bims-mikwok Biomed News
on Mitochondrial quality control
Issue of 2023–05–07
nine papers selected by
Avinash N. Mukkala, University of Toronto
  1. Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress.
  2. MICU1 occludes the mitochondrial calcium uniporter in divalent-free conditions.
  3. Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT.
  4. Harnessing mitochondrial transplantation to sustain cardiac function: Another step forward.
  5. Trends and prospects in mitochondrial genome editing.
  6. Switch-like compaction of poly(ADP-ribose) upon cation binding.
  7. Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation.
  8. Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses.
  9. A phosphate-sensing organelle regulates phosphate and tissue homeostasis.
  1. Sci Adv. 2023 May 03. 9(18): eadf0138
    Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress.
    Ramya S Kuna, Avi Kumar, Karl A Wessendorf-Rodriguez, Hector Galvez, Courtney R Green, Grace H McGregor, Thekla Cordes, Reuben J Shaw, Robert U Svensson, Christian M Metallo.
      Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA homeostasis under such stresses is critically important. To this end, we applied 13C isotope tracing cell lines deficient in these mitochondrial [ATP-citrate lyase (ACLY)]-, cytosolic [acetyl-CoA synthetase (ACSS2)]-, and peroxisomal [peroxisomal biogenesis factor 5 (PEX5)]-dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting that alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation in cells lacking ACLY, highlighting a role for inter-organelle cross-talk in supporting cell survival in response to nutrient fluctuations.
    DOI:  https://doi.org/10.1126/sciadv.adf0138
  2. Proc Natl Acad Sci U S A. 2023 May 09. 120(19): e2218999120
    MICU1 occludes the mitochondrial calcium uniporter in divalent-free conditions.
    Macarena Rodríguez-Prados, Elena Berezhnaya, Maria Teresa Castromonte, Sergio L Menezes-Filho, Melanie Paillard, György Hajnóczky.
      Mitochondrial Ca2+ uptake is mediated by the mitochondrial uniporter complex (mtCU) that includes a tetramer of the pore-forming subunit, MCU, a scaffold protein, EMRE, and the EF-hand regulatory subunit, MICU1 either homodimerized or heterodimerized with MICU2/3. MICU1 has been proposed to regulate Ca2+ uptake via the mtCU by physically occluding the pore and preventing Ca2+ flux at resting cytoplasmic [Ca2+] (free calcium concentration) and to increase Ca2+ flux at high [Ca2+] due to cooperative activation of MICUs EF-hands. However, mtCU and MICU1 functioning when its EF-hands are unoccupied by Ca2+ is poorly studied due to technical limitations. To overcome this barrier, we have studied the mtCU in divalent-free conditions by assessing the Ru265-sensitive Na+ influx using fluorescence-based measurement of mitochondrial matrix [Na+] (free sodium concentration) rise and the ensuing depolarization and swelling. We show an increase in all these measures of Na+ uptake in MICU1KO cells as compared to wild-type (WT) and rescued MICU1KO HEK cells. However, mitochondria in WT cells and MICU1 stable-rescued cells still allowed some Ru265-sensitive Na+ influx that was prevented by MICU1 in excess upon acute overexpression. Thus, MICU1 restricts the cation flux across the mtCU in the absence of Ca2+, but even in cells with high endogenous MICU1 expression such as HEK, some mtCU seem to lack MICU1-dependent gating. We also show rearrangement of the mtCU and altered number of functional channels in MICU1KO and different rescues, and loss of MICU1 during mitoplast preparation, that together might have obscured the pore-blocking function of MICU1 in divalent-free conditions in previous studies.
    Keywords:  EMRE; MICU1; Na+; mitochondrial calcium uniporter; mitoplast
    DOI:  https://doi.org/10.1073/pnas.2218999120
  3. Hum Mol Genet. 2023 May 02. pii: ddad062. [Epub ahead of print]
    Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT.
    Iman Al Khatib, Jingti Deng, Yuanjiu Lei, Sylvia Torres-Odio, Gladys R Rojas, Laura E Newman, Brian K Chung, Andrew Symes, Hongliang Zhang, Shar-Yin N Huang, Yves Pommier, Aneal Khan, Gerald S Shadel, A Phillip West, William T Gibson, Timothy E Shutt.
