bims-mecosi Biomed News
on Membrane contact sites
Issue of 2025–02–09
six papers selected by
Verena Kohler, Umeå University
  1. Moving the fat: Emerging roles of rab GTPases in the regulation of lipid droplet contact sites.
  2. Mitochondrial-ER Contact Sites and Tethers Influence the Biosynthesis and Function of Coenzyme Q.
  3. The Wheat NLR Protein PM3b Localises to Endoplasmic Reticulum-Plasma Membrane Contact Sites and Interacts With AVRPM3b2/c2 Through Its LRR Domain.
  4. Optimizing In Situ Proximity Ligation Assays for Mitochondria, ER, or MERC Markers in Skeletal Muscle Tissue and Cells.
  5. The ER-PM interaction is essential for cytokinesis and recruits the actin cytoskeleton through the SCAR/WAVE complex.
  6. Regulation of calcium signaling prevents neuronal death mediated by NIST DEP in xenoferroptotic cell death conditions.
  1. Curr Opin Cell Biol. 2025 Feb 01. pii: S0955-0674(25)00004-3. [Epub ahead of print]93 102466
    Moving the fat: Emerging roles of rab GTPases in the regulation of lipid droplet contact sites.
    Mariano Alonso-Bivou, Albert Pol, Harriet P Lo.
      Lipid droplets (LDs) play crucial roles in lipid metabolism, energy homeostasis, and cellular stress. Throughout their lifecycle, LDs establish membrane contact sites (MCSs) with the endoplasmic reticulum, mitochondria, peroxisomes, endosomes, lysosomes, and phagosomes. LD MCSs are dynamically generated in response to metabolic or immune cues to ensure that LD lipids (and proteins) are timely delivered to optimize valuable substrates and avoid lipotoxicity. It is increasingly evident that many Rab GTPases are involved in LD dynamics. Here, we summarize our current understanding of how and when Rab proteins dynamically drive the generation of LD MCSs and regulate a variety of LD functions.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102466
  2. Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251316350
    Mitochondrial-ER Contact Sites and Tethers Influence the Biosynthesis and Function of Coenzyme Q.
    Noelle Alexa Novales, Hadar Meyer, Yeynit Asraf, Maya Schuldiner, Catherine F Clarke.
      Coenzyme Q (CoQ) is an essential redox-active lipid that plays a major role in the electron transport chain, driving mitochondrial ATP synthesis. In Saccharomyces cerevisiae (yeast), CoQ biosