion of PARL, spontaneously initiate ferroptosis in primary spermatocytes in vivo by simultaneous effects on GPX4 and CoQ, the two major ferroptosis-inhibitors. Ferroptosis warrants to be further scrutinized in the pathogenesis of mitochondrial diseases and male infertility.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.84710
  2. Antioxidants (Basel). 2023 Jul 24. pii: 1477. [Epub ahead of print]12(7):
    Complex II Biology in Aging, Health, and Disease.
    Eric Goetzman, Zhenwei Gong, Bob Zhang, Radhika Muzumdar.
      Aging is associated with a decline in mitochondrial function which may contribute to age-related diseases such as neurodegeneration, cancer, and cardiovascular diseases. Recently, mitochondrial Complex II has emerged as an important player in the aging process. Mitochondrial Complex II converts succinate to fumarate and plays an essential role in both the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC). The dysfunction of Complex II not only limits mitochondrial energy production; it may also promote oxidative stress, contributing, over time, to cellular damage, aging, and disease. Intriguingly, succinate, the substrate for Complex II which accumulates during mitochondrial dysfunction, has been shown to have widespread effects as a signaling molecule. Here, we review recent advances related to understanding the function of Complex II, succinate signaling, and their combined roles in aging and aging-related diseases.
    Keywords:  Complex II; aging; reactive oxygen species; succinate dehydrogenase
    DOI:  https://doi.org/10.3390/antiox12071477
  3. bioRxiv. 2023 Jul 11. pii: 2023.07.11.548594. [Epub ahead of print]
    Purification of functional mouse skeletal muscle mitochondria using Percoll density gradient centrifugation.
    Rea Victoria P Anunciado-Koza, Anyonya R Guntur, Calvin P Vary, Carlos A Gartner, Madeleine Nowak, Robert A Koza.
       Objective: Our goal was to isolate purified mitochondria from mouse skeletal muscle using a Percoll density gradient and to assess bioenergetic function and purity via Seahorse Extracellular Flux (XF) Analyses and mass spectrometry.
    Results: Mitochondria isolated from murine quadriceps femoris skeletal muscle using a Percoll density gradient method allowed for minimally contaminated preparations with time from tissue harvest to mitochondrial isolation and quantification in about 3-4 hours. Percoll purification from 100-200 mg fresh tissue yielded ∼200-400 ug protein. Mitochondrial bioenergetics evaluated using the Seahorse XFe96 analyzer, a high-throughput respirometry platform, showed optimum mitochondrial input at 500 ng with respiratory control ratio ranging from 3.9-7.1 using various substrates demonstrating a high degree of functionality. Furthermore, proteomic analysis of Percoll-enriched mitochondria isolated from skeletal muscle using this method showed significant enrichment of mitochondrial proteins indicating high sample purity. This study established a methodology that ensures sufficient high quality mitochondria for downstream analyses such as mitochondrial bioenergetics and proteomics.
    DOI:  https://doi.org/10.1101/2023.07.11.548594
  4. Heliyon. 2023 Jun;9(6): e17392
    Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD+ precursor nicotinamide riboside.
    Sharath Anugula, Zhiquan Li, Yuan Li, Alexander Hendriksen, Peter Bjarn Christensen, Lin Wang, Jonathan M Monk, Niels de Wind, Vilhelm A Bohr, Claus Desler, Robert K Naviaux, Lene Juel Rasmussen.
      Replication stress, caused by Rev1 deficiency, is associated with mitochondrial dysfunction, and metabolic stress. However, the overall metabolic alterations and possible interventions to rescue the deficits due to Rev1 loss remain unclear. Here, we report that loss of Rev1 leads to intense changes in metabolites and that this can be manipulated by NAD + supplementation. Autophagy decreases in Rev1-/- mouse embryonic fibroblasts (MEFs) and can be restored by supplementing the NAD+ precursor nicotinamide riboside (NR). The abnormal mitochondrial morphology in Rev1-/- MEFs can be partially reversed by NR supplementation, which also protects the mitochondrial cristae from rotenone-induced degeneration. In nematodes rev-1 deficiency causes sensitivity to oxidative stress but this cannot be rescued by NR supplementation. In conclusion, Rev1 deficiency leads to metabolic dysregulation of especially lipid and nucleotide metabolism, impaired autophagy, and mitochondrial anomalies, and all of these phenotypes can be improved by NR replenishment in MEFs.
    Keywords:  Autophagy; Healthspan; Mitochondria; NAD+; Nicotinamide riboside; Replication stress; Rev1
    DOI:  https://doi.org/10.1016/j.heliyon.2023.e17392
  5. Biology (Basel). 2023 Jul 03. pii: 953. [Epub ahead of print]12(7):
    A Novel ENU-Induced Mfn2 Mutation Causes Motor Deficits in Mice without Causing Peripheral Neuropathy.
    Timothy J Hines, Janice Bailey, Hedi Liu, Anyonya R Guntur, Kevin L Seburn, Samia L Pratt, Jonathan R Funke, Lisa M Tarantino, Robert W Burgess.
      Mitochondrial fission and fusion are required for maintaining functional mitochondria. The mitofusins (MFN1 and MFN2) are known for their roles in mediating mitochondrial fusion. Recently, MFN2 has been implicated in other important cellular functions, such as mitophagy, mitochondrial motility, and coordinating endoplasmic reticulum-mitochondria communication. In humans, over 100 MFN2 mutations are associated with a form of inherited peripheral neuropathy, Charcot-Marie-Tooth disease type 2A (CMT2A). Here we describe an ENU-induced mutant mouse line with a recessive neuromuscular phenotype. Behavioral screening showed progressive weight loss and rapid deterioration of motor function beginning at 8 weeks. Mapping and sequencing revealed a missense mutation in exon 18 of Mfn2 (T1928C; Leu643Pro), within the transmembrane domain. Compared to wild-type and heterozygous littermates, Mfn2L643P/L643P mice exhibited diminished rotarod performance and decreases in activity in the open field test, muscular endurance, mean mitochondrial diameter, sensory tests, mitochondrial DNA content, and MFN2 protein levels. However, tests of peripheral nerve physiology and histology were largely normal. Mutant leg bones had reduced cortical bone thickness and bone area fraction. Together, our data indicate that Mfn2L643P causes a recessive motor phenotype with mild bone and mitochondrial defects in mice. Lack of apparent nerve pathology notwithstanding, this is the first reported mouse model with a mutation in the transmembrane domain of the protein, which may be valuable for researchers studying MFN2 biology.
    Keywords:  CMT2A; Charcot–Marie–Tooth disease; mitofusin 2; neuromuscular disease
    DOI:  https://doi.org/10.3390/biology12070953
  6. Biochem Biophys Res Commun. 2023 Jul 14. pii: S0006-291X(23)00879-3. [Epub ahead of print]676 48-57
    Promotion of mitochondrial fragmentation suppresses the formation of mitochondrial spherical compartmentation in PINK1B9Drosophila melanogaster.
    Yi Li, Wen Chen, Danling Wang.
      Mitochondria undergo structural changes reflective of functional statuses. Ultrastructural characterizing of mitochondria is valuable for understanding mitochondrial dysfunction in various pathological conditions. PINK1, a Parkinson's disease (PD) associated gene, plays key roles in maintaining mitochondrial function and integrity. In Drosophila melanogaster, deficiency of PINK1 results in PD-like pathologies due to mitochondrial abnormalities. Here, we report the existence of a new type of mitochondrial-membrane deformity, mitochondrial spherical compartmentation (MSC), caused by PINK1 deficiency in Drosophila. The MSC is a three-dimensional spheroid-like mitochondrial membrane structure encompassing nonselective contents. Upregulation of dDrp1, downregulation of dMarf, and upregulation of dArgK1-A-all resulting in mitochondrial fragmentation-were able to suppress the formation of MSC. Furthermore, arginine kinase, only when localizing to the vicinity of mitochondria, induced mitochondrial fragmentation and reversed the MSC phenotype. In summary, this study demonstrates that loss of dPINK1 leads to the formation of mitochondrial-membrane deformity MSC, which responds to mitochondrial dynamics. In addition, our data suggest a new perspective of how phosphagen energy-buffer system might regulate mitochondrial dynamics.
    Keywords:  Arginine kinase; Mitochondrial spherical compartmentation; Mitochondrial-membrane deformity; PINK1; Transmission electron microscopy
    DOI:  https://doi.org/10.1016/j.bbrc.2023.07.022
  7. Adv Exp Med Biol. 2023 ;1429 173-189
    Gene Editing Technologies Targeting TFAM and Its Relation to Mitochondrial Diseases.
    Vanessa Cristina de Oliveira, Kelly Cristine Santos Roballo, Clesio Gomes Mariano Junior, Carlos Eduardo Ambrósio.
      Mitochondria are organelles present in the cytoplasm of eukaryotic cells; they play a key role in adenosine triphosphate (ATP) synthesis and oxidative phosphorylation. Mitochondria have their own DNA, mitochondrial DNA (mtDNA), keeping the function of the mitochondria. Mitochondrial transcription factor A (TFAM) is a member of the HMGB subfamily that binds to mtDNA promoters is and considered essential in mtDNA replication and transcription. More recently, TFAM has been shown to play a central role in the maintenance and regulation of mitochondrial copy number, inflammatory response, expression regulation, and mitochondrial genome activity. Gene editing tools such as the CRISPR-Cas 9 technique, TALENs, and other gene editing tools have been used to investigate the role of TFAM in mitochondrial mechanics and biogenesis as well as its correlation to mitochondrial disorders. Thus this chapter brings a summary of mitochondria function, dysfunction, the importance of TFAM in the maintenance of mitochondria, and state of the art of gene editing tools involving TFAM and mtDNA.
    DOI:  https://doi.org/10.1007/978-3-031-33325-5_10
  8. Res Sq. 2023 Jul 18. pii: rs.3.rs-3088175. [Epub ahead of print]
    Mitochondrial Magnesium is the cationic rheostat for MCU-mediated mitochondrial Ca2+ uptake.
    Santhanam Shanmughapriya, Thiruvelselvan Ponnusamy, Prema Velusamy, Amrendra Kumar, Daniel Morris, Xueqian Zhang, Gang Ning, Marianne Klinger, Jean Copper, Sudarsan Rajan, Joseph Cheung, Natarajaseenivasan Kalimuthusamy, Nelli Mnatsakanyan.