      The recognition that cytosolic mtDNA activates cGAS-STING innate immune signaling has unlocked novel disease mechanisms. Here, an uncharacterized variant predicted to affect TOP1MT function, P193L, was discovered in a family with multiple early-onset autoimmune diseases, including Systemic Lupus Erythematosus (SLE). Although there was no previous genetic association between TOP1MT and autoimmune disease, the role of TOP1MT as a regulator of mtDNA led us to investigate whether TOP1MT could mediate the release of mtDNA to the cytosol, where it could then activate the cGAS-STING innate immune pathway known to be activated in SLE and other autoimmune diseases. Through analysis of cells with reduced TOP1MT expression, we show that loss of TOP1MT results in release of mtDNA to the cytosol, which activates the cGAS-STING pathway. We also characterized the P193L variant for its ability to rescue several TOP1MT functions when expressed in TOP1MT knockout cells. We show that the P193L variant is not fully functional, as its re-expression at high levels was unable to rescue mitochondrial respiration deficits, and only showed partial rescue for other functions, including repletion of mtDNA replication following depletion, nucleoid size, steady state mtDNA transcripts levels, and mitochondrial morphology. Additionally, expression of P193L at endogenous levels was unable to rescue mtDNA release-mediated cGAS-STING signaling. Overall, we report a link between TOP1MT and mtDNA release leading to cGAS-STING activation. Moreover, we show that the P193L variant has partial loss of function that may contribute to autoimmune disease susceptibility via cGAS-STING mediated activation of the innate immune system.
    DOI:  https://doi.org/10.1093/hmg/ddad062
  4. Mol Ther. 2023 May 03. pii: S1525-0016(23)00201-0. [Epub ahead of print]31(5): 1201-1203
    Harnessing mitochondrial transplantation to sustain cardiac function: Another step forward.
    Yuhao Li, Kroekkiat Chinda, Yaozu Xiang, Hao Zhou, Dachun Xu, Sang-Ging Ong, Sang-Bing Ong.
      
    DOI:  https://doi.org/10.1016/j.ymthe.2023.04.003
  5. Exp Mol Med. 2023 May 01.
    Trends and prospects in mitochondrial genome editing.
    Hong Thi Lam Phan, Hyunji Lee, Kyoungmi Kim.
      Mitochondria are of fundamental importance in programmed cell death, cellular metabolism, and intracellular calcium concentration modulation, and inheritable mitochondrial disorders via mitochondrial DNA (mtDNA) mutation cause several diseases in various organs and systems. Nevertheless, mtDNA editing, which plays an essential role in the treatment of mitochondrial disorders, still faces several challenges. Recently, programmable editing tools for mtDNA base editing, such as cytosine base editors derived from DddA (DdCBEs), transcription activator-like effector (TALE)-linked deaminase (TALED), and zinc finger deaminase (ZFD), have emerged with considerable potential for correcting pathogenic mtDNA variants. In this review, we depict recent advances in the field, including structural biology and repair mechanisms, and discuss the prospects of using base editing tools on mtDNA to broaden insight into their medical applicability for treating mitochondrial diseases.
    DOI:  https://doi.org/10.1038/s12276-023-00973-7
  6. Proc Natl Acad Sci U S A. 2023 May 09. 120(19): e2215068120
    Switch-like compaction of poly(ADP-ribose) upon cation binding.
    Mohsen Badiee, Adam L Kenet, Laura R Ganser, Tapas Paul, Sua Myong, Anthony K L Leung.
      Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a posttranslational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine4+). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.
    Keywords:  PAR-binding protein; persistence length; poly(ADP-ribose); single molecule FRET
    DOI:  https://doi.org/10.1073/pnas.2215068120
  7. Nat Commun. 2023 May 05. 14(1): 2610
    Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation.
    Yafeng Li, Jessica S Hook, Qing Ding, Xue Xiao, Stephen S Chung, Marcel Mettlen, Lin Xu, Jessica G Moreland, Michalis Agathocleous.
      Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in patients with COVID-19. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19 and healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism. Metabolic changes in neutrophils from patients with severe COVID-19 were consistent with reduced activity of the glycolytic enzyme GAPDH. Inhibition of GAPDH blocked glycolysis and promoted pentose phosphate pathway activity but blunted the neutrophil respiratory burst. Inhibition of GAPDH was sufficient to cause neutrophil extracellular trap (NET) formation which required neutrophil elastase activity. GAPDH inhibition increased neutrophil pH, and blocking this increase prevented cell death and NET formation. These findings indicate that neutrophils in severe COVID-19 have an aberrant metabolism which can contribute to their dysfunction. Our work also shows that NET formation, a pathogenic feature of many inflammatory diseases, is actively suppressed in neutrophils by a cell-intrinsic mechanism controlled by GAPDH.
