bims-mecosi 2024-10-13 papers

bims-mecosi

Biomed News

on Membrane contact sites

Issue of 2024–10–13
nine papers selected by
Verena Kohler, Umeå University

Crosstalk between mitochondria-ER contact sites and the apoptotic machinery as a novel health meter.
Imaging and proteomics toolkits for studying organelle contact sites.
The lysosomal lipid transporter LIMP-2/SCARB2 is part of lysosome-endoplasmic reticulum STARD3-VAPB-dependent contact sites.
CISD2 counteracts the inhibition of ER-mitochondrial calcium transfer by anti-apoptotic BCL-2.
ER-mitochondria distance is a critical parameter for efficient mitochondrial Ca2+ uptake and oxidative metabolism.
TBC1D15-regulated mitochondria-lysosome membrane contact exerts neuroprotective effects by alleviating mitochondrial calcium overload in seizure.
Better Together: Interorganellar Communication in the Regulation of Proteostasis.
Mitochondrial apolipoprotein MIC26 is a metabolic rheostat regulating central cellular fuel pathways.
Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM.

Trends Cell Biol. 2024 Oct 07. pii: S0962-8924(24)00185-5. [Epub ahead of print]

Crosstalk between mitochondria-ER contact sites and the apoptotic machinery as a novel health meter.

Alvaro Larrañaga-SanMiguel, Nora Bengoa-Vergniory, Hector Flores-Romero.

  Mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) function as transient signaling platforms that regulate essential cellular functions. MERCS are enriched in specific proteins and lipids that connect mitochondria and the ER together and modulate their activities. Dysregulation of MERCS is associated with several human pathologies including Alzheimer's disease (AD), Parkinson's disease (PD), and cancer. BCL-2 family proteins can locate at MERCS and control essential cellular functions such as calcium signaling and autophagy in addition to their role in mitochondrial apoptosis. Moreover, the BCL-2-mediated apoptotic machinery was recently found to trigger cGAS-STING pathway activation and a proinflammatory response, a recognized hallmark of these diseases that requires mitochondria-ER interplay. This review underscores the pivotal role of MERCS in regulating essential cellular functions, focusing on their crosstalk with BCL-2 family proteins, and discusses how their dysregulation is linked to disease.

Keywords:  MAMs; MERCS; apoptosis; cancer; inflammation; neurodegeneration

DOI:  https://doi.org/10.1016/j.tcb.2024.08.007
Front Cell Dev Biol. 2024 ;12 1466915

Imaging and proteomics toolkits for studying organelle contact sites.

Rico Gamuyao, Chi-Lun Chang.

  Organelle contact sites are regions where two heterologous membranes are juxtaposed by molecular tethering complexes. These contact sites are important in inter-organelle communication and cellular functional integration. However, visualizing these minute foci and identifying contact site proteomes have been challenging. In recent years, fluorescence-based methods have been developed to visualize the dynamic physical interaction of organelles while proximity labeling approaches facilitate the profiling of proteomes at contact sites. In this review, we explain the design principle for these contact site reporters: a dual-organelle interaction mechanism based on how endogenous tethers and/or tethering complexes localize to contact sites. We classify the contact site reporters into three categories: (i) single-protein systems, (ii) two-component systems with activated reporter signal upon organelle proximity, and (iii) reporters for contact site proteomes. We also highlight advanced imaging analysis with high temporal-spatial resolution and the use of machine-learning algorithms for detecting contact sites.

Keywords:  bimolecular complementation; electron microscopy; light microscopy; organelle contact sites; proximity labeling; split fluorescent protein; split-TurboID; splitFAST

DOI:  https://doi.org/10.3389/fcell.2024.1466915
J Cell Sci. 2024 Oct 07. pii: jcs.261810. [Epub ahead of print]

The lysosomal lipid transporter LIMP-2/SCARB2 is part of lysosome-endoplasmic reticulum STARD3-VAPB-dependent contact sites.

Sönke Rudnik, Saskia Heybrock, Etienne Coyaud, Zizhen Xu, Dante Neculai, Brian Raught, Viola Oorschot, Cecilia Heus, Judith Klumperman, Paul Saftig.