      Calcium (Ca2+) uptake by mitochondria is essential in regulating bioenergetics, cell death, and cytosolic Ca2+ transients. Mitochondrial Calcium Uniporter (MCU) mediates the mitochondrial Ca2+ uptake. MCU is a hetero-oligomeric complex with a pore-forming component and accessory proteins required for channel activity. Though MCU regulation by MICUs is unequivocally established, there needs to be more knowledge of whether divalent cations regulate MCU. Here we set out to understand the mitochondrial matrix Mg2+-dependent regulation of MCU activity. We showed Mrs2 as the authentic mammalian mitochondrial Mg2+ channel using the planar lipid bilayer recordings. Using a liver-specific Mrs2 KO mouse model, we showed that decreased matrix [Mg2+] is associated with increased MCU activity and matrix Ca2+ overload. The disruption of Mg2+-dependent MCU regulation significantly prompted mitochondrial permeability transition pore opening-mediated cell death during tissue IR injury. Our findings support a critical role for mMg2+ in regulating MCU activity and attenuating mCa2+ overload.
    DOI:  https://doi.org/10.21203/rs.3.rs-3088175/v1
  9. bioRxiv. 2023 Jul 11. pii: 2023.07.11.548601. [Epub ahead of print]
    Mitochondrial proteostasis mediated by CRL5 Ozz and Alix maintains skeletal muscle function.
    Yvan Campos, Ricardo Rodriguez-Enriquez, Gustavo Palacios, Diantha Van de Vlekkert, Xiaohui Qiu, Jayce Weesner, Elida Gomero, Jeroen Demmers, Tulio Bertorini, Joseph T Opferman, Gerard C Grosveld, Alessandra d'Azzo.
      High energy-demanding tissues, such as skeletal muscle, require mitochondrial proteostasis to function properly. Two quality-control mechanisms, the ubiquitin proteasome system (UPS) and the release of mitochondria-derived vesicles, safeguard mitochondrial proteostasis. However, whether these processes interact is unknown. Here we show that the E3 ligase CRL5 Ozz , a member of the UPS, and its substrate Alix control the mitochondrial concentration of Slc25A4, a solute carrier that is essential for ATP production. The mitochondria in Ozz -/- or Alix -/- skeletal muscle share overt morphologic alterations (they are supernumerary, swollen, and dysmorphic) and have abnormal metabolomic profiles. We found that CRL5 Ozz ubiquitinates Slc25A4 and promotes its proteasomal degradation, while Alix facilitates SLC25A4 loading into exosomes destined for lysosomal destruction. The loss of Ozz or Alix offsets steady-state levels of Slc25A4, which disturbs mitochondrial metabolism and alters muscle fiber composition. These findings reveal hitherto unknown regulatory functions of Ozz and Alix in mitochondrial proteostasis.
    DOI:  https://doi.org/10.1101/2023.07.11.548601
  10. Biology (Basel). 2023 Jul 08. pii: 972. [Epub ahead of print]12(7):
    Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's.
    Luigi Del Giudice, Paola Pontieri, Mariarosaria Aletta, Matteo Calcagnile.
      Currently, numerous research endeavors are dedicated to unraveling the intricate nature of neurodegenerative diseases. These conditions are characterized by the gradual and progressive impairment of specific neuronal systems that exhibit anatomical or physiological connections. In particular, in the last twenty years, remarkable efforts have been made to elucidate neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, despite extensive research endeavors, no cure or effective treatment has been discovered thus far. With the emergence of studies shedding light on the contribution of mitochondria to the onset and advancement of mitochondrial neurodegenerative disorders, researchers are now directing their investigations toward the development of therapies. These therapies include molecules designed to protect mitochondria and neurons from the detrimental effects of aging, as well as mutant proteins. Our objective is to discuss and evaluate the recent discovery of three mitochondrial ribosomal proteins linked to Alzheimer's and Parkinson's diseases. These proteins represent an intermediate stage in the pathway connecting damaged genes to the two mitochondrial neurological pathologies. This discovery potentially could open new avenues for the production of medicinal substances with curative potential for the treatment of these diseases.
    Keywords:  Alzheimer’s disease; GEP3; MRPL44; NAM9; Parkinson’s disease; mitochondrial neurodegenerative diseases; mitochondrial ribosomal proteins
    DOI:  https://doi.org/10.3390/biology12070972
  11. Antioxidants (Basel). 2023 Jul 21. pii: 1469. [Epub ahead of print]12(7):
    Biosynthesis, Deficiency, and Supplementation of Coenzyme Q.
    Carmine Staiano, Laura García-Corzo, David Mantle, Nadia Turton, Lauren E Millichap, Gloria Brea-Calvo, Iain Hargreaves.
      Originally identified as a key component of the mitochondrial respiratory chain, Coenzyme Q (CoQ or CoQ10 for human tissues) has recently been revealed to be essential for many different redox processes, not only in the mitochondria, but elsewhere within other cellular membrane types. Cells rely on endogenous CoQ biosynthesis, and defects in this still-not-completely understood pathway result in primary CoQ deficiencies, a group of conditions biochemically characterised by decreased tissue CoQ levels, which in turn are linked to functional defects. Secondary CoQ deficiencies may result from a wide variety of cellular dysfunctions not directly linked to primary synthesis. In this article, we review the current knowledge on CoQ biosynthesis, the defects leading to diminished CoQ10 levels in human tissues and their associated clinical manifestations.
    Keywords:  CoQ biosynthesis; CoQ deficiency; Coenzyme Q; blood-brain barrier; statins
    DOI:  https://doi.org/10.3390/antiox12071469
  12. Neural Regen Res. 2024 Feb;19(2): 405-406
    Mitochondrial DNA methylation and mitochondria-related epigenetics in neurodegeneration.
    Fabio Coppedè.
      
    DOI:  https://doi.org/10.4103/1673-5374.379045
  13. Free Radic Biol Med. 2023 Jul 23. pii: S0891-5849(23)00552-X. [Epub ahead of print]
    Assembly of mitochondrial succinate dehydrogenase in human health and disease.
    Ke Cao, Jie Xu, Wenli Cao, Xueqiang Wang, Weiqiang Lv, Mengqi Zeng, Xuan Zou, Jiankang Liu, Zhihui Feng.
      Mitochondrial succinate dehydrogenase (SDH), also known as electron transport chain (ETC) Complex II, is the only enzyme complex engaged in both oxidative phosphorylation and the tricarboxylic acid (TCA) cycle. SDH has received increasing attention due to its crucial role in regulating mitochondrial metabolism and human health. Despite having the fewest subunits among the four ETC complexes, functional SDH is formed via a sequential and well-coordinated assembly of subunits. Along with the discovery of subunit-specific assembly factors, the dynamic involvement of the SDH assembly process in a broad range of diseases has been revealed. Recently, we reported that perturbation of SDH assembly in different tissues leads to interesting and distinct pathophysiological changes in mice, indicating a need to understand the intricate SDH assembly process in human health and diseases. Thus, in this review, we summarize recent findings on SDH pathogenesis with respect to disease and a focus on SDH assembly.
    Keywords:  Mitochondria; Succinate dehydrogenase; Succinate dehydrogenase assembly factors; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.07.023
  14. bioRxiv. 2023 Jul 23. pii: 2023.07.18.549409. [Epub ahead of print]
    Loss of the mitochondrial citrate carrier, Slc25a1/CIC disrupts embryogenesis via 2-Hydroxyglutarate.
    Anna Kasprzyk-Pawelec, Mingjun Tan, Yu Leng Phua, Raneen Rahhal, Alec McIntosh, Harvey Fernandez, Rami Mosaoa, Michael Girgis, Amrita Cheema, Lei Jiang, Lawrence F Kroemer, Anastas Popratiloff, Cheryl Clarkson, Brian M Kirmsa, Gray W Pearson, Eric Glasgow, Christopher Albanese, Jerry Vockley, Maria Laura Avantaggiati.
      Biallelic germline mutations in the SLC25A1 gene lead to combined D/L-2-hydroxyglutaric aciduria (D/L-2HGA), a fatal systemic disease uniquely characterized by the accumulation of both enantiomers of 2-hydroxyglutaric acid (2HG). How SLC25A1 deficiency contributes to D/L-2HGA and the role played by 2HG is unclear and no therapy exists. Both enantiomers act as oncometabolites, but their activities in normal tissues remain understudied. Here we show that mice lacking both SLC25A1 alleles exhibit developmental abnormalities that mirror human D/L-2HGA. SLC25A1 deficient cells undergo premature mitochondrial dysfunction associated senescence, suggesting that loss of proliferative capacity underlies the pathogenesis of D/L-2HGA. Remarkably, D- and L-2HG directly induce mitochondrial respiratory deficit and treatment of zebrafish embryos with the combination of D- and L-2HG phenocopies SLC25A1 loss, leading to developmental abnormalities in an additive fashion relative to either enantiomer alone. Metabolic analyses demonstrated that loss of SLC25A1 leads to global remodeling towards glutamine metabolism, with glutamine serving as a source for 2HG synthesis. Therefore, we explored the pre-clinical relevance of phenylbutyrate, an FDA-approved drug that reduces the blood glutamine levels, and found that it reduces 2HG accumulation reversing metabolic abnormalities in patients affected by D/L-2HGA. These results reveal pathogenic and growth suppressive activities of 2HG in the context of SLC25A1 deficiency and expose metabolic vulnerabilities for the clinical management of this disease.
    DOI:  https://doi.org/10.1101/2023.07.18.549409
  15. Cell Rep. 2023 Jul 26. pii: S2211-1247(23)00906-3. [Epub ahead of print]42(8): 112895
    PGAM5 is an MFN2 phosphatase that plays an essential role in the regulation of mitochondrial dynamics.
    Sudeshna Nag, Kaitlin Szederkenyi, Olena Gorbenko, Hannah Tyrrell, Christopher M Yip, G Angus McQuibban.
      Mitochondrial morphology is regulated by the post-translational modifications of the dynamin family GTPase proteins including mitofusin 1 (MFN1), MFN2, and dynamin-related protein 1 (DRP1). Mitochondrial phosphatase phosphoglycerate mutase 5 (PGAM5) is emerging as a regulator of these post-translational modifications; however, its precise role in the regulation of mitochondrial morphology is unknown. We show that PGAM5 interacts with MFN2 and DRP1 in a stress-sensitive manner. PGAM5 regulates MFN2 phosphorylation and consequently protects it from ubiquitination and degradation. Further, phosphorylation and dephosphorylation modification of MFN2 regulates its fusion ability. Phosphorylation enhances fission and degradation, whereas dephosphorylation enhances fusion. PGAM5 dephosphorylates MFN2 to promote mitochondrial network formation. Further, using a Drosophila genetic model, we demonstrate that the MFN2 homolog Marf and dPGAM5 are in the same biological pathway. Our results identify MFN2 dephosphorylation as a regulator of mitochondrial fusion and PGAM5 as an MFN2 phosphatase.
