bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2022–05–08
twenty papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. Glycine decarboxylase maintains mitochondrial protein lipoylation to support tumor growth.
  2. HAX1-dependent control of mitochondrial proteostasis governs neutrophil granulocyte differentiation.
  3. Structural basis for feedforward control in the PINK1/Parkin pathway.
  4. Pantothenate kinase 2 interacts with PINK1 to regulate mitochondrial quality control via acetyl-CoA metabolism.
  5. An optimized FusX assembly-based technique to introduce mitochondrial TC-to-TT variations in human cell lines.
  6. Novel roles of RTN4 and CLIMP-63 in regulating mitochondrial structure, bioenergetics and apoptosis.
  7. The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei.
  8. Intra-mitochondrial reaction for cancer cell imaging and anti-cancer therapy by aggregation-induced emission.
  9. Protein import in mitochondria biogenesis: guided by targeting signals and sustained by dedicated chaperones.
  10. Altered Brown Adipose Tissue Mitochondrial Function in Newborn Fragile X Syndrome Mice.
  11. The role of mitochondrial fission in cardiovascular health and disease.
  12. Loss of mitochondrial ATPase ATAD3A contributes to non-alcoholic fatty liver disease through accumulation of lipids and damaged mitochondria.
  13. Extracellular Flux Analysis of Mitochondrial Function in Pluripotent Stem Cells.
  14. Regulation of mitochondrial network homeostasis by O-GlcNAcylation.
  15. Stress Responses Elicited by Misfolded Proteins Targeted to Mitochondria.
  16. High-content high-throughput imaging reveals distinct connections between mitochondrial morphology and functionality for OXPHOS complex I, III, and V inhibitors.
  17. The MFN1 and MFN2 mitofusins promote clustering between mitochondria and peroxisomes.
  18. Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant.
  19. The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context.
  20. Mitochondrial calcium uptake regulates tumour progression in embryonal rhabdomyosarcoma.
  1. Cell Metab. 2022 May 03. pii: S1550-4131(22)00133-4. [Epub ahead of print]34(5): 775-782.e9
    Glycine decarboxylase maintains mitochondrial protein lipoylation to support tumor growth.
    Dzmitry Mukha, Mariam Fokra, Alona Feldman, Boris Sarvin, Nikita Sarvin, Keren Nevo-Dinur, Elazar Besser, Elior Hallo, Elina Aizenshtein, Zachary T Schug, Tomer Shlomi.
      The folic acid cycle mediates the transfer of one-carbon (1C) units to support nucleotide biosynthesis. While the importance of serine as a mitochondrial and cytosolic donor of folate-mediated 1C units in cancer cells has been thoroughly investigated, a potential role of glycine oxidation remains unclear. We developed an approach for quantifying mitochondrial glycine cleavage system (GCS) flux by combining stable and radioactive isotope tracing with computational flux decomposition. We find high GCS flux in hepatocellular carcinoma (HCC), supporting nucleotide biosynthesis. Surprisingly, other than supplying 1C units, we found that GCS is important for maintaining protein lipoylation and mitochondrial activity. Genetic silencing of glycine decarboxylase inhibits the lipoylation and activity of pyruvate dehydrogenase and impairs tumor growth, suggesting a novel drug target for HCC. Considering the physiological role of liver glycine cleavage, our results support the notion that tissue of origin plays an important role in tumor-specific metabolic rewiring.
    Keywords:  GCS; GLDC; PDH; glycine cleavage system; glycine decarboxylase; hepatocellular carcinoma; one-carbon metabolism; protein P; protein lipoylation; pyruvate dehydrogenase
    DOI:  https://doi.org/10.1016/j.cmet.2022.04.006
  2. J Clin Invest. 2022 May 02. pii: e153153. [Epub ahead of print]132(9):
    HAX1-dependent control of mitochondrial proteostasis governs neutrophil granulocyte differentiation.
    Yanxin Fan, Marta Murgia, Monika I Linder, Yoko Mizoguchi, Cong Wang, Marcin Łyszkiewicz, Natalia Ziȩtara, Yanshan Liu, Stephanie Frenz, Gabriela Sciuccati, Armando Partida-Gaytan, Zahra Alizadeh, Nima Rezaei, Peter Rehling, Sven Dennerlein, Matthias Mann, Christoph Klein.
      The relevance of molecular mechanisms governing mitochondrial proteostasis to the differentiation and function of hematopoietic and immune cells is largely elusive. Through dissection of the network of proteins related to HCLS1-associated protein X-1, we defined a potentially novel functional CLPB/HAX1/(PRKD2)/HSP27 axis with critical importance for the differentiation of neutrophil granulocytes and, thus, elucidated molecular and metabolic mechanisms underlying congenital neutropenia in patients with HAX1 deficiency as well as bi- and monoallelic mutations in CLPB. As shown by stable isotope labeling by amino acids in cell culture (SILAC) proteomics, CLPB and HAX1 control the balance of mitochondrial protein synthesis and persistence crucial for proper mitochondrial function. Impaired mitochondrial protein dynamics are associated with decreased abundance of the serine-threonine kinase PRKD2 and HSP27 phosphorylated on serines 78 and 82. Cellular defects in HAX1-/- cells can be functionally reconstituted by HSP27. Thus, mitochondrial proteostasis emerges as a critical molecular and metabolic mechanism governing the differentiation and function of neutrophil granulocytes.
    Keywords:  Cell Biology; Immunology; Mitochondria; Neutrophils
    DOI:  https://doi.org/10.1172/JCI153153
  3. EMBO J. 2022 May 02. e109460
    Structural basis for feedforward control in the PINK1/Parkin pathway.
    Véronique Sauvé, George Sung, Emma J MacDougall, Guennadi Kozlov, Anshu Saran, Rayan Fakih, Edward A Fon, Kalle Gehring.
      PINK1 and parkin constitute a mitochondrial quality control system mutated in Parkinson's disease. PINK1, a kinase, phosphorylates ubiquitin to recruit parkin, an E3 ubiquitin ligase, to mitochondria. PINK1 controls both parkin localization and activity through phosphorylation of both ubiquitin and the ubiquitin-like (Ubl) domain of parkin. Here, we observed that phospho-ubiquitin can bind to two distinct sites on parkin, a high-affinity site on RING1 that controls parkin localization and a low-affinity site on RING0 that releases parkin autoinhibition. Surprisingly, ubiquitin vinyl sulfone assays, ITC, and NMR titrations showed that the RING0 site has higher affinity for phospho-ubiquitin than phosphorylated Ubl in trans. We observed parkin activation by micromolar concentrations of tetra-phospho-ubiquitin chains that mimic mitochondria bearing multiple phosphorylated ubiquitins. A chimeric form of parkin with the Ubl domain replaced by ubiquitin was readily activated by PINK1 phosphorylation. In all cases, mutation of the binding site on RING0 abolished parkin activation. The feedforward mechanism of parkin activation confers robustness and rapidity to the PINK1-parkin pathway and likely represents an intermediate step in its evolutionary development.
    Keywords:  Parkinson's disease; autophagy; mitophagy; open-loop control; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2021109460
  4. Nat Commun. 2022 May 03. 13(1): 2412
    Pantothenate kinase 2 interacts with PINK1 to regulate mitochondrial quality control via acetyl-CoA metabolism.
    Yunpeng Huang, Zhihui Wan, Yinglu Tang, Junxuan Xu, Bretton Laboret, Sree Nallamothu, Chenyu Yang, Boxiang Liu, Rongze Olivia Lu, Bingwei Lu, Juan Feng, Jing Cao, Susan Hayflick, Zhihao Wu, Bing Zhou.
      Human neurodegenerative disorders often exhibit similar pathologies, suggesting a shared aetiology. Key pathological features of Parkinson's disease (PD) are also observed in other neurodegenerative diseases. Pantothenate Kinase-Associated Neurodegeneration (PKAN) is caused by mutations in the human PANK2 gene, which catalyzes the initial step of de novo CoA synthesis. Here, we show that fumble (fbl), the human PANK2 homolog in Drosophila, interacts with PINK1 genetically. fbl and PINK1 mutants display similar mitochondrial abnormalities, and overexpression of mitochondrial Fbl rescues PINK1 loss-of-function (LOF) defects. Dietary vitamin B5 derivatives effectively rescue CoA/acetyl-CoA levels and mitochondrial function, reversing the PINK1 deficiency phenotype. Mechanistically, Fbl regulates Ref(2)P (p62/SQSTM1 homolog) by acetylation to promote mitophagy, whereas PINK1 regulates fbl translation by anchoring mRNA molecules to the outer mitochondrial membrane. In conclusion, Fbl (or PANK2) acts downstream of PINK1, regulating CoA/acetyl-CoA metabolism to promote mitophagy, uncovering a potential therapeutic intervention strategy in PD treatment.