  SCARB2/LIMP-2 is an abundant lysosomal membrane protein. Previous studies have shown LIMP-2 functions as a virus receptor, a chaperone for lysosomal enzyme targeting, and a lipid transporter. The large luminal domain of LIMP-2 contains a hydrophobic tunnel that enables transport of phospholipids, sphingosine and cholesterol from the lysosomal lumen to the membrane. The question about the fate of the lipids after LIMP-2-mediated transport is largely unexplored. To elucidate whether LIMP-2 is part of contact sites between lysosomes and the endoplasmic reticulum (ER), we performed a proximity-based interaction screen. This revealed that LIMP-2 interacts with the endosomal protein STARD3 and the ER-resident protein VAPB. Using imaging and co-immunoprecipitation, we demonstrated colocalization and physical interaction between LIMP-2 and these proteins. Moreover, we found that interaction of LIMP-2 with VAPB required the presence of STARD3. Our findings suggest that LIMP-2 is part of ER-lysosome contact sites, possibly facilitating cholesterol transport from the lysosomal to the ER membrane. This suggests a novel mechanism for inter-organelle communication and lipid trafficking mediated by LIMP-2.

Keywords:  Endoplasmic reticulum; LIMP-2; Lysosome; Membrane contact sites; SCARB2; STARD3; VAPB

DOI:  https://doi.org/10.1242/jcs.261810
Biochim Biophys Acta Mol Cell Res. 2024 Oct 04. pii: S0167-4889(24)00200-3. [Epub ahead of print]1872(1): 119857

CISD2 counteracts the inhibition of ER-mitochondrial calcium transfer by anti-apoptotic BCL-2.

Jens Loncke, Ian de Ridder, Justin Kale, Larry Wagner, Allen Kaasik, Jan B Parys, Martijn Kerkhofs, David W Andrews, David Yule, Tim Vervliet, Geert Bultynck.

  CISD2, a 2Fe2S cluster domain-containing protein, is implicated in Wolfram syndrome type 2, longevity and cancer. CISD2 is part of a ternary complex with IP3 receptors (IP3Rs) and anti-apoptotic BCL-2 proteins and enhances BCL-2's anti-autophagic function. Here, we examined how CISD2 impacted the function of BCL-2 in apoptosis and in controlling IP3R-mediated Ca2+ signaling. Using purified proteins, we found a direct interaction between the cytosolic region of CISD2 and BCL-2's BH4 domain with a submicromolar affinity. At the functional level, the cytosolic region of CISD2, as a purified protein, did not affect the ability of BCL-2 to inhibit BAX-pore formation. In a cellular context, loss of CISD2 did not impede the suppression of apoptosis by BCL-2. Also, in Ca2+-signaling assays, absence of CISD2 did not affect the inhibition of IP3R-mediated Ca2+ release by BCL-2. Combined, these experiments indicate that CISD2 is not essential for BCL-2 function in apoptosis and cytosolic Ca2+ signaling. Instead, CISD2 overexpression enhanced BCL-2-mediated suppression of cytosolic IP3R-mediated Ca2+ release. However, consistent with the presence of CISD2 and BCL-2 at mitochondria-associated ER membranes (MAMs), the most striking effect was observed at the level of ER-mitochondrial Ca2+ transfer. While BCL-2 overexpression inhibited ER-mitochondrial Ca2+ transfer, overexpression of CISD2 together with BCL-2 abrogated the effect of BCL-2. The underlying mechanism is linked to ER-mitochondrial contact sites, since BCL-2 reduced ER-mitochondrial contact sites while co-expression of CISD2 together with BCL-2 abolished this effect. These findings reveal a unique interplay between BCL-2 and CISD2 at Ca2+-signaling nanodomains between ER and mitochondria.

Keywords:  BCL-2; Calcium signaling; IP(3) receptor; Iron‑sulfur cluster proteins; Naf-1

DOI:  https://doi.org/10.1016/j.bbamcr.2024.119857
Commun Biol. 2024 Oct 10. 7(1): 1294

ER-mitochondria distance is a critical parameter for efficient mitochondrial Ca2+ uptake and oxidative metabolism.