    Keywords:  CP: Molecular biology; DRP1; MFN2; PGAM5; mitochondrial morphology
    DOI:  https://doi.org/10.1016/j.celrep.2023.112895
  16. J Biol Chem. 2023 Jul 24. pii: S0021-9258(23)02115-4. [Epub ahead of print] 105087
    Hyper-ubiquitylation of DNA helicase RECQL4 by E3 ligase MITOL prevents mitochondrial entry and potentiates mitophagy.
    Mansoor Hussain, Aftab Mohammed, Shabnam Saifi, Swati Priya, Sagar Sengupta.
      Mutations in the DNA helicase RECQL4 lead to Rothmund-Thomson Syndrome (RTS), a disorder characterized by mitochondrial dysfunctions, premature aging, and genomic instability. However, the mechanisms by which these mutations lead to pathology are unclear. Here we report that RECQL4 is ubiquitylated by a mitochondrial E3 ligase, MITOL, at two lysine residues (K1101, K1154) via K6 linkage. This ubiquitylation hampers the interaction of RECQL4 with mitochondrial importer Tom20, thereby restricting its own entry into mitochondria. We show the RECQL4 2K mutant (where both K1101 and K1154 are mutated) has increased entry into mitochondria and demonstrates enhanced mtDNA replication. We observed that the three tested RTS patient mutants were unable to enter the mitochondria and showed decreased mtDNA replication. Furthermore, we found that RECQL4 in RTS patient mutants are hyper-ubiquitylated by MITOL and form insoluble aggregate-like structures on the outer mitochondrial surface. However, depletion of MITOL allows RECQL4 expressed in these RTS mutants to enter mitochondria and rescue mtDNA replication. Finally, we show increased accumulation of hyper-ubiquitylated RECQL4 outside the mitochondria leads to the cells being potentiated to increased mitophagy. Hence, we conclude regulating the turnover of RECQL4 by MITOL may have a therapeutic effect in RTS patients.
    Keywords:  E3 ligases; RecQ helicases; Rothmund Thomson Syndrome; autophagy; mitochondrial replication
    DOI:  https://doi.org/10.1016/j.jbc.2023.105087
  17. Cell Rep. 2023 Jul 26. pii: S2211-1247(23)00894-X. [Epub ahead of print]42(8): 112883
    COPI-regulated mitochondria-ER contact site formation maintains axonal integrity.
    Daniel C Maddison, Bilal Malik, Leonardo Amadio, Dana M Bis-Brewer, Stephan Züchner, Owen M Peters, Gaynor A Smith.
      Coat protein complex I (COPI) is best known for its role in Golgi-endoplasmic reticulum (ER) trafficking, responsible for the retrograde transport of ER-resident proteins. The ER is crucial to neuronal function, regulating Ca2+ homeostasis and the distribution and function of other organelles such as endosomes, peroxisomes, and mitochondria via functional contact sites. Here we demonstrate that disruption of COPI results in mitochondrial dysfunction in Drosophila axons and human cells. The ER network is also disrupted, and the neurons undergo rapid degeneration. We demonstrate that mitochondria-ER contact sites (MERCS) are decreased in COPI-deficient axons, leading to Ca2+ dysregulation, heightened mitophagy, and a decrease in respiratory capacity. Reintroducing MERCS is sufficient to rescue not only mitochondrial distribution and Ca2+ uptake but also ER morphology, dramatically delaying neurodegeneration. This work demonstrates an important role for COPI-mediated trafficking in MERC formation, which is an essential process for maintaining axonal integrity.
    Keywords:  Axon transport; COPI; CP: Cell biology; Calcium homeostasis; Endoplasmic reticulum; Golgi; Mitochondria; Neuronal cell biology; Vesicle trafficking
    DOI:  https://doi.org/10.1016/j.celrep.2023.112883
  18. Genome Res. 2023 Jul 24. pii: gr.277755.123. [Epub ahead of print]
    Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins.
    Rosario Avolio, Ilenia Agliarulo, Daniela Criscuolo, Daniela Sarnataro, Margherita Auriemma, Sabrina De Lella, Sara Pennacchio, Giovanni Calice, Martin Y Ng, Carlotta Giorgi, Paolo Pinton, Barry Cooperman, Matteo Landriscina, Franca Esposito, Danilo Swann Matassa.
      A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein we identify the molecular mechanisms involved, demonstrating that TRAP1: i) binds both mitochondrial and cytosolic ribosomes as well as translation elongation factors, ii) slows down translation elongation rate, and iii) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
    DOI:  https://doi.org/10.1101/gr.277755.123
  19. Curr Issues Mol Biol. 2023 Jul 21. 45(7): 6097-6115
    Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling.
    Raquel A Adams, Zheng Liu, Chongere Hsieh, Michael Marko, W Jonathan Lederer, M Saleet Jafri, Carmen Mannella.
      Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, and organelle location within rat cardiac myocytes. A tomographic analysis guided the definition of four classes of crista morphology: lamellar, tubular, mixed and transitional, the last associated with remodeling between lamellar and tubular cristae. Correlations include an apparent bias for mitochondria with lamellar cristae to be located in the regions between myofibrils and a two-fold larger crista membrane density in mitochondria with lamellar cristae relative to mitochondria with tubular cristae. The examination of individual cristae inside mitochondria reveals local variations in crista topology, such as extent of branching, alignment of fenestrations and progressive changes in membrane morphology and packing density. The findings suggest both a rationale for the interfibrillar location of lamellar mitochondria and a pathway for crista remodeling from lamellar to tubular morphology.
    Keywords:  cardiomyocytes; cristae; electron microscopy; electron tomography; membrane remodeling; mitochondria; myofibrils
    DOI:  https://doi.org/10.3390/cimb45070385
  20. bioRxiv. 2023 Jul 21. pii: 2023.07.20.549963. [Epub ahead of print]
    Coenzyme Q 4 is a functional substitute for coenzyme Q 10 and can be targeted to the mitochondria.
    Laura H Steenberge, Andrew Y Sung, Jing Fan, David J Pagliarini.
      Coenzyme Q 10 (CoQ 10 ) is an important cofactor and antioxidant for numerous cellular processes, and its deficiency has been linked to human disorders including mitochondrial disease, heart failure, Parkinson's disease, and hypertension. Unfortunately, treatment with exogenous oral CoQ 10 is often ineffective, likely due to the extreme hydrophobicity and high molecular weight of CoQ 10 . Here, we show that less hydrophobic CoQ species with shorter isoprenoid tails can serve as viable substitutes for CoQ 10 in human cells. We demonstrate that CoQ 4 can perform multiple functions of CoQ 10 in CoQ-deficient cells at markedly lower treatment concentrations, motivating further investigation of CoQ 4 as a supplement for CoQ 10 deficiencies. In addition, we describe the synthesis and evaluation of an initial set of compounds designed to target CoQ 4 selectively to mitochondria using triphenylphosphonium (TPP). Our results indicate that select versions of these compounds can successfully be delivered to mitochondria in a cell model and be cleaved to produce CoQ 4 , laying the groundwork for further development.
    DOI:  https://doi.org/10.1101/2023.07.20.549963
  21. J Am Chem Soc. 2023 Jul 25.
    Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I.
    Hyunho Kim, Patricia Saura, Maximilian C Pöverlein, Ana P Gamiz-Hernandez, Ville R I Kaila.
      Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
    DOI:  https://doi.org/10.1021/jacs.3c03086
  22. ACS Synth Biol. 2023 Jul 28.
    A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types.
    Sierra K Lear, Jose A Nunez, Seth L Shipman.
      Efficient metabolic engineering and the development of mitochondrial therapeutics often rely upon the specific and strong import of foreign proteins into mitochondria. Fusing a protein to a mitochondria-bound signal peptide is a common method to localize proteins to mitochondria, but this strategy is not universally effective, with particular proteins empirically failing to localize. To help overcome this barrier, this work develops a generalizable and open-source framework to design proteins for mitochondrial import and quantify their specific localization. This Python-based pipeline quantitatively assesses the colocalization of different proteins previously used for precise genome editing in a high-throughput manner to reveal signal peptide-protein combinations that localize well in mitochondria.
    Keywords:  Python; digital image analysis; high-throughput imaging; mitochondria; protein engineering; subcellular localization
    DOI:  https://doi.org/10.1021/acssynbio.3c00349
  23. Res Sq. 2023 Jul 12. pii: rs.3.rs-3152718. [Epub ahead of print]
    FUS Unveiled in Mitochondrial DNA Repair and Targeted Ligase-1 Expression Rescues Repair-Defects in FUS-Linked Neurodegeneration.
    Muralidhar Hegde, Kodavati Manohar, Haibo Wang, Wenting Gao, Joy Mitra, Pavana Hegde, Vincent Provasek, Vikas Rao, Indira Vedula, Aijun Zhang, Sankar Mitra, Alan Tomkinson, Ludo Van Den Bosch, Dale Hamilton.
      This study establishes the physiological role of Fused in Sarcoma (FUS) in mitochondrial DNA (mtDNA) repair and highlights its implications to the pathogenesis of FUS-associated neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS). Endogenous FUS interacts with and recruits mtDNA Ligase IIIα (mtLig3) to DNA damage sites within mitochondria, a relationship essential for maintaining mtDNA repair and integrity in healthy cells. Using ALS patient-derived FUS mutant cell lines, a transgenic mouse model, and human autopsy samples, we discovered that compromised FUS functionality hinders mtLig3's repair role, resulting in increased mtDNA damage and mutations. These alterations cause various manifestations of mitochondrial dysfunction, particularly under stress conditions relevant to disease pathology. Importantly, rectifying FUS mutations in patient-derived induced pluripotent cells (iPSCs) preserves mtDNA integrity. Similarly, targeted introduction of human DNA Ligase 1 restores repair mechanisms and mitochondrial activity in FUS mutant cells, suggesting a potential therapeutic approach. Our findings unveil FUS's critical role in mitochondrial health and mtDNA repair, offering valuable insights into the mechanisms underlying mitochondrial dysfunction in FUS-associated neurodegeneration.