    DOI:  https://doi.org/10.1038/s41467-022-30178-x
  5. STAR Protoc. 2022 Jun 17. 3(2): 101288
    An optimized FusX assembly-based technique to introduce mitochondrial TC-to-TT variations in human cell lines.
    Bibekananda Kar, Ankit Sabharwal, Santiago Restrepo-Castillo, Brandon W Simone, Karl J Clark, Stephen C Ekker.
      The FusX TALE Based Editor (FusXTBE) is a programmable base editing platform that can introduce specific TC-to-TT variations in the mitochondrial DNA (mtDNA). Here, we provide a protocol describing the synthesis and testing of the FusXTBE plasmids in cultured human cell lines. This tool is designed to be easily modified to work in diverse applications where editing of mitochondrial DNA is desired. For complete details on the use and execution of this protocol, please refer to Sabharwal et al. (2021) and Ma et al. (2016).
    Keywords:  CRISPR; Cell Biology; Genetics; Molecular Biology; Sequencing
    DOI:  https://doi.org/10.1016/j.xpro.2022.101288
  6. Cell Death Dis. 2022 May 04. 13(5): 436
    Novel roles of RTN4 and CLIMP-63 in regulating mitochondrial structure, bioenergetics and apoptosis.
    Rachel J Carter, Mateus Milani, Alison J Beckett, Shiyu Liu, Ian A Prior, Gerald M Cohen, Shankar Varadarajan.
      The recruitment of DRP1 to mitochondrial membranes prior to fission is facilitated by the wrapping of endoplasmic reticulum (ER) membranes around the mitochondria. To investigate the complex interplay between the ER membranes and DRP1 in the context of mitochondrial structure and function, we downregulate two key ER shaping proteins, RTN4 and CLIMP-63, and demonstrate pronounced mitochondrial hyperfusion and reduced ER-mitochondria contacts, despite their differential regulation of ER architecture. Although mitochondrial recruitment of DRP1 is unaltered in cells lacking RTN4 or CLIMP-63, several aspects of mitochondrial function, such as mtDNA-encoded translation, respiratory capacity and apoptosis are significantly hampered. Further mechanistic studies reveal that CLIMP-63 is required for cristae remodeling (OPA1 proteolysis) and DRP1-mediated mitochondrial fission, whereas both RTN4 and CLIMP-63 regulate the recruitment of BAX to ER and mitochondrial membranes to enable cytochrome c release and apoptosis, thereby performing novel and distinct roles in the regulation of mitochondrial structure and function.
    DOI:  https://doi.org/10.1038/s41419-022-04869-8
  7. PLoS Pathog. 2022 May 02. 18(5): e1009717
    The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei.
    Advaitha Iyer, Moritz Niemann, Mauro Serricchio, Caroline E Dewar, Silke Oeljeklaus, Luce Farine, Bettina Warscheid, André Schneider, Peter Bütikofer.
      The endoplasmic reticulum membrane complex (EMC) is a versatile complex that plays a key role in membrane protein biogenesis in the ER. Deletion of the complex has wide-ranging consequences including ER stress, disturbance in lipid transport and organelle tethering, among others. Here we report the function and organization of the evolutionarily conserved EMC (TbEMC) in the highly diverged eukaryote, Trypanosoma brucei. Using (co-) immunoprecipitation experiments in combination with mass spectrometry and whole cell proteomic analyses of parasites after depletion of select TbEMC subunits, we demonstrate that the TbEMC is composed of 9 subunits that are present in a high molecular mass complex localizing to the mitochondrial-endoplasmic reticulum interface. Knocking out or knocking down of single TbEMC subunits led to growth defects of T. brucei procyclic forms in culture. Interestingly, we found that depletion of individual TbEMC subunits lead to disruption of de novo synthesis of phosphatidylcholine (PC) or phosphatidylethanolamine (PE), the two most abundant phospholipid classes in T. brucei. Downregulation of TbEMC1 or TbEMC3 inhibited formation of PC while depletion of TbEMC8 inhibited PE synthesis, pointing to a role of the TbEMC in phospholipid synthesis. In addition, we found that in TbEMC7 knock-out parasites, TbEMC3 is released from the complex, implying that TbEMC7 is essential for the formation or the maintenance of the TbEMC.
