bims-midtic Biomed News
on Mitochondrial dynamics and trafficking in cells
Issue of 2024–04–21
nine papers selected by
Omkar Joshi, Turku Bioscience
  1. The Structure of the Drp1 Lattice on Membrane.
  2. PGC-1a mediated mitochondrial biogenesis promotes recovery and survival of neuronal cells from cellular degeneration.
  3. OMA1 clears traffic jam in TOM tunnel in mammals.
  4. Cdk8/CDK19 promotes mitochondrial fission through Drp1 phosphorylation and can phenotypically suppress pink1 deficiency in Drosophila.
  5. Attenuating mitochondrial dysfunction and morphological disruption with PT320 delays dopamine degeneration in MitoPark mice.
  6. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies.
  7. RNF31 alleviates liver steatosis by promoting p53/BNIP3-related mitophagy in hepatocytes.
  8. Positioning regulation of organelle network via Chinese microneedle.
  9. Endothelial Mitochondria-Associated Membranes (MAMs) Isolation by Percoll Step Gradients.
  1. bioRxiv. 2024 Apr 04. pii: 2024.04.04.588123. [Epub ahead of print]
    The Structure of the Drp1 Lattice on Membrane.
    Ruizhi Peng, Kristy Rochon, Scott M Stagg, Jason A Mears.
      Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
    SUMMARY: This study provides new insights into the structure of Drp1 on lipid membranes. A locally ordered Drp1 lattice structure is solved and reveals intermolecular contacts and conformational rearrangements that suggest a mechanism for constriction of mitochondrial membranes.
    DOI:  https://doi.org/10.1101/2024.04.04.588123
  2. Cell Death Discov. 2024 Apr 17. 10(1): 180
    PGC-1a mediated mitochondrial biogenesis promotes recovery and survival of neuronal cells from cellular degeneration.
    Wenting You, Kèvin Knoops, Tos T J M Berendschot, Birke J Benedikter, Carroll A B Webers, Chris P M Reutelingsperger, Theo G M F Gorgels.
      Neurodegenerative disorders are characterized by the progressive loss of structure and function of neurons, often including the death of the neuron. Previously, we reported that, by removing the cell death stimulus, dying/injured neurons could survive and recover from the process of regulated cell death, even if the cells already displayed various signs of cellular damage. Now we investigated the role of mitochondrial dynamics (fission/fusion, biogenesis, mitophagy) in both degeneration and in recovery of neuronal cells. In neuronal PC12 cells, exposure to ethanol (EtOH) induced massive neurite loss along with widespread mitochondrial fragmentation, mitochondrial membrane potential loss, reduced ATP production, and decreased total mitochondrial volume. By removing EtOH timely all these mitochondrial parameters recovered to normal levels. Meanwhile, cells regrew neurites and survived. Study of the mitochondrial dynamics showed that autophagy was activated only during the cellular degeneration phase (EtOH treatment) but not in the recovery phase (EtOH removed), and it was not dependent on the Parkin/PINK1 mediated mitophagy pathway. Protein expression of key regulators of mitochondrial fission, phospho-Drp1Ser616 and S-OPA1, increased during EtOH treatment and recovered to normal levels after removing EtOH. In addition, the critical role of PGC-1α mediated mitochondrial biogenesis in cellular recovery was revealed: inhibition of PGC-1α using SR-18292 after EtOH removal significantly impeded recovery of mitochondrial damage, regeneration of neurites, and cell survival in a concentration-dependent manner. Taken together, our study showed reversibility of mitochondrial morphological and functional damage in stressed neuronal cells and revealed that PGC-1α mediated mitochondrial biogenesis played a critical role in the cellular recovery. This molecular mechanism could be a target for neuroprotection and neurorescue in neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41420-024-01953-0
  3. J Cell Biol. 2024 May 06. pii: e202403190. [Epub ahead of print]223(5):
    OMA1 clears traffic jam in TOM tunnel in mammals.
    Shiori Sekine, Yusuke Sekine.
      Using an engineered mitochondrial clogger, Krakowczyk et al. (https://doi.org/10.1083/jcb.202306051) identified the OMA1 protease as a critical component that eliminates import failure at the TOM translocase in mammalian cells, providing a novel quality control mechanism that is distinct from those described in yeast.
    DOI:  https://doi.org/10.1083/jcb.202403190
  4. Nat Commun. 2024 Apr 18. 15(1): 3326
    Cdk8/CDK19 promotes mitochondrial fission through Drp1 phosphorylation and can phenotypically suppress pink1 deficiency in Drosophila.