    DOI:  https://doi.org/10.21203/rs.3.rs-3152718/v1
  24. PLoS One. 2023 ;18(7): e0276147
    A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer.
    Brad Ebanks, Pola Kwiecinska, Nicoleta Moisoi, Lisa Chakrabarti.
      High-resolution respirometry methods allow for the assessment of oxygen consumption by the electron transfer systems within cells, tissue samples, and isolated mitochondrial preparations. As mitochondrial integrity is compromised by the process of cryopreservation, these methods have been limited to fresh samples. Here we present a simple method to assess the activity of mitochondria respiratory complexes I and II in previously cryopreserved murine skeletal muscle tissue homogenates, as well as previously frozen D. melanogaster, as a function of oxygen consumption.
    DOI:  https://doi.org/10.1371/journal.pone.0276147
  25. Int J Mol Sci. 2023 Jul 21. pii: 11734. [Epub ahead of print]24(14):
    Understanding the Molecular Basis of the Multiple Mitochondrial Dysfunctions Syndrome 2: The Disease-Causing His96Arg Mutation of BOLA3.
    Beatrice Bargagna, Lucia Banci, Francesca Camponeschi.
      Multiple mitochondrial dysfunctions syndrome type 2 with hyperglycinemia (MMDS2) is a severe disorder of mitochondrial energy metabolism, associated with biallelic mutations in the gene encoding for BOLA3, a protein with a not yet completely understood role in iron-sulfur (Fe-S) cluster biogenesis, but essential for the maturation of mitochondrial [4Fe-4S] proteins. To better understand the role of BOLA3 in MMDS2, we have investigated the impact of the p.His96Arg (c.287A > G) point mutation, which involves a highly conserved residue, previously identified as a [2Fe-2S] cluster ligand in the BOLA3-[2Fe-2S]-GLRX5 heterocomplex, on the structural and functional properties of BOLA3 protein. The His96Arg mutation has been associated with a severe MMDS2 phenotype, characterized by defects in the activity of mitochondrial respiratory complexes and lipoic acid-dependent enzymes. Size exclusion chromatography, NMR, UV-visible, circular dichroism, and EPR spectroscopy characterization have shown that the His96Arg mutation does not impair the interaction of BOLA3 with its protein partner GLRX5, but leads to the formation of an aberrant BOLA3-[2Fe-2S]-GLRX5 heterocomplex, that is not functional anymore in the assembly of a [4Fe-4S] cluster on NFU1. These results allowed us to rationalize the severe phenotype observed in MMDS2 caused by His96Arg mutation.
    Keywords:  BOLA3; GLRX5; ISC machinery; MMDS2; iron-sulfur cluster biogenesis; iron-sulfur clusters; mitochondria; multiple mitochondrial dysfunctions syndrome
    DOI:  https://doi.org/10.3390/ijms241411734
  26. Cells. 2023 Jul 20. pii: 1897. [Epub ahead of print]12(14):
    The Role of Mitochondrial Dynamics and Mitotic Fission in Regulating the Cell Cycle in Cancer and Pulmonary Arterial Hypertension: Implications for Dynamin-Related Protein 1 and Mitofusin2 in Hyperproliferative Diseases.
    Pierce Colpman, Asish Dasgupta, Stephen L Archer.
      Mitochondria, which generate ATP through aerobic respiration, also have important noncanonical functions. Mitochondria are dynamic organelles, that engage in fission (division), fusion (joining) and translocation. They also regulate intracellular calcium homeostasis, serve as oxygen-sensors, regulate inflammation, participate in cellular and organellar quality control and regulate the cell cycle. Mitochondrial fission is mediated by the large GTPase, dynamin-related protein 1 (Drp1) which, when activated, translocates to the outer mitochondrial membrane (OMM) where it interacts with binding proteins (Fis1, MFF, MiD49 and MiD51). At a site demarcated by the endoplasmic reticulum, fission proteins create a macromolecular ring that divides the organelle. The functional consequence of fission is contextual. Physiological fission in healthy, nonproliferating cells mediates organellar quality control, eliminating dysfunctional portions of the mitochondria via mitophagy. Pathological fission in somatic cells generates reactive oxygen species and triggers cell death. In dividing cells, Drp1-mediated mitotic fission is critical to cell cycle progression, ensuring that daughter cells receive equitable distribution of mitochondria. Mitochondrial fusion is regulated by the large GTPases mitofusin-1 (Mfn1) and mitofusin-2 (Mfn2), which fuse the OMM, and optic atrophy 1 (OPA-1), which fuses the inner mitochondrial membrane. Mitochondrial fusion mediates complementation, an important mitochondrial quality control mechanism. Fusion also favors oxidative metabolism, intracellular calcium homeostasis and inhibits cell proliferation. Mitochondrial lipids, cardiolipin and phosphatidic acid, also regulate fission and fusion, respectively. Here we review the role of mitochondrial dynamics in health and disease and discuss emerging concepts in the field, such as the role of central versus peripheral fission and the potential role of dynamin 2 (DNM2) as a fission mediator. In hyperproliferative diseases, such as pulmonary arterial hypertension and cancer, Drp1 and its binding partners are upregulated and activated, positing mitochondrial fission as an emerging therapeutic target.
    Keywords:  apoptosis; cancer; cardiolipin (CL); dynamin 2 (DNM2); dynamin-related protein 1 (Drp1); mitochondrial dynamics protein of 49 kDa (MiD49); mitochondrial dynamics protein of 51 kDa (MiD51); mitochondrial fission factor (MFF); mitochondrial fission protein 1 (Fis1); mitophagy; mitotic fission; phosphatidic acid (PA); pulmonary arterial hypertension
    DOI:  https://doi.org/10.3390/cells12141897
  27. Proc Natl Acad Sci U S A. 2023 08;120(31): e2300475120
    Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface.
    Qingqing Liu, Benjamin Fong, Seungmin Yoo, Jay R Unruh, Fengli Guo, Zulin Yu, Jingjing Chen, Kausik Si, Rong Li, Chuankai Zhou.
      Eukaryotes organize cellular contents into membrane-bound organelles and membrane-less condensates, for example, protein aggregates. An unsolved question is why the ubiquitously distributed proteins throughout the cytosol give rise to spatially localized protein aggregates on the organellar surface, like mitochondria. We report that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in budding yeast and human cells. This is because misfolded cytosolic proteins do not autonomously aggregate in vivo; instead, they are recruited to the condensation sites initiated by Tom70's substrates (nascent mitochondrial proteins) on the organellar membrane using multivalent hydrophobic interactions. Knocking out Tom70 partially impairs, while overexpressing Tom70 increases the formation and association between cytosolic protein aggregates and mitochondria. In addition, ectopic targeting Tom70 and its substrates to the vacuole surface is able to redirect the localized aggregation from mitochondria to the vacuolar surface. Although other redundant mechanisms may exist, this nascent mitochondrial proteins-based initiation of protein aggregation likely explains the localized condensation of otherwise ubiquitously distributed molecules on the mitochondria. Disrupting the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
    Keywords:  condensate; mitochondria; protein aggregation
    DOI:  https://doi.org/10.1073/pnas.2300475120
  28. Pharmacol Ther. 2023 Jul 21. pii: S0163-7258(23)00165-1. [Epub ahead of print] 108501
    Pathophysiological mechanisms of complications associated with propionic acidemia.
    Hannah Marchukq, You Wang, Zachary Alec Ladd, Xiaoxin Chen, Guo-Fang Zhang.
      Propionic acidemia (PA) is a genetic metabolic disorder caused by mutations in the mitochondrial enzyme, propionyl-CoA carboxylase (PCC), which is responsible for converting propionyl-CoA to methylmalonyl-CoA for further metabolism in the tricarboxylic acid cycle. When this process is disrupted, propionyl-CoA and its metabolites accumulate, leading to a variety of complications including life-threatening cardiac diseases and other metabolic strokes. While the clinical symptoms and diagnosis of PA are well established, the underlying pathophysiological mechanisms of PA-induced diseases are not fully understood. As a result, there are currently few effective therapies for PA beyond dietary restriction. This review focuses on the pathophysiological mechanisms of the various complications associated with PA, drawing on extensive research and clinical reports. Most research suggests that propionyl-CoA and its metabolites can impair mitochondrial energy metabolism and cause cellular damage by inducing oxidative stress. However, direct evidence from in vivo studies is still lacking. Additionally, elevated levels of ammonia can be toxic, although not all PA patients develop hyperammonemia. The discovery of pathophysiological mechanisms underlying various complications associated with PA can aid in the development of more effective therapeutic treatments. The consequences of elevated odd-chain fatty acids in lipid metabolism and potential gene expression changes mediated by histone propionylation also warrant further investigation.
    Keywords:  PCCA; PCCB; Propionic acidemia; cardiac disease; gene mutation; gene therapy; liver transplant; neurological disorder; propionyl-CoA
    DOI:  https://doi.org/10.1016/j.pharmthera.2023.108501
  29. Res Sq. 2023 Jul 10. pii: rs.3.rs-3029860. [Epub ahead of print]
    Repression of ferroptotic cell death by mitochondrial calcium signaling.
    Haitao Wen, Jianwen Chen, Bao Zhao, Shen Wang, Anjun Ma, Hong Dong, Xiang Cheng, Shengyin Lin, Xinghui Li, Laura Herring, Gang Xin, Qin Ma, Kai He, Ruili Xie, Yu Lei, Irina Ingold, Xiaolin Cheng, Zihai Li.
      The uptake of Ca 2+ into and extrusion of calcium from the mitochondrial matrix, regulated by the mitochondrial Ca 2+ uniporter (MCU), is a fundamental biological process that has crucial impacts on cellular metabolism, signaling, growth and survival. Herein, we report that the embryonic lethality of Mcu -deficient mice is fully rescued by orally supplementing ferroptosis inhibitor lipophilic antioxidant vitamin E and ubiquinol. Mechanistically, we found MCU promotes acetyl-CoA-mediated GPX4 acetylation at K90 residue, and K90R mutation impaired the GPX4 enzymatic activity, a step that is crucial for ferroptosis. Structural analysis supports the possibility that GPX4 K90R mutation alters the conformational state of the molecule, resulting in disruption of a salt bridge formation with D23, which was confirmed by mutagenesis studies. Finally, we report that deletion of MCU in cancer cells caused a marked reduction in tumor growth in multiple cancer models. In summary, our study provides a first direct link between mitochondrial calcium level and sustained GPX4 enzymatic activity to regulate ferroptosis, which consequently protects cancer cells from ferroptosis.
    DOI:  https://doi.org/10.21203/rs.3.rs-3029860/v1
  30. Biomolecules. 2023 Jul 17. pii: 1138. [Epub ahead of print]13(7):
    Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane.
    Andriy Anishkin, Kiran Kumar Adepu, Dipendra Bhandari, Sean H Adams, Sree V Chintapalli.
      Myoglobin (Mb) interaction with the outer mitochondrial membrane (OMM) promotes oxygen (O2) release. However, comprehensive molecular details on specific contact regions of the OMM with oxygenated (oxy-) and deoxygenated (deoxy-)Mb are missing. We used molecular dynamics (MD) simulations to explore the interaction of oxy- and deoxy-Mb with the membrane lipids of the OMM in two lipid compositions: (a) a typical whole membrane on average, and (b) specifically the cardiolipin-enriched cristae region (contact site). Unrestrained relaxations showed that on average, both the oxy- and deoxy-Mb established more stable contacts with the lipids typical of the cristae contact site, then with those of the average OMM. However, in steered detachment simulations, deoxy-Mb clung more tightly to the average OMM, and oxy-Mb strongly preferred the contact sites of the OMM. The MD simulation analysis further indicated that a non-specific binding, mediated by local electrostatic interactions, existed between charged or polar groups of Mb and the membrane, for stable interaction. To the best of our knowledge, this is the first computational study providing the molecular details of the direct Mb-mitochondria interaction that assisted in distinguishing the preferred localization of oxy- and deoxy-Mb on the OMM. Our findings support the existing experimental evidence on Mb-mitochondrial association and shed more insights on Mb-mediated O2 transport for cellular bioenergetics.
    Keywords:  diffusion; mitochondria; myoglobin
    DOI:  https://doi.org/10.3390/biom13071138
  31. EMBO Rep. 2023 Jul 28. e55859
    UBQLN2 and HSP70 participate in Parkin-mediated mitophagy by facilitating outer mitochondrial membrane rupture.
    Qilian Ma, Jiaqi Xin, Qiang Peng, Ningning Li, Shan Sun, Hongyu Hou, Guoqiang Ma, Nana Wang, Li Zhang, Kin Yip Tam, Heiko Dussmann, Jochen Hm Prehn, Hongfeng Wang, Zheng Ying.
      Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two aging-related neurodegenerative diseases that share common key features, including aggregation of pathogenic proteins, dysfunction of mitochondria, and impairment of autophagy. Mutations in ubiquilin 2 (UBQLN2), a shuttle protein in the ubiquitin-proteasome system (UPS), can cause ALS/FTD, but the mechanism underlying UBQLN2-mediated pathogenesis is still uncertain. Recent studies indicate that mitophagy, a selective form of autophagy which is crucial for mitochondrial quality control, is tightly associated with neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and ALS. In this study, we show that after Parkin-dependent ubiquitination of damaged mitochondria, UBQLN2 is recruited to poly-ubiquitinated mitochondria through the UBA domain. UBQLN2 cooperates with the chaperone HSP70 to promote UPS-driven degradation of outer mitochondrial membrane (OMM) proteins. The resulting rupture of the OMM triggers the autophagosomal recognition of the inner mitochondrial membrane receptor PHB2. UBQLN2 is required for Parkin-mediated mitophagy and neuronal survival upon mitochondrial damage, and the ALS/FTD pathogenic mutations in UBQLN2 impair mitophagy in primary cultured neurons. Taken together, our findings link dysfunctional mitophagy to UBQLN2-mediated neurodegeneration.
    Keywords:  ALS; Parkin; UBQLN2; mitophagy; ubiquitin
    DOI:  https://doi.org/10.15252/embr.202255859
  32. J Transl Med. 2023 07 26. 21(1): 503
    Mitochondrial dysfunction: roles in skeletal muscle atrophy.
    Xin Chen, Yanan Ji, Ruiqi Liu, Xucheng Zhu, Kexin Wang, Xiaoming Yang, Boya Liu, Zihui Gao, Yan Huang, Yuntian Shen, Hua Liu, Hualin Sun.
      Mitochondria play important roles in maintaining cellular homeostasis and skeletal muscle health, and damage to mitochondria can lead to a series of pathophysiological changes. Mitochondrial dysfunction can lead to skeletal muscle atrophy, and its molecular mechanism leading to skeletal muscle atrophy is complex. Understanding the pathogenesis of mitochondrial dysfunction is useful for the prevention and treatment of skeletal muscle atrophy, and finding drugs and methods to target and modulate mitochondrial function are urgent tasks in the prevention and treatment of skeletal muscle atrophy. In this review, we first discussed the roles of normal mitochondria in skeletal muscle. Importantly, we described the effect of mitochondrial dysfunction on skeletal muscle atrophy and the molecular mechanisms involved. Furthermore, the regulatory roles of different signaling pathways (AMPK-SIRT1-PGC-1α, IGF-1-PI3K-Akt-mTOR, FoxOs, JAK-STAT3, TGF-β-Smad2/3 and NF-κB pathways, etc.) and the roles of mitochondrial factors were investigated in mitochondrial dysfunction. Next, we analyzed the manifestations of mitochondrial dysfunction in muscle atrophy caused by different diseases. Finally, we summarized the preventive and therapeutic effects of targeted regulation of mitochondrial function on skeletal muscle atrophy, including drug therapy, exercise and diet, gene therapy, stem cell therapy and physical therapy. This review is of great significance for the holistic understanding of the important role of mitochondria in skeletal muscle, which is helpful for researchers to further understanding the molecular regulatory mechanism of skeletal muscle atrophy, and has an important inspiring role for the development of therapeutic strategies for muscle atrophy targeting mitochondria in the future.
    Keywords:  Antioxidants; Mitochondrial dysfunction; Muscle atrophy; Therapy
    DOI:  https://doi.org/10.1186/s12967-023-04369-z
  33. Am J Pathol. 2023 Jul 20. pii: S0002-9440(23)00245-6. [Epub ahead of print]
    Current advances of Mitochondrial dysfunction and cardiovascular disease and promising therapeutic strategies.
    Dexiang Xia, Yue Liu, Peng Wu, Dangheng Wei.
      Mitochondria are "cellular power stations" and essential organelles for maintaining cellular homeostasis. Dysfunctional mitochondria have emerged as a key factor in the occurrence and development of cardiovascular disease. This review focuses on the advances in the relationship between mitochondrial dysfunction and cardiovascular diseases such as atherosclerosis, heart failure, myocardial ischemia reperfusion injury, and pulmonary arterial hypertension. Moreover, the clinical value and challenges of mitochondria-targeted strategies, including mitochondria-targeted antioxidants, mitochondrial quality control modulators, mitochondrial function protectors, mitochondrial biogenesis promoters, and recently developed mitochondrial transplants, are also discussed.
    Keywords:  Cardiovascular disease; Mitochondrial dysfunction; Therapeutics
    DOI:  https://doi.org/10.1016/j.ajpath.2023.06.013
  34. Cell Calcium. 2023 Jul 17. pii: S0143-4160(23)00093-3. [Epub ahead of print]114 102782
    Human IP3 receptor triple knockout stem cells remain pluripotent despite altered mitochondrial metabolism.
    Julius Rönkkö, Yago Rodriguez, Tiina Rasila, Rubén Torregrosa-Muñumer, Jana Pennonen, Jouni Kvist, Emilia Kuuluvainen, Ludo Van Den Bosch, Ville Hietakangas, Geert Bultynck, Henna Tyynismaa, Emil Ylikallio.
      Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ER Ca2+-release channels that control a broad set of cellular processes. Animal models lacking IP3Rs in different combinations display severe developmental phenotypes. Given the importance of IP3Rs in human diseases, we investigated their role in human induced pluripotent stem cells (hiPSC) by developing single IP3R and triple IP3R knockouts (TKO). Genome edited TKO-hiPSC lacking all three IP3R isoforms, IP3R1, IP3R2, IP3R3, failed to generate Ca2+ signals in response to agonists activating GPCRs, but retained stemness and pluripotency. Steady state metabolite profiling and flux analysis of TKO-hiPSC indicated distinct alterations in tricarboxylic acid cycle metabolites consistent with a deficiency in their pyruvate utilization via pyruvate dehydrogenase, shifting towards pyruvate carboxylase pathway. These results demonstrate that IP3Rs are not essential for hiPSC identity and pluripotency but regulate mitochondrial metabolism. This set of knockout hiPSC is a valuable resource for investigating IP3Rs in human cell types of interest.
    Keywords:  Ca(2+) signaling; IP(3)R1; IP(3)R2; IP(3)R3; Induced pluripotent stem cells; Inositol 1,4,5-trisphosphate receptors; Mitochondria; TCA; iPSC
    DOI:  https://doi.org/10.1016/j.ceca.2023.102782
  35. Biology (Basel). 2023 Jul 03. pii: 956. [Epub ahead of print]12(7):
    Mitochondrial Proteome Changes in Rett Syndrome.
    Gocha Golubiani, Laura van Agen, Lia Tsverava, Revaz Solomonia, Michael Müller.
      Rett syndrome (RTT) is a genetic neurodevelopmental disorder with mutations in the X-chromosomal MECP2 (methyl-CpG-binding protein 2) gene. Most patients are young girls. For 7-18 months after birth, they hardly present any symptoms; later they develop mental problems, a lack of communication, irregular sleep and breathing, motor dysfunction, hand stereotypies, and seizures. The complex pathology involves mitochondrial structure and function. Mecp2-/y hippocampal astrocytes show increased mitochondrial contents. Neurons and glia suffer from oxidative stress, a lack of ATP, and increased hypoxia vulnerability. This spectrum of changes demands comprehensive molecular studies of mitochondria to further define their pathogenic role in RTT. Therefore, we applied a comparative proteomic approach for the first time to study the entity of mitochondrial proteins in a mouse model of RTT. In the neocortex and hippocampus of symptomatic male mice, two-dimensional gel electrophoresis and subsequent mass-spectrometry identified various differentially expressed mitochondrial proteins, including components of respiratory chain complexes I and III and the ATP-synthase FoF1 complex. The NADH-ubiquinone oxidoreductase 75 kDa subunit, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, NADH dehydrogenase [ubiquinone] flavoprotein 2, cytochrome b-c1 complex subunit 1, and ATP synthase subunit d are upregulated either in the hippocampus alone or both the hippocampus and neocortex of Mecp2-/y mice. Furthermore, the regulatory mitochondrial proteins mitofusin-1, HSP60, and 14-3-3 protein theta are decreased in the Mecp2-/y neocortex. The expressional changes identified provide further details of the altered mitochondrial function and morphology in RTT. They emphasize brain-region-specific alterations of the mitochondrial proteome and support the notion of a metabolic component of this devastating disorder.