    DOI:  https://doi.org/10.1371/journal.ppat.1009717
  8. RSC Adv. 2020 Nov 27. 10(71): 43383-43388
    Intra-mitochondrial reaction for cancer cell imaging and anti-cancer therapy by aggregation-induced emission.
    Sangpil Kim, Juhee Kim, Batakrishna Jana, Ja-Hyoung Ryu.
      Controlled intracellular chemical reactions to regulate cellular functions remain a challenge in biology mimetic systems. Herein, we developed an intra-mitochondrial bio-orthogonal reaction to induce aggregation induced emission. In situ carbonyl ligation inside mitochondria drives the molecules to form nano-aggregates with green fluorescence, which leads to depolarization of the mitochondrial membrane, generation of ROS, and subsequently mitochondrial dysfunction. This intra-mitochondrial carbonyl ligation shows great potential for anticancer treatment in various cancer cell lines.
    DOI:  https://doi.org/10.1039/d0ra07471c
  9. RSC Adv. 2021 Sep 27. 11(51): 32476-32493
    Protein import in mitochondria biogenesis: guided by targeting signals and sustained by dedicated chaperones.
    Anna-Roza Dimogkioka, Jamie Lees, Erik Lacko, Kostas Tokatlidis.
      Mitochondria have a central role in cellular metabolism; they are responsible for the biosynthesis of amino acids, lipids, iron-sulphur clusters and regulate apoptosis. About 99% of mitochondrial proteins are encoded by nuclear genes, so the biogenesis of mitochondria heavily depends on protein import pathways into the organelle. An intricate system of well-studied import machinery facilitates the import of mitochondrial proteins. In addition, folding of the newly synthesized proteins takes place in a busy environment. A system of folding helper proteins, molecular chaperones and co-chaperones, are present to maintain proper conformation and thus avoid protein aggregation and premature damage. The components of the import machinery are well characterised, but the targeting signals and how they are recognised and decoded remains in some cases unclear. Here we provide some detail on the types of targeting signals involved in the protein import process. Furthermore, we discuss the very elaborate chaperone systems of the intermembrane space that are needed to overcome the particular challenges for the folding process in this compartment. The mechanisms that sustain productive folding in the face of aggregation and damage in mitochondria are critical components of the stress response and play an important role in cell homeostasis.
    DOI:  https://doi.org/10.1039/d1ra04497d
  10. Mitochondrion. 2022 Apr 29. pii: S1567-7249(22)00037-X. [Epub ahead of print]
    Altered Brown Adipose Tissue Mitochondrial Function in Newborn Fragile X Syndrome Mice.
    Yash R Somnay, Aili Wang, Keren K Griffiths, Richard J Levy.
      Brown adipose tissue (BAT) mitochondria generate heat via uncoupled respiration due to excessive proton leak through uncoupling proteins (UCPs). We previously found hyperthermia in a newborn mouse model of fragile X syndrome and excessive leak in Fmr1 KO forebrain mitochondria caused by CoQ deficiency. The inefficient thermogenic nature of Fmr1 mutant forebrain mitochondria was reminiscent of BAT metabolic features. Thus, we aimed to characterize BAT mitochondrial function in these hyperthermic mice using a top-down approach. Although there was no change in steady-state levels of UCP1 expression between strains, BAT weighed significantly less in Fmr1 mutants compared with controls. Fmr1 KO BAT mitochondria demonstrated impaired substrate oxidation, lower mitochondrial membrane potentials and rates of respiration, and CoQ deficiency. The CoQ analog decylubiquinone normalized CoQ-dependent electron flux and unmasked excessive proton leak. Unlike mutant forebrain, where such deficiency resulted in pathological proton leak, CoQ deficiency within BAT mitochondria resulted largely in abnormal substrate oxidation. This suggests that CoQ is important in BAT for uncoupled respiration to produce heat during development. Although our data provide further evidence of a link between fragile X mental retardation protein (FMRP) and CoQ biosynthesis, the results highlight the importance of CoQ in developing tissues and suggest tissue-specific differences from CoQ deficiency. Because BAT mitochondria are primarily responsible for regulating core body temperature, the defects we describe in Fmr1 KOs could manifest as an adaptive downregulated response to hyperthermia or could result from FMRP deficiency directly.