Giulia Dematteis, Laura Tapella, Claudio Casali, Maria Talmon, Elisa Tonelli, Simone Reano, Adele Ariotti, Emanuela Pessolano, Justyna Malecka, Gabriela Chrostek, Gabrielė Kulkovienė, Danielius Umbrasas, Carla Distasi, Mariagrazia Grilli, Graham Ladds, Nicoletta Filigheddu, Luigia Grazia Fresu, Katsuhiko Mikoshiba, Carlos Matute, Paula Ramos-Gonzalez, Aiste Jekabsone, Tito Calì, Marisa Brini, Marco Biggiogera, Fabio Cavaliere, Riccardo Miggiano, Armando A Genazzani, Dmitry Lim.

IP3 receptor (IP3R)-mediated Ca2+ transfer at the mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) drives mitochondrial Ca2+ uptake and oxidative metabolism and is linked to different pathologies, including Parkinson's disease (PD). The dependence of Ca2+ transfer efficiency on the ER-mitochondria distance remains unexplored. Employing molecular rulers that stabilize ER-mitochondrial distances at 5 nm resolution, and using genetically encoded Ca2+ indicators targeting the ER lumen and the sub-mitochondrial compartments, we now show that a distance of ~20 nm is optimal for Ca2+ transfer and mitochondrial oxidative metabolism due to enrichment of IP3R at MERCS. In human iPSC-derived astrocytes from PD patients, 20 nm MERCS were specifically reduced, which correlated with a reduction of mitochondrial Ca2+ uptake. Stabilization of the ER-mitochondrial interaction at 20 nm, but not at 10 nm, fully rescued mitochondrial Ca2+ uptake in PD astrocytes. Our work determines with precision the optimal distance for Ca2+ flux between ER and mitochondria and suggests a new paradigm for fine control over mitochondrial function.

DOI: https://doi.org/10.1038/s42003-024-06933-9
Sci Rep. 2024 10 10. 14(1): 23782

TBC1D15-regulated mitochondria-lysosome membrane contact exerts neuroprotective effects by alleviating mitochondrial calcium overload in seizure.

Yinyin Xie, Wanwan Zhang, Tingting Peng, Xiaoyi Wang, Xiaolei Lian, Jiao He, Cui Wang, Nanchang Xie.

  Mitochondrial calcium overload plays an important role in the neurological insults in seizure. The Rab7 GTPase-activating protein, Tre-2/Bub2/Cdc16 domain family member 15 (TBC1D15), is involved in the regulation of mitochondrial calcium dynamics by mediating mitochondria-lysosome membrane contact. However, whether TBC1D15-regulated mitochondria-lysosome membrane contact and mitochondrial calcium participate in neuronal injury in seizure is unclear. We aimed to investigate the effect of TBC1D15-regulated mitochondria-lysosome membrane contact on epileptiform discharge-induced neuronal damage and further explore the underlying mechanism. Lentiviral vectors (Lv) infection and stereotaxic adeno-associated virus (AAV) injection were used to regulate TBC1D15 expression before establishing in vitro epileptiform discharge and in vivo status epilepticus (SE) models. TBC1D15's effect on inter-organellar interactions, mitochondrial calcium levels and neuronal injury in seizure was evaluated. The results showed that abnormalities in mitochondria-lysosome membrane contact, mitochondrial calcium overload, mitochondrial dysfunction, increased levels of reactive oxygen species, and prominent neuronal damage were partly relieved by TBC1D15 overexpression, whereas TBC1D15 knockdown markedly deteriorated these phenomena. Further examination revealed that epileptiform discharge-induced mitochondrial calcium overload in primary hippocampal neurons was closely associated with abnormal mitochondria-lysosome membrane contact. This study highlights the crucial role played by TBC1D15-regulated mitochondria-lysosome membrane contact in epileptiform discharge-induced neuronal injury by alleviating mitochondrial calcium overload.