    Keywords:  Mecp2; Rett syndrome; hippocampus; mitochondria; mouse model; neocortex; proteomics
    DOI:  https://doi.org/10.3390/biology12070956
  36. Biomed J. 2023 Jul 25. pii: S2319-4170(23)00073-2. [Epub ahead of print] 100636
    Exercise, mitochondrial dysfunction and inflammasomes in skeletal muscle.
    Mikhaela B Slavin, Priyanka Khemraj, David A Hood.
      In the broad field of inflammation, skeletal muscle is a tissue that is understudied. Yet it represents about 40% of body mass in non-obese individuals and is therefore of fundamental importance for whole body metabolism and health. This article provides an overview of the unique features of skeletal muscle tissue, as well as its adaptability to exercise. This ability to adapt, particularly with respect to mitochondrial content and function, confers a level of metabolic "protection" against energy consuming events, and adds a measure of quality control that determines the phenotypic response to stress. Thus, we describe the particular role of mitochondria in promoting inflammasome activation in skeletal muscle, contributing to muscle wasting and dysfunction in aging, disuse and metabolic disease. We will then discuss how exercise training can be anti-inflammatory, mitigating the chronic inflammation that is observed in these conditions, potentially through improvements in mitochondrial quality and function.
    Keywords:  aging; exercise; inflammation; mitochondria; muscle disuse; skeletal muscle
    DOI:  https://doi.org/10.1016/j.bj.2023.100636
  37. Metabolites. 2023 Jun 27. pii: 793. [Epub ahead of print]13(7):
    Red Blood Cell Metabolism In Vivo and In Vitro.
    Angelo D'Alessandro, Alkmini T Anastasiadi, Vassilis L Tzounakas, Travis Nemkov, Julie A Reisz, Anastsios G Kriebardis, James C Zimring, Steven L Spitalnik, Michael P Busch.
      Red blood cells (RBC) are the most abundant cell in the human body, with a central role in oxygen transport and its delivery to tissues. However, omics technologies recently revealed the unanticipated complexity of the RBC proteome and metabolome, paving the way for a reinterpretation of the mechanisms by which RBC metabolism regulates systems biology beyond oxygen transport. The new data and analytical tools also informed the dissection of the changes that RBCs undergo during refrigerated storage under blood bank conditions, a logistic necessity that makes >100 million units available for life-saving transfusions every year worldwide. In this narrative review, we summarize the last decade of advances in the field of RBC metabolism in vivo and in the blood bank in vitro, a narrative largely influenced by the authors' own journeys in this field. We hope that this review will stimulate further research in this interesting and medically important area or, at least, serve as a testament to our fascination with this simple, yet complex, cell.
    Keywords:  erythrocyte; hematology; hemolysis; iron; mitochondria; red blood cell; spleen; storage lesion; transfusion medicine
    DOI:  https://doi.org/10.3390/metabo13070793
  38. Am J Med Genet C Semin Med Genet. 2023 Jul 28.
    Applications of artificial intelligence in clinical laboratory genomics.
    Swaroop Aradhya, Flavia M Facio, Hillery Metz, Toby Manders, Alexandre Colavin, Yuya Kobayashi, Keith Nykamp, Britt Johnson, Robert L Nussbaum.
      The transition from analog to digital technologies in clinical laboratory genomics is ushering in an era of "big data" in ways that will exceed human capacity to rapidly and reproducibly analyze those data using conventional approaches. Accurately evaluating complex molecular data to facilitate timely diagnosis and management of genomic disorders will require supportive artificial intelligence methods. These are already being introduced into clinical laboratory genomics to identify variants in DNA sequencing data, predict the effects of DNA variants on protein structure and function to inform clinical interpretation of pathogenicity, link phenotype ontologies to genetic variants identified through exome or genome sequencing to help clinicians reach diagnostic answers faster, correlate genomic data with tumor staging and treatment approaches, utilize natural language processing to identify critical published medical literature during analysis of genomic data, and use interactive chatbots to identify individuals who qualify for genetic testing or to provide pre-test and post-test education. With careful and ethical development and validation of artificial intelligence for clinical laboratory genomics, these advances are expected to significantly enhance the abilities of geneticists to translate complex data into clearly synthesized information for clinicians to use in managing the care of their patients at scale.
    Keywords:  deep learning; germline genetic testing; in silico prediction algorithms; machine learning; precision medicine; variant classification
    DOI:  https://doi.org/10.1002/ajmg.c.32057
  39. Front Bioinform. 2023 ;3 1101505
    Visualization of automatically combined disease maps and pathway diagrams for rare diseases.
    Piotr Gawron, David Hoksza, Janet Piñero, Maria Peña-Chilet, Marina Esteban-Medina, Jose Luis Fernandez-Rueda, Vincenza Colonna, Ewa Smula, Laurent Heirendt, François Ancien, Valentin Groues, Venkata P Satagopam, Reinhard Schneider, Joaquin Dopazo, Laura I Furlong, Marek Ostaszewski.
      Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower. Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer. Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets. Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/.
    Keywords:  disease maps; gene-disease association; pathway diagrams; rare diseases (RD); systems biomedicine
    DOI:  https://doi.org/10.3389/fbinf.2023.1101505
  40. Nat Aging. 2023 Jul 24.
    Impaired BCAA catabolism in adipose tissues promotes age-associated metabolic derangement.
    Hye-Sook Han, Eunyong Ahn, Eun Seo Park, Tom Huh, Seri Choi, Yongmin Kwon, Byeong Hun Choi, Jueun Lee, Yoon Ha Choi, Yujin L Jeong, Gwang Bin Lee, Minji Kim, Je Kyung Seong, Hyun Mu Shin, Hang-Rae Kim, Myeong Hee Moon, Jong Kyoung Kim, Geum-Sook Hwang, Seung-Hoi Koo.
      Adipose tissues are central in controlling metabolic homeostasis and failure in their preservation is associated with age-related metabolic disorders. The exact role of mature adipocytes in this phenomenon remains elusive. Here we describe the role of adipose branched-chain amino acid (BCAA) catabolism in this process. We found that adipocyte-specific Crtc2 knockout protected mice from age-associated metabolic decline. Multiomics analysis revealed that BCAA catabolism was impaired in aged visceral adipose tissues, leading to the activation of mechanistic target of rapamycin complex (mTORC1) signaling and the resultant cellular senescence, which was restored by Crtc2 knockout in adipocytes. Using single-cell RNA sequencing analysis, we found that age-associated decline in adipogenic potential of visceral adipose tissues was reinstated by Crtc2 knockout, via the reduction of BCAA-mTORC1 senescence-associated secretory phenotype axis. Collectively, we propose that perturbation of BCAA catabolism by CRTC2 is critical in instigating age-associated remodeling of adipose tissue and the resultant metabolic decline in vivo.
    DOI:  https://doi.org/10.1038/s43587-023-00460-8
  41. bioRxiv. 2023 Jul 11. pii: 2023.07.11.548587. [Epub ahead of print]
    The AAA+ protein Msp1 selects substrates by recognizing a hydrophobic mismatch between the substrate transmembrane domain and the lipid bilayer.
    Heidi L Fresenius, Deepika Gaur, Matthew L Wohlever.
      An essential aspect of protein quality control is enzymatic removal of membrane proteins from the lipid bilayer. Failures in this essential cellular process are associated with neurodegenerative diseases and cancer. Msp1 is a AAA+ ( A TPases A ssociated with diverse cellular A ctivities) protein that removes mistargeted proteins from the outer mitochondrial membrane (OMM). How Msp1 selectively recognizes and extracts substrates within the complex OMM ecosystem, and the role of the lipid bilayer on these processes is unknown. Here, we describe the development of fully defined, rapid, and quantitative extraction assay that retains physiological substrate selectivity. Using this new assay, we systematically modified both substrates and the lipid environment to demonstrate that Msp1 recognizes substrates by a hydrophobic mismatch between the substrate TMD and the lipid bilayer. We further demonstrate that the rate limiting step in Msp1 activity is extraction of the TMD from the lipid bilayer. Together, these results provide foundational insights into how the lipid bilayer influences AAA+ mediated membrane protein extraction.
    DOI:  https://doi.org/10.1101/2023.07.11.548587
  42. Nat Rev Genet. 2023 Jul 25.
    Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans.
    Shinya Yamamoto, Oguz Kanca, Michael F Wangler, Hugo J Bellen.
      Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
    DOI:  https://doi.org/10.1038/s41576-023-00633-6
  43. Mitochondrion. 2023 Jul 24. pii: S1567-7249(23)00068-5. [Epub ahead of print]
    Molecular Understanding of ER-MT Communication Dysfunction during Neurodegeneration.
    Shivkumar S Sammeta, Trupti A Banarase, Sandip R Rahangdale, Nitu L Wankhede, Manish M Aglawe, Brijesh G Taksande, Shubhada V Mangrulkar, Aman B Upaganlawar, Sushruta Koppula, Spandana Rajendra Kopalli, Milind J Umekar, Mayur B Kale.
      Biological researchers are seeing organelles in a new light. These cellular entities have been believed to be singular and distinctive structures that performed specialized purposes for a very long time. But in recentpast years, scientists have learned that organelles become dynamic and make physical contact. Additionally, Biological processes are regulated by organelles interactions and its alteration play an important role in cell malfunctioning and several pathologies, including neurodegenerative diseases. Mitochondrial-ER contact sites (MERCS) have received considerable attention in the domain of cell homeostasis and dysfunction, specifically in the area of neurodegeneration. This is largely due to the significant role of this subcellular compartment in a diverse array of vital cellular functions, including Ca2+ homeostasis, transport, bioenergetics and turnover, mitochondrial dynamics, apoptotic signaling, ER stress, and inflammation. A significant number of disease-associated proteins were found to physically interact with the ER-Mitochondria (ER-MT) interface, causing structural and/or functional alterations in this compartment. In this review, we summarize current knowledge about the structure and functions of the ER-MT contact sites, as well as the possible repercussions of their alteration in notable neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and fronto-temporal dementia. The constraints and complexities in defining the nature and origin of the highlighted defects in ER-MT communication, as well as their concise contribution to the neurodegenerative process, are illustrated in particular. The possibility of using MERCS as a potential drug target to prevent neuronal damage and ultimately neurodegeneration is the topic of our final discussion.