    Keywords:  Mitochondria; brown adipose tissue; coenzyme Q; fragile X syndrome; hyperthermia; uncoupling proteins
    DOI:  https://doi.org/10.1016/j.mito.2022.04.003
  11. Nat Rev Cardiol. 2022 May 06.
    The role of mitochondrial fission in cardiovascular health and disease.
    Justin M Quiles, Åsa B Gustafsson.
      Mitochondria are organelles involved in the regulation of various important cellular processes, ranging from ATP generation to immune activation. A healthy mitochondrial network is essential for cardiovascular function and adaptation to pathological stressors. Mitochondria undergo fission or fusion in response to various environmental cues, and these dynamic changes are vital for mitochondrial function and health. In particular, mitochondrial fission is closely coordinated with the cell cycle and is linked to changes in mitochondrial respiration and membrane permeability. Another key function of fission is the segregation of damaged mitochondrial components for degradation by mitochondrial autophagy (mitophagy). Mitochondrial fission is induced by the large GTPase dynamin-related protein 1 (DRP1) and is subject to sophisticated regulation. Activation requires various post-translational modifications of DRP1, actin polymerization and the involvement of other organelles such as the endoplasmic reticulum, Golgi apparatus and lysosomes. A decrease in mitochondrial fusion can also shift the balance towards mitochondrial fission. Although mitochondrial fission is necessary for cellular homeostasis, this process is often aberrantly activated in cardiovascular disease. Indeed, strong evidence exists that abnormal mitochondrial fission directly contributes to disease development. In this Review, we compare the physiological and pathophysiological roles of mitochondrial fission and discuss the therapeutic potential of preventing excessive mitochondrial fission in the heart and vasculature.
    DOI:  https://doi.org/10.1038/s41569-022-00703-y
  12. J Biol Chem. 2022 May 02. pii: S0021-9258(22)00448-3. [Epub ahead of print] 102008
    Loss of mitochondrial ATPase ATAD3A contributes to non-alcoholic fatty liver disease through accumulation of lipids and damaged mitochondria.
    Liting Chen, Yuchang Li, Chantal Sottas, Anthoula Lazaris, Stephanie K Petrillo, Peter Metrakos, Lu Li, Yuji Ishida, Takeshi Saito, Samuel Garza, Vassilios Papadopoulos.
      Mitochondrial ATPase ATAD3A is essential for cholesterol transport, mitochondrial structure, and cell survival. However, the relationship between ATAD3A and non-alcoholic fatty liver disease (NAFLD) is largely unknown. In this study, we found that ATAD3A was upregulated in the progression of NAFLD in livers from rats with diet-induced non-alcoholic steatohepatitis and in human livers from patients diagnosed with NAFLD. We used CRISPR-Cas9 to delete ATAD3A in Huh7 human hepatocellular carcinoma cells, and used RNAi to silence ATAD3A expression in human hepatocytes isolated from humanized liver-chimeric mice to assess the influence of ATAD3A deletion on liver cells with free cholesterol (FC) overload induced by treatment with cholesterol plus 58035, an inhibitor of acetyl-CoA acetyltransferase. Our results showed that ATAD3A KO exacerbated FC accumulation under FC overload in Huh7 cells, and also that triglyceride (TG) levels were significantly increased in ATAD3A KO Huh7 cells following inhibition of lipolysis mediated by upregulation of lipid droplet-binding protein perilipin-2. Moreover, loss of ATAD3A upregulated autophagosome-associated light chain 3-II protein and p62 in Huh7 cells and fresh human hepatocytes through blockage of autophagosome degradation. Finally, we show the mitophagy mediator, PTEN-induced kinase 1, was downregulated in ATAD3A KO Huh7 cells, suggesting that ATAD3A KO inhibits mitophagy. These results also showed that loss of ATAD3A impaired mitochondrial basal respiration and ATP production in Huh7 cells under FC overload, accompanied by downregulation of mitochondrial ATP synthase. Taken together, we conclude that loss of ATAD3A promotes the progression of NAFLD through the accumulation of FC, TG, and damaged mitochondria in hepatocytes.