    Jenny Zhe Liao, Hyung-Lok Chung, Claire Shih, Kenneth Kin Lam Wong, Debdeep Dutta, Zelha Nil, Catherine Grace Burns, Oguz Kanca, Ye-Jin Park, Zhongyuan Zuo, Paul C Marcogliese, Katherine Sew, Hugo J Bellen, Esther M Verheyen.
      Cdk8 in Drosophila is the orthologue of vertebrate CDK8 and CDK19. These proteins have been shown to modulate transcriptional control by RNA polymerase II. We found that neuronal loss of Cdk8 severely reduces fly lifespan and causes bang sensitivity. Remarkably, these defects can be rescued by expression of human CDK19, found in the cytoplasm of neurons, suggesting a non-nuclear function of CDK19/Cdk8. Here we show that Cdk8 plays a critical role in the cytoplasm, with its loss causing elongated mitochondria in both muscles and neurons. We find that endogenous GFP-tagged Cdk8 can be found in both the cytoplasm and nucleus. We show that Cdk8 promotes the phosphorylation of Drp1 at S616, a protein required for mitochondrial fission. Interestingly, Pink1, a mitochondrial kinase implicated in Parkinson's disease, also phosphorylates Drp1 at the same residue. Indeed, overexpression of Cdk8 significantly suppresses the phenotypes observed in flies with low levels of Pink1, including elevated levels of ROS, mitochondrial dysmorphology, and behavioral defects. In summary, we propose that Pink1 and Cdk8 perform similar functions to promote Drp1-mediated fission.
    DOI:  https://doi.org/10.1038/s41467-024-47623-8
  5. J Biomed Sci. 2024 Apr 17. 31(1): 38
    Attenuating mitochondrial dysfunction and morphological disruption with PT320 delays dopamine degeneration in MitoPark mice.
    Vicki Wang, Kuan-Yin Tseng, Tung-Tai Kuo, Eagle Yi-Kung Huang, Kuo-Lun Lan, Zi-Rong Chen, Kuo-Hsing Ma, Nigel H Greig, Jin Jung, Ho-Ii Choi, Lars Olson, Barry J Hoffer, Yuan-Hao Chen.
       BACKGROUND: Mitochondria are essential organelles involved in cellular energy production. Changes in mitochondrial function can lead to dysfunction and cell death in aging and age-related disorders. Recent research suggests that mitochondrial dysfunction is closely linked to neurodegenerative diseases. Glucagon-like peptide-1 receptor (GLP-1R) agonist has gained interest as a potential treatment for Parkinson's disease (PD). However, the exact mechanisms responsible for the therapeutic effects of GLP-1R-related agonists are not yet fully understood.
    METHODS: In this study, we explores the effects of early treatment with PT320, a sustained release formulation of the GLP-1R agonist Exenatide, on mitochondrial functions and morphology in a progressive PD mouse model, the MitoPark (MP) mouse.
    RESULTS: Our findings demonstrate that administration of a clinically translatable dose of PT320 ameliorates the reduction in tyrosine hydroxylase expression, lowers reactive oxygen species (ROS) levels, and inhibits mitochondrial cytochrome c release during nigrostriatal dopaminergic denervation in MP mice. PT320 treatment significantly preserved mitochondrial function and morphology but did not influence the reduction in mitochondria numbers during PD progression in MP mice. Genetic analysis indicated that the cytoprotective effect of PT320 is attributed to a reduction in the expression of mitochondrial fission protein 1 (Fis1) and an increase in the expression of optic atrophy type 1 (Opa1), which is known to play a role in maintaining mitochondrial homeostasis and decreasing cytochrome c release through remodeling of the cristae.
    CONCLUSION: Our findings suggest that the early administration of PT320 shows potential as a neuroprotective treatment for PD, as it can preserve mitochondrial function. Through enhancing mitochondrial health by regulating Opa1 and Fis1, PT320 presents a new neuroprotective therapy in PD.
    Keywords:  Exenatide; Glucagon-like peptide-1 receptor agonist; MitoPark mouse; Mitochondria; PT320; Parkinson’s disease
    DOI:  https://doi.org/10.1186/s12929-024-01025-6
  6. Nat Commun. 2024 Apr 17. 15(1): 3290
    Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies.
    Ying Zhu, Kerem Can Akkaya, Julia Ruta, Nanako Yokoyama, Cong Wang, Max Ruwolt, Diogo Borges Lima, Martin Lehmann, Fan Liu.
      The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
    DOI:  https://doi.org/10.1038/s41467-024-47569-x
  7. Free Radic Biol Med. 2024 Apr 12. pii: S0891-5849(24)00385-X. [Epub ahead of print]
    RNF31 alleviates liver steatosis by promoting p53/BNIP3-related mitophagy in hepatocytes.