    Keywords:  Alzheimer’s disease; Amyotrophic lateral sclerosis; Mitochondria–ER contact sites (MERCS); Parkinson’s disease; mitochondria–ER-associated membrane (MAM); neurodegeneration
    DOI:  https://doi.org/10.1016/j.mito.2023.07.005
  44. Int J Mol Sci. 2023 Jul 18. pii: 11594. [Epub ahead of print]24(14):
    Single Cell Transcriptomic Analysis in a Mouse Model of Barth Syndrome Reveals Cell-Specific Alterations in Gene Expression and Intercellular Communication.
    Gayani Perera, Liam Power, Amy Larson, Christina J Codden, Junya Awata, Rebecca Batorsky, Douglas Strathdee, Michael T Chin.
      Barth Syndrome, a rare X-linked disorder affecting 1:300,000 live births, results from defects in Tafazzin, an acyltransferase that remodels cardiolipin and is essential for mitochondrial respiration. Barth Syndrome patients develop cardiomyopathy, muscular hypotonia and cyclic neutropenia during childhood, rarely surviving to middle age. At present, no effective therapy exists, and downstream transcriptional effects of Tafazzin dysfunction are incompletely understood. To identify novel, cell-specific, pathological pathways that mediate heart dysfunction, we performed single-nucleus RNA-sequencing (snRNA-seq) on wild-type (WT) and Tafazzin-knockout (Taz-KO) mouse hearts. We determined differentially expressed genes (DEGs) and inferred predicted cell-cell communication networks from these data. Surprisingly, DEGs were distributed heterogeneously across the cell types, with fibroblasts, cardiomyocytes, endothelial cells, macrophages, adipocytes and pericytes exhibiting the greatest number of DEGs between genotypes. One differentially expressed gene was detected for the lymphatic endothelial and mesothelial cell types, while no significant DEGs were found in the lymphocytes. A Gene Ontology (GO) analysis of these DEGs showed cell-specific effects on biological processes such as fatty acid metabolism in adipocytes and cardiomyocytes, increased translation in cardiomyocytes, endothelial cells and fibroblasts, in addition to other cell-specific processes. Analysis of ligand-receptor pair expression, to infer intercellular communication patterns, revealed the strongest dysregulated communication involved adipocytes and cardiomyocytes. For the knockout hearts, there was a strong loss of ligand-receptor pair expression involving adipocytes, and cardiomyocyte expression of ligand-receptor pairs underwent reorganization. These findings suggest that adipocyte and cardiomyocyte mitochondria may be most sensitive to mitochondrial Tafazzin deficiency and that rescuing adipocyte mitochondrial dysfunction, in addition to cardiomyocyte mitochondrial dysfunction, may provide therapeutic benefit in Barth Syndrome patients.
    Keywords:  Barth Syndrome; Tafazzin; cardiomyopathy; gene expression; metabolism; mitochondria; single-nucleus RNA sequencing
    DOI:  https://doi.org/10.3390/ijms241411594
  45. Dis Model Mech. 2023 Jul 27. pii: dmm.050266. [Epub ahead of print]
    OPA1 deficiency impacts oxidative metabolism in cycling cells: a translational approach for degenerative diseases.
    Aurélie M C Millet, Corentin Coustham, Camille Champigny, Marlène Botella, Christine Demeilliers, Anne Devin, Anne Galinier, Pascale Belenguer, Joel Bordeneuve-Guibé, Noélie Davezac.
      Dominant optic atrophy is an optic neuropathy which displays varying clinical symptoms and progression. A severe disorder is associated with certain OPA1 mutations and includes additional symptoms for more than 20% of patients. This underscores the consequences of OPA1 mutations in different cellular populations, not only retinal ganglionic cells. We assessed the consequences of OPA1 loss of function on oxidative metabolism and antioxidant defences using an RNA silencing strategy in a human epithelial cell line. We observed a decrease of the mitochondrial respiratory chain complexes that was associated with a reduction of aconitase activity related to an increase in reactive oxygen species (ROS) production. In response, the NRF2 transcription factor was translocated into the nucleus and upregulated SOD1 and GSTP1. This paper highlights the effects of OPA1 deficiency on oxidative metabolism in replicative cells, as already shown in neurons. It underlines a translational process to use cycling cells to circumvent and deeply describe the oxidative metabolism. Moreover, it paves the way to predict the evolution of the disease using mathematical models that consider mitochondrial ROS production and their detoxifying pathways.
    Keywords:  Mathematical model; Mitochondria; Neurodegenerative disease; Oxidative metabolism
    DOI:  https://doi.org/10.1242/dmm.050266
  46. Cell Metab. 2023 Jul 20. pii: S1550-4131(23)00250-4. [Epub ahead of print]
    The lncRNA HOXA11os regulates mitochondrial function in myeloid cells to maintain intestinal homeostasis.
    Liraz Shmuel-Galia, Fiachra Humphries, Tim Vierbuchen, Zhaozhao Jiang, Nolan Santos, John Johnson, Boris Shklyar, Leonel Joannas, Nicholas Mustone, Shany Sherman, Doyle Ward, JeanMarie Houghton, Christina E Baer, Aisling O'Hara, Jorge Henao-Mejia, Kasper Hoebe, Katherine A Fitzgerald.
      This study reveals a previously uncharacterized mechanism to restrict intestinal inflammation via a regulatory RNA transcribed from a noncoding genomic locus. We identified a novel transcript of the lncRNA HOXA11os specifically expressed in the distal colon that is reduced to undetectable levels in colitis. HOXA11os is localized to mitochondria under basal conditions and interacts with a core subunit of complex 1 of the electron transport chain (ETC) to maintain its activity. Deficiency of HOXA11os in colonic myeloid cells results in complex I deficiency, dysfunctional oxidative phosphorylation (OXPHOS), and the production of mitochondrial reactive oxygen species (mtROS). As a result, HOXA11os-deficient mice develop spontaneous intestinal inflammation and are hypersusceptible to colitis. Collectively, these studies identify a new regulatory axis whereby a lncRNA maintains intestinal homeostasis and restricts inflammation in the colon through the regulation of complex I activity.
    Keywords:  IBD; Krebs cycle; OXPHOS; colitis; complex I; intestinal inflammation; lncRNA; mitochondria; mtROS; mucosal inflammation; ncRNA
    DOI:  https://doi.org/10.1016/j.cmet.2023.06.019
  47. Genes (Basel). 2023 Jul 07. pii: 1408. [Epub ahead of print]14(7):
    Riboflavin 1 Transporter Deficiency: Novel SLC52A1 Variants and Expansion of the Phenotypic Spectrum.
    Sarah C Grünert, Athanasia Ziagaki, André Heinen, Anke Schumann, Sara Tucci, Ute Spiekerkoetter, Miriam Schmidts.
      Riboflavin transporter 1 (RFVT1) deficiency is an ultrarare metabolic disorder due to autosomal dominant pathogenic variants in SLC52A1. The RFVT1 protein is mainly expressed in the placenta and intestine. To our knowledge, only five cases of RFVT1 deficiency from three families have been reported so far. While newborns and infants with SLC52A1 variants mainly showed a multiple acyl-CoA dehydrogenase deficiency-like presentation, individuals identified in adulthood were usually clinically asymptomatic. We report two patients with novel heterozygous SLC52A1 variants. Patient 1 presented at the age of 62 with mild hyperammonemia following gastroenteritis. An acylcarnitine analysis in dried blood spots was abnormal with a multiple acyl-CoA dehydrogenase deficiency-like pattern, and genetic analysis confirmed a heterozygous SLC52A1 variant, c.68C > A, p. Ser23Tyr. Patient 2 presented with recurrent seizures and hypsarrhythmia at the age of 7 months. Metabolic investigations yielded unremarkable results. However, whole exome sequencing revealed a heterozygous start loss variant, c.3G > A, p. Met1Ile in SLC52A1. These two cases expand the clinical spectrum of riboflavin transporter 1 deficiency and demonstrate that symptomatic presentation in adulthood is possible.
    Keywords:  MADD; SLC52A1; riboflavin; riboflavin transporter; vitamin B2
    DOI:  https://doi.org/10.3390/genes14071408
  48. J Biol Chem. 2023 Jul 20. pii: S0021-9258(23)02103-8. [Epub ahead of print] 105075
    Lipoylation is dependent on the ferredoxin FDX1 and dispensable under hypoxia in human cells.
    Pallavi R Joshi, Shayan Sadre, Xiaoyan A Guo, Jason G McCoy, Vamsi K Mootha.
      Iron sulfur clusters (ISC) are essential cofactors that participate in electron transfer, environmental sensing, and catalysis. Amongst the most ancient ISC containing proteins are the ferredoxin family of electron carriers. Humans have two ferredoxins, FDX1 and FDX2, both of which are localized to mitochondria, and the latter of which is itself important for ISC synthesis. We have previously shown that hypoxia can eliminate the requirement for some components of the ISC biosynthetic pathway, but ferredoxins were not included in that study. Here we report that FDX1, but not FDX2, is dispensable under 1% O2 in cultured human cells. We find that FDX1 is essential for production of the lipoic acid cofactor, which is synthesized by the ISC containing enzyme lipoyl synthase (LIAS). While hypoxia can rescue the growth phenotype of either FDX1 or LIAS knockout cells, lipoylation in these same cells is not rescued, arguing against an alternative biosynthetic route or salvage pathway for lipoate in hypoxia. Our work reveals the divergent roles of FDX1 and FDX2 in mitochondria, identifies a role for FDX1 in lipoate synthesis, and suggests that loss of lipoic acid can be tolerated under low oxygen tensions in cell culture.
    Keywords:  Energy Metabolism; Hypoxia; Iron-Sulfur Protein; Lipoate; Mitochondria; S-adenosyl methionine
    DOI:  https://doi.org/10.1016/j.jbc.2023.105075
  49. Am J Med Genet A. 2023 Jul 28.
    An evaluation of clinical presentation and genetic testing approaches for patients with neuromuscular disorders.
    Amanda Rosenberg, Cuixia Tian, Hua He, Elizabeth Ulm, Kathleen Collins Ruff, Chinmayee B Nagaraj.