    Keywords:  ATAD3A; NAFLD; autophagy; cholesterol; fatty acid oxidation; free fatty acid; mitochondrial respiration; mitophagy; triglyceride
    DOI:  https://doi.org/10.1016/j.jbc.2022.102008
  13. Methods Mol Biol. 2022 ;2429 85-102
    Extracellular Flux Analysis of Mitochondrial Function in Pluripotent Stem Cells.
    Enkhtuul Tsogtbaatar, Katherine Minter-Dykhouse, Alicia Saarinen, Clifford D L Folmes.
      Mitochondrial function and energy metabolism are increasingly recognized not only as regulators of pluripotent stem cell function and fate, but also as critical targets in disease pathogenesis and aging. Therefore across the downstream applications of pluripotent stem cells, including development and disease modeling, drug screening, and cell-based therapies, it is crucial to be able to measure mitochondrial function and metabolism in a high-throughput, real-time and label-free manner. Here we describe the application of Seahorse extracellular flux analysis to measure mitochondrial function in pluripotent stem cells and their derivatives. Specifically, we highlight two assays, the Mitochondrial Stress Test, which quantifies overall mitochondrial function including basal, maximal and ATP-couple oxygen consumption rates, and the Electron Transport Chain Complex Specific assay, that quantifies function of individual complexes within the electron transport chain.
    Keywords:  Differentiation; Embryonic stem cells; Induced pluripotent stem cells; Mitochondrial respiration; Oxidative metabolism; Oxidative phosphorylation
    DOI:  https://doi.org/10.1007/978-1-0716-1979-7_7
  14. Mitochondrion. 2022 May 02. pii: S1567-7249(22)00041-1. [Epub ahead of print]
    Regulation of mitochondrial network homeostasis by O-GlcNAcylation.
    Qiu Xue, Ru Yan, Shengtao Ji, Shu Yu.
      O-GlcNAcylation, a ubiquitous post-translational modification, rapidly modulates protein activity through the reversible addition and removal of O-GlcNAc groups from serine or threonine residues in target proteins, and is involved in multiple metabolic pathways. With the discovery of enzymes and substrates for O-GlcNAc cycling in mitochondria, mitochondrial O-GlcNAc modification and its regulatory role in mitochondrial function deserve extensive attention. Adaptive regulation of the O-GlcNAc cycling in response to energy perturbations is demonstrated to be important in maintaining mitochondrial homeostasis. Dysregulation of O-GlcNAcylation in mitochondria has been associated with various mitochondrial dysfunctions, such as abnormal mitochondrial dynamics, reduced mitochondrial biosynthesis, disruption of the electron transport chain, oxidative stress and the calcium paradox, as well as activation of mitochondrial apoptosis pathways. Here, we outline the current understanding of O-GlcNAc modification in mitochondria and the key discovery of O-GlcNAcylation in regulating mitochondrial network homeostasis. This review will provide insights into targeting mitochondrial O-GlcNAcylation, as well as the mechanisms linking mitochondrial dysfunction and disease.
    Keywords:  Cellular bioenergetics; Metabolism; Mitochondrial homeostasis; Nutrient sensing; O-GlcNAcylation
    DOI:  https://doi.org/10.1016/j.mito.2022.04.007
  15. J Mol Biol. 2022 Apr 29. pii: S0022-2836(22)00198-X. [Epub ahead of print] 167618
    Stress Responses Elicited by Misfolded Proteins Targeted to Mitochondria.
    Kannan Boosi Narayana Rao, Pratima Pandey, Rajasri Sarkar, Asmita Ghosh, Shemin Mansuri, Mudassar Ali, Priyanka Majumder, K Ranjith Kumar, Arjun Ray, Swasti Raychaudhuri, Koyeli Mapa.