    Yifei Chen, Fuji Yang, Yujie Shi, Jingyu Sheng, Yanjin Wang, Liting Zhang, Jing Zhou, Yi Jin, Yongmin Yan.
       BACKGROUND & AIMS: Non-alcoholic fatty liver disease (NAFLD) is one of the liver illnesses that may be affected by mitophagy, which is the selective removal of damaged mitochondria. RNF31, an E3 ubiquitin ligase, is carcinogenic in many malignancies. However, the influence of RNF31 on mitochondrial homeostasis and NAFLD development remains unknown.
    METHODS: Oleic-palmitic acid treated hepatocytes and high-fat diet (HFD)-fed mice were established to observe the effect of RNF31 on hepatocyte mitophagy and steatosis. Mitophagy processes were comprehensively assessed by mt-Keima fluorescence imaging, while global changes in hepatic gene expression were measured by RNA-seq.
    RESULTS: The present study discovered a reduction in RNF31 expression in lipotoxic hepatocytes with mitochondrial dysfunction. The observed decrease in RNF31 expression was associated with reduced mitochondrial membrane potential, disturbed mitophagy, and increased steatosis. Additionally, the findings indicated that RNF31 is a pivotal factor in the initiation of mitophagy and the facilitation of mitochondrial homeostasis, resulting in a decrease in steatosis in lipotoxic hepatocytes. Mechanistically, RNF31 enhanced p53 ubiquitination and subsequent proteasomal degradation. Down-regulation of p53 led to increased expression of the mitophagy receptor protein BCL2 and adenovirus E1B 19 kDa-interacting protein 3 (BNIP3), thereby promoting mitophagy in hepatocytes. Furthermore, it was demonstrated that the transportation of RNF31 via small extracellular vesicles derived from mesenchymal stem cells (referred to as sEV) had a substantial influence on reducing hepatic steatosis and restoring liver function in HFD-fed mice.
    CONCLUSIONS: The findings highlight RNF31's essential role in the regulation of mitochondrial homeostasis in hepatocytes, emphasizing its potential as a therapeutic target for NAFLD.
    Keywords:  Extracellular vesicles; Mitophagy; RNF31; Steatosis
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.04.214
  8. Sci Adv. 2024 Apr 19. 10(16): eadl3063
    Positioning regulation of organelle network via Chinese microneedle.
    Feng Lin, Lei Xiang, Longxi Wu, Yupu Liu, Qinzhe Jiang, Lianfu Deng, Wenguo Cui.
      The organelle network is a key factor in the repair and regeneration of lesion. However, effectively intervening in the organelle network which has complex interaction mechanisms is challenging. In this study, on the basis of electromagnetic laws, we constructed a biomaterial-based physical/chemical restraint device. This device was designed to jointly constrain electrical and biological factors in a conductive screw-threaded microneedle (ST-needle) system, identifying dual positioning regulation of the organelle network. The unique physical properties of this system could accurately locate the lesion and restrict the current path to the lesion cells through electromagnetic laws, and dynamic Van der Waals forces were activated to release functionalized hydrogel microspheres. Subsequently, the mitochondria-endoplasmic reticulum (ER) complex was synergistically targeted by increasing mitochondrial ATP supply to the ER via electrical stimulation and by blocking calcium current from the ER to the mitochondria using microspheres, and then the life activity of the lesion cells was effectively restored.
    DOI:  https://doi.org/10.1126/sciadv.adl3063
  9. Methods Mol Biol. 2024 ;2782 113-122
    Endothelial Mitochondria-Associated Membranes (MAMs) Isolation by Percoll Step Gradients.
    Margaret Baldini, Cheng Zhang, Jun Yu.
      Mitochondria-associated membranes (MAMs) are regions where the endoplasmic reticulum (ER) interacts with mitochondria and regulate lipid trafficking, calcium signaling, ER stress, and inflammation activation. Isolation of MAMs from endothelial cells is vital for studying insight into the immune regulation of many inflammatory diseases. Endothelial cells (ECs) are critical innate immune cells due to their paracrine function of secreting interleukins, chemokines, cytokines, and growth factors, as well as expressing levels of pattern recognition receptors including toll-like receptors (TLRs). Furthermore, ECs regulate and recruit monocytes by expressing adhesion molecules including vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), P-selectin, and E-selectin, to facilitate monocyte diapedesis in areas of damage and inflammation. This protocol consists of step-by-step instructions on isolating pure MAMs and other subcellular fractions from endothelial cells, which is critical to understanding ER and mitochondria crosstalks in endothelial functions in health and disease.
    Keywords:  Endoplasmic reticulum; Endothelial cells; Immunity; Inflammation; Mitochondria; Mitochondria-associated membranes; Subcellular fractions
    DOI:  https://doi.org/10.1007/978-1-0716-3754-8_8
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