      Inherited neuromuscular disorders (NMDs) are a large group of genetic conditions characterized by impaired peripheral nerve, motor neuron, neuromuscular junction, or skeletal muscle function. These conditions are also known to have clinical and genetic heterogeneity and variable ages of onset. Clinical evaluation for NMDs has increasingly incorporated molecular genetics. However, genetic testing is complicated by the variety of testing options and the ambiguity of NMD phenotypes. Examining test selection and yield may elucidate testing recommendations and improve the diagnostic journey for these patients. This retrospective chart review evaluated the clinical presentations, genetic testing approaches, and diagnostic outcomes of 155 patients with suspected NMDs at Cincinnati Children's Hospital Medical Center. A total of 262 individual tests were ordered, averaging 1.7 tests per patient. The clinic utilized 26 separate genetic tests, with test yields ranging from 0% to 66%. Overall, 21% of patients received a genetic diagnosis. Of all the clinical findings evaluated, elevated CPK levels with or without muscle weakness were the most informative symptoms correlated with a diagnostic result. This study highlights several genetic testing considerations for NMDs, including the variability of diagnostic outcomes. This knowledge is relevant to clinicians and patients, especially during the pretest counseling and consenting process.
    Keywords:  diagnostic techniques; genetic testing; neuromuscular diseases; retrospective study
    DOI:  https://doi.org/10.1002/ajmg.a.63356
  50. Int J Mol Sci. 2023 Jul 24. pii: 11872. [Epub ahead of print]24(14):
    Choosing Variant Interpretation Tools for Clinical Applications: Context Matters.
    Josu Aguirre, Natàlia Padilla, Selen Özkan, Casandra Riera, Lídia Feliubadaló, Xavier de la Cruz.
      Pathogenicity predictors are computational tools that classify genetic variants as benign or pathogenic; this is currently a major challenge in genomic medicine. With more than fifty such predictors available, selecting the most suitable tool for clinical applications like genetic screening, molecular diagnostics, and companion diagnostics has become increasingly challenging. To address this issue, we have developed a cost-based framework that naturally considers the various components of the problem. This framework encodes clinical scenarios using a minimal set of parameters and treats pathogenicity predictors as rejection classifiers, a common practice in clinical applications where low-confidence predictions are routinely rejected. We illustrate our approach in four examples where we compare different numbers of pathogenicity predictors for missense variants. Our results show that no single predictor is optimal for all clinical scenarios and that considering rejection yields a different perspective on classifiers.
    Keywords:  classification with rejection; clinical variant interpretation; cost models; healthcare costs; in silico tools; molecular diagnostics; pathogenicity prediction; personalized medicine
    DOI:  https://doi.org/10.3390/ijms241411872
  51. J Inherit Metab Dis. 2023 Jul 26.
    Oral enzyme therapy for maple syrup urine disease (MSUD) suppresses plasma leucine levels in intermediate MSUD mice and healthy non-human primates.
    Kristen Skvorak, Joyce Liu, Nikki Kruse, Roasa Mehmood, Subhamoy Das, Stephan Jenne, Chinping Chng, U Loi Lao, Da Duan, Jonathan Asfaha, Faye Du, Leann Teadt, Antionette Sero, Charlene Ching, James Riggins, Lianne Pope, Ping Yan, Harminder Mashiana, Moulay Hicham Alaoui Ismaili, Kerryn McCluskie, Gjalt Huisman, Adam P Silverman.
      Maple Syrup Urine Disease (MSUD) is an inborn error of branched-chain amino acid metabolism affecting several thousand individuals worldwide. MSUD patients have elevated levels of plasma leucine and its metabolic product α-ketoisocaproate (KIC), which can lead to severe neurotoxicity, coma, and death. Patients must maintain a strict diet of protein restriction and medical formula, and periods of non-compliance or illness can lead to acute metabolic decompensation or cumulative neurological impairment. Given the lack of therapeutic options for MSUD patients, we sought to develop an oral enzyme therapy that can degrade leucine within the gastrointestinal tract prior to its systemic absorption and thus enable patients to maintain acceptable plasma leucine levels while broadening their access to natural protein. We identified a highly active leucine decarboxylase enzyme from Planctomycetaceae bacterium and used directed evolution to engineer the enzyme for stability to gastric and intestinal conditions. Following high-throughput screening of over 12 000 enzyme variants over 9 iterative rounds of evolution, we identified a lead variant, LDCv10, which retains activity following simulated gastric or intestinal conditions in vitro. In intermediate MSUD mice or healthy non-human primates given a whey protein meal, oral treatment with LDCv10 suppressed the spike in plasma leucine and KIC and reduced the leucine AUC in a dose-dependent manner. Reduction in plasma leucine correlated with decreased brain leucine levels following oral LDCv10 treatment. Collectively, these data support further development of LDCv10 as a potential new therapy for MSUD patients. This article is protected by copyright. All rights reserved.
    Keywords:  branched-chain amino acid deficiency; enzyme engineering; enzyme replacement therapy; inborn errors of metabolism; leucine decarboxylase; maple syrup urine disease
    DOI:  https://doi.org/10.1002/jimd.12662
  52. J Transl Med. 2023 Jul 28. 21(1): 512
    RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors.
    Jiaoyan Ma, Liankun Sun, Weinan Gao, Yang Li, Delu Dong.
      Mitochondria are the only organelles regulated by two genomes. The coordinated translation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), which together co-encode the subunits of the oxidative phosphorylation (OXPHOS) complex, is critical for determining the metabolic plasticity of tumor cells. RNA-binding protein (RBP) is a post-transcriptional regulatory factor that plays a pivotal role in determining the fate of mRNA. RBP rapidly and effectively reshapes the mitochondrial proteome in response to intracellular and extracellular stressors, mediating the cytoplasmic and mitochondrial translation balance to adjust mitochondrial respiratory capacity and provide energy for tumor cells to adapt to different environmental pressures and growth needs. This review highlights the ability of RBPs to use liquid-liquid phase separation (LLPS) as a platform for translation regulation, integrating nuclear-mitochondrial positive and retrograde signals to coordinate cross-department translation, reshape mitochondrial energy metabolism, and promote the development and survival of tumor cells.
    Keywords:  Cytoplasmic translation; LLPS; Mitochondrial translation; OXPHOS; Retrograde signals
    DOI:  https://doi.org/10.1186/s12967-023-04373-3
  53. Antioxidants (Basel). 2023 Jul 06. pii: 1391. [Epub ahead of print]12(7):
    New Insights on the Uptake and Trafficking of Coenzyme Q.
    Michael D Guile, Akash Jain, Kyle A Anderson, Catherine F Clarke.
      Coenzyme Q (CoQ) is an essential lipid with many cellular functions, such as electron transport for cellular respiration, antioxidant protection, redox homeostasis, and ferroptosis suppression. Deficiencies in CoQ due to aging, genetic disease, or medication can be ameliorated by high-dose supplementation. As such, an understanding of the uptake and transport of CoQ may inform methods of clinical use and identify how to better treat deficiency. Here, we review what is known about the cellular uptake and intracellular distribution of CoQ from yeast, mammalian cell culture, and rodent models, as well as its absorption at the organism level. We discuss the use of these model organisms to probe the mechanisms of uptake and distribution. The literature indicates that CoQ uptake and distribution are multifaceted processes likely to have redundancies in its transport, utilizing the endomembrane system and newly identified proteins that function as lipid transporters. Impairment of the trafficking of either endogenous or exogenous CoQ exerts profound effects on metabolism and stress response. This review also highlights significant gaps in our knowledge of how CoQ is distributed within the cell and suggests future directions of research to better understand this process.
    Keywords:  coenzyme Q; lipid trafficking; membrane contact sites; mitochondria transport; ubiquinone
    DOI:  https://doi.org/10.3390/antiox12071391
  54. bioRxiv. 2023 Jul 14. pii: 2023.07.14.549063. [Epub ahead of print]
    Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines.
    Connon I Thomas, Melissa A Ryan, Naomi Kamasawa, Benjamin Scholl.
      Postsynaptic mitochondria are critical to the development, plasticity, and maintenance of synaptic inputs. However, their relationship to synaptic structure and functional activity is unknown. We examined a correlative dataset from ferret visual cortex with in vivo two-photon calcium imaging of dendritic spines during visual stimulation and electron microscopy (EM) reconstructions of spine ultrastructure, investigating mitochondrial abundance near functionally- and structurally-characterized spines. Surprisingly, we found no correlation to structural measures of synaptic strength. Instead, we found that mitochondria are positioned near spines with orientation preferences that are dissimilar to the somatic preference. Additionally, we found that mitochondria are positioned near groups of spines with heterogeneous orientation preferences. For a subset of spines with a mitochondrion in the head or neck, synapses were larger and exhibited greater selectivity to visual stimuli than those without a mitochondrion. Our data suggest mitochondria are not necessarily positioned to support the energy needs of strong spines, but rather support the structurally and functionally diverse inputs innervating the basal dendrites of cortical neurons.
    DOI:  https://doi.org/10.1101/2023.07.14.549063
  55. Metabolites. 2023 Jun 24. pii: 787. [Epub ahead of print]13(7):
    Inborn Errors of Purine Salvage and Catabolism.
    Marcella Camici, Mercedes Garcia-Gil, Simone Allegrini, Rossana Pesi, Giulia Bernardini, Vanna Micheli, Maria Grazia Tozzi.
      Cellular purine nucleotides derive mainly from de novo synthesis or nucleic acid turnover and, only marginally, from dietary intake. They are subjected to catabolism, eventually forming uric acid in humans, while bases and nucleosides may be converted back to nucleotides through the salvage pathways. Inborn errors of the purine salvage pathway and catabolism have been described by several researchers and are usually referred to as rare diseases. Since purine compounds play a fundamental role, it is not surprising that their dysmetabolism is accompanied by devastating symptoms. Nevertheless, some of these manifestations are unexpected and, so far, have no explanation or therapy. Herein, we describe several known inborn errors of purine metabolism, highlighting their unexplained pathological aspects. Our intent is to offer new points of view on this topic and suggest diagnostic tools that may possibly indicate to clinicians that the inborn errors of purine metabolism may not be very rare diseases after all.
    Keywords:  inborn errors; metabolism; metabolites; neurological disorders; neurological syndromes; purine catabolism; purine salvage; uric acid
    DOI:  https://doi.org/10.3390/metabo13070787
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