      The double-membrane-bound architecture of mitochondria, essential for ATP production, sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix possess contrasting oxido-reductive environments and discrete protein quality control (PQC) machineries resulting inherent differences in their protein folding environments. To understand the nature of stress response elicited by equivalent proteotoxic stress to these sub-mitochondrial compartments, we took misfolding and aggregation-prone stressor proteins and fused it to well described signal sequences to specifically target and impart stress to yeast mitochondrial IMS or matrix. We show, mitochondrial proteotoxicity leads to growth arrest of yeast cells of varying degrees depending on nature of stressor proteins and the intra-mitochondrial location of stress. Next, by employing transcriptomics and proteomics, we report a comprehensive stress response elicited by stressor proteins specifically targeted to mitochondrial matrix or IMS. A general response to proteotoxic stress by mitochondria-targeted misfolded proteins is mitochondrial fragmentation, and an adaptive abrogation of mitochondrial respiration with concomitant upregulation of glycolysis. Beyond shared stress responses, specific signatures due to stress within mitochondrial sub-compartments are also revealed. We report that stress-imparted by bipartite signal sequence-fused stressor proteins to IMS, leads to specific upregulation of IMS-chaperones and TOM complex components. In contrast, matrix-targeted stressors lead to specific upregulation of matrix-chaperones and cytosolic PQC components. Finally, by systematic genetic interaction using deletion strains of differentially upregulated genes, we found prominent modulatory role of TOM complex components during IMS-stress response. In contrast, VMS1 markedly modulates the stress response originated from matrix.
    Keywords:  Mitochondrial Unfolded Protein Response; Molecular Chaperone; Protein misfolding; Proteostasis; Proteotoxic stress; Ribosome Quality Control; Stress Response; TOM complex; Vms1
    DOI:  https://doi.org/10.1016/j.jmb.2022.167618
  16. Cell Biol Toxicol. 2022 May 04.
    High-content high-throughput imaging reveals distinct connections between mitochondrial morphology and functionality for OXPHOS complex I, III, and V inhibitors.
    Wanda van der Stel, Huan Yang, Sylvia E le Dévédec, Bob van de Water, Joost B Beltman, Erik H J Danen.
      Cells can adjust their mitochondrial morphology by altering the balance between mitochondrial fission and fusion to adapt to stressful conditions. The connection between a chemical perturbation, changes in mitochondrial function, and altered mitochondrial morphology is not well understood. Here, we made use of high-throughput high-content confocal microscopy to assess the effects of distinct classes of oxidative phosphorylation (OXPHOS) complex inhibitors on mitochondrial parameters in a concentration and time resolved manner. Mitochondrial morphology phenotypes were clustered based on machine learning algorithms and mitochondrial integrity patterns were mapped. In parallel, changes in mitochondrial membrane potential (MMP), mitochondrial and cellular ATP levels, and viability were microscopically assessed. We found that inhibition of MMP, mitochondrial ATP production, and oxygen consumption rate (OCR) using sublethal concentrations of complex I and III inhibitors did not trigger mitochondrial fragmentation. Instead, complex V inhibitors that suppressed ATP and OCR but increased MMP provoked a more fragmented mitochondrial morphology. In agreement, complex V but not complex I or III inhibitors triggered proteolytic cleavage of the mitochondrial fusion protein, OPA1. The relation between increased MMP and fragmentation did not extend beyond OXPHOS complex inhibitors: increasing MMP by blocking the mPTP pore did not lead to OPA1 cleavage or mitochondrial fragmentation and the OXPHOS uncoupler FCCP was associated with OPA1 cleavage and MMP reduction. Altogether, our findings connect vital mitochondrial functions and phenotypes in a high-throughput high-content confocal microscopy approach that help understanding of chemical-induced toxicity caused by OXPHOS complex perturbing chemicals.
    Keywords:  ATP; Machine learning; Membrane potential; Mitochondria; Morphology
    DOI:  https://doi.org/10.1007/s10565-022-09712-6
  17. Commun Biol. 2022 May 06. 5(1): 423
    The MFN1 and MFN2 mitofusins promote clustering between mitochondria and peroxisomes.
    Yinbo Huo, Weiping Sun, Tiezhu Shi, Song Gao, Min Zhuang.