    DOI:  https://doi.org/10.1038/s41467-023-37567-w
  8. Cell Rep Med. 2023 Apr 25. pii: S2666-3791(23)00134-9. [Epub ahead of print] 101024
    Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses.
    Gustavo Garcia, Joseph Ignatius Irudayam, Arjit Vijey Jeyachandran, Swati Dubey, Christina Chang, Sebastian Castillo Cario, Nate Price, Sathya Arumugam, Angelica L Marquez, Aayushi Shah, Amir Fanaei, Nikhil Chakravarty, Shantanu Joshi, Sanjeev Sinha, Samuel W French, Mark S Parcells, Arunachalam Ramaiah, Vaithilingaraja Arumugaswami.
      RNA viruses continue to remain a threat for potential pandemics due to their rapid evolution. Potentiating host antiviral pathways to prevent or limit viral infections is a promising strategy. Thus, by testing a library of innate immune agonists targeting pathogen recognition receptors, we observe that Toll-like receptor 3 (TLR3), stimulator of interferon genes (STING), TLR8, and Dectin-1 ligands inhibit arboviruses, Chikungunya virus (CHIKV), West Nile virus, and Zika virus to varying degrees. STING agonists (cAIMP, diABZI, and 2',3'-cGAMP) and Dectin-1 agonist scleroglucan demonstrate the most potent, broad-spectrum antiviral function. Furthermore, STING agonists inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and enterovirus-D68 (EV-D68) infection in cardiomyocytes. Transcriptome analysis reveals that cAIMP treatment rescue cells from CHIKV-induced dysregulation of cell repair, immune, and metabolic pathways. In addition, cAIMP provides protection against CHIKV in a chronic CHIKV-arthritis mouse model. Our study describes innate immune signaling circuits crucial for RNA virus replication and identifies broad-spectrum antivirals effective against multiple families of pandemic potential RNA viruses.
    Keywords:  Chikungunya virus; SARS-CoV-2; West Nile virus; Zika virus; cAIMP; cGAS-STING pathway; enterovirus-D68; pattern-recognition receptors; respiratory syncytial virus; scleroglucan
    DOI:  https://doi.org/10.1016/j.xcrm.2023.101024
  9. Nature. 2023 May 03.
    A phosphate-sensing organelle regulates phosphate and tissue homeostasis.
    Chiwei Xu, Jun Xu, Hong-Wen Tang, Maria Ericsson, Jui-Hsia Weng, Jonathan DiRusso, Yanhui Hu, Wenzhe Ma, John M Asara, Norbert Perrimon.
      Inorganic phosphate (Pi) is one of the essential molecules for life. However, little is known about intracellular Pi metabolism and signalling in animal tissues1. Following the observation that chronic Pi starvation causes hyperproliferation in the digestive epithelium of Drosophila melanogaster, we determined that Pi starvation triggers the downregulation of the Pi transporter PXo. In line with Pi starvation, PXo deficiency caused midgut hyperproliferation. Interestingly, immunostaining and ultrastructural analyses showed that PXo specifically marks non-canonical multilamellar organelles (PXo bodies). Further, by Pi imaging with a Förster resonance energy transfer (FRET)-based Pi sensor2, we found that PXo restricts cytosolic Pi levels. PXo bodies require PXo for biogenesis and undergo degradation following Pi starvation. Proteomic and lipidomic characterization of PXo bodies unveiled their distinct feature as an intracellular Pi reserve. Therefore, Pi starvation triggers PXo downregulation and PXo body degradation as a compensatory mechanism to increase cytosolic Pi. Finally, we identified connector of kinase to AP-1 (Cka), a component of the STRIPAK complex and JNK signalling3, as the mediator of PXo knockdown- or Pi starvation-induced hyperproliferation. Altogether, our study uncovers PXo bodies as a critical regulator of cytosolic Pi levels and identifies a Pi-dependent PXo-Cka-JNK signalling cascade controlling tissue homeostasis.
    DOI:  https://doi.org/10.1038/s41586-023-06039-y
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