Keywords:  Mitochondrial calcium overload; Mitochondria–lysosome membrane contact; Seizure; TBC1D15

DOI:  https://doi.org/10.1038/s41598-024-74388-3
Contact (Thousand Oaks). 2024 Jan-Dec;7:7 25152564241272245

Better Together: Interorganellar Communication in the Regulation of Proteostasis.

Andreas Kohler, Verena Kohler.

  An extensive network of chaperones and folding factors is responsible for maintaining a functional proteome, which is the basis for cellular life. The underlying proteostatic mechanisms are not isolated within organelles, rather they are connected over organellar borders via signalling processes or direct association via contact sites. This review aims to provide a conceptual understanding of proteostatic mechanisms across organelle borders, not focussing on individual organelles. This discussion highlights the precision of these finely tuned systems, emphasising the complicated balance between cellular protection and adaptation to stress. In this review, we discuss widely accepted aspects while shedding light on newly discovered perspectives.

Keywords:  calcium; chaperones; protein homeostasis; protein misfolding; reactive oxygen species; stress response

DOI:  https://doi.org/10.1177/25152564241272245
Life Sci Alliance. 2024 Dec;pii: e202403038. [Epub ahead of print]7(12):

Mitochondrial apolipoprotein MIC26 is a metabolic rheostat regulating central cellular fuel pathways.

Melissa Damiecki, Ritam Naha, Yulia Schaumkessel, Philipp Westhoff, Nika Atanelov, Anja Stefanski, Patrick Petzsch, Kai Stühler, Karl Köhrer, Andreas Pm Weber, Ruchika Anand, Andreas S Reichert, Arun Kumar Kondadi.

Mitochondria play central roles in metabolism and metabolic disorders such as type 2 diabetes. MIC26, a mitochondrial contact site and cristae organising system complex subunit, was linked to diabetes and modulation of lipid metabolism. Yet, the functional role of MIC26 in regulating metabolism under hyperglycemia is not understood. We used a multi-omics approach combined with functional assays using WT and MIC26 KO cells cultured in normoglycemia or hyperglycemia, mimicking altered nutrient availability. We show that MIC26 has an inhibitory role in glycolysis and cholesterol/lipid metabolism under normoglycemic conditions. Under hyperglycemia, this inhibitory role is reversed demonstrating that MIC26 is critical for metabolic adaptations. This is partially mediated by alterations of mitochondrial metabolite transporters. Furthermore, MIC26 deletion led to a major metabolic rewiring of glutamine use and oxidative phosphorylation. We propose that MIC26 acts as a metabolic "rheostat," that modulates mitochondrial metabolite exchange via regulating mitochondrial cristae, allowing cells to cope with nutrient overload.

DOI: https://doi.org/10.26508/lsa.202403038
bioRxiv. 2024 Sep 28. pii: 2024.09.28.615015. [Epub ahead of print]

Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM.

Michael G Hanna, Hely O Rodriguez Cruz, Kenshiro Fujise, Zhuonging Li, Mara Monetti, Pietro De Camilli.

Recent studies have identified a family of rod-shaped proteins which includes VPS13 and ATG2 and are thought to mediate unidirectional lipid transport at intracellular membrane contacts by a bridge-like mechanism. Here, we show that one such protein, BLTP3A/UHRF1BP1, associates with VAMP7-positive vesicles via its C-terminal region and anchors them to lysosomes via the binding of its chorein domain containing N-terminal region to Rab7. Upon damage of lysosomal membranes and resulting mATG8 recruitment to their surface by CASM, BLTP3A first dissociates from lysosomes but then reassociates with them via an interaction of its LIR motif with mATG8. Such interaction is mutually exclusive to the binding of BLTP3A to vesicles and leaves its N-terminal chorein domain, i.e. the proposed entry site of lipids into this family of proteins, available for binding to another membrane, possibly the ER. Our findings reveal that BLTP3A is an effector CASM, potentially as part of a mechanism to help repair or minimize lysosome damage by delivering lipids.

DOI: https://doi.org/10.1101/2024.09.28.615015