      Mitochondria and peroxisomes are two types of functionally close-related organelles, and both play essential roles in lipid and ROS metabolism. However, how they physically interact with each other is not well understood. In this study, we apply the proximity labeling method with peroxisomal proteins and report that mitochondrial protein mitofusins (MFNs) are in proximity to peroxisomes. Overexpression of MFNs induces not only the mitochondria clustering but also the co-clustering of peroxisomes. We also report the enrichment of MFNs at the mitochondria-peroxisome interface. Induced mitofusin expression gives rise to more mitochondria-peroxisome contacting sites. Furthermore, the tethering of peroxisomes to mitochondria can be inhibited by the expression of a truncated MFN2, which lacks the transmembrane region. Collectively, our study suggests MFNs as regulators for mitochondria-peroxisome contacts. Our findings are essential for future studies of inter-organelle metabolism regulation and signaling, and may help understand the pathogenesis of mitofusin dysfunction-related disease.
    DOI:  https://doi.org/10.1038/s42003-022-03377-x
  18. PLoS One. 2022 ;17(5): e0254296
    Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant.
    Prita R Asih, Anne Poljak, Michael Kassiou, Yazi D Ke, Lars M Ittner.
      The translocator protein (TSPO) has been implicated in mitochondrial transmembrane cholesterol transport, brain inflammation, and other mitochondrial functions. It is upregulated in glial cells during neuroinflammation in Alzheimer's disease. High affinity TSPO imaging radioligands are utilized to visualize neuroinflammation. However, this is hampered by the common A147T polymorphism which compromises ligand binding. Furthermore, this polymorphism has been linked to increased risk of neuropsychiatric disorders, and possibly reduces TSPO protein stability. Here, we used immunoprecipitation coupled to mass-spectrometry (IP-MS) to establish a mitochondrial protein binding profile of wild-type (WT) TSPO and the A147T polymorphism variant. Using mitochondria from human glial cells expressing either WT or A147T TSPO, we identified 30 WT TSPO binding partners, yet only 23 for A147T TSPO. Confirming that A147T polymorphism of the TSPO might confer loss of function, we found that one of the identified interactors of WT TSPO, 14-3-3 theta (YWHAQ), a protein involved in regulating mitochondrial membrane proteins, interacts much less with A147T TSPO. Our data presents a network of mitochondrial interactions of TSPO and its A147T polymorphism variant in human glial cells and indicate functional relevance of A147T in mitochondrial protein networks.
    DOI:  https://doi.org/10.1371/journal.pone.0254296
  19. Nucleic Acids Res. 2022 May 07. pii: gkac306. [Epub ahead of print]
    The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context.
    Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann.
      Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterized by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It, however, lacked functions aimed at integrating mitochondria in the cellular context and thus identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade, we implemented two novel integrative functions, network analysis and transcription factor enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualization, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species and an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.
    DOI:  https://doi.org/10.1093/nar/gkac306
  20. Cell Death Dis. 2022 Apr 30. 13(4): 419
    Mitochondrial calcium uptake regulates tumour progression in embryonal rhabdomyosarcoma.
    Hsin Yao Chiu, Amos Hong Pheng Loh, Reshma Taneja.
      Embryonal rhabdomyosarcoma (ERMS) is characterised by a failure of cells to complete skeletal muscle differentiation. Although ERMS cells are vulnerable to oxidative stress, the relevance of mitochondrial calcium homoeostasis in oncogenesis is unclear. Here, we show that ERMS cell lines as well as primary tumours exhibit elevated expression of the mitochondrial calcium uniporter (MCU). MCU knockdown resulted in impaired mitochondrial calcium uptake and a reduction in mitochondrial reactive oxygen species (mROS) levels. Phenotypically, MCU knockdown cells exhibited reduced cellular proliferation and motility, with an increased propensity to differentiate in vitro and in vivo. RNA-sequencing of MCU knockdown cells revealed a significant reduction in genes involved in TGFβ signalling that play prominent roles in oncogenesis and inhibition of myogenic differentiation. Interestingly, modulation of mROS production impacted TGFβ signalling. Our study elucidates mechanisms by which mitochondrial calcium dysregulation promotes tumour progression and suggests that targeting the MCU complex to restore mitochondrial calcium homoeostasis could be a therapeutic avenue in ERMS.
    DOI:  https://doi.org/10.1038/s41419-022-04835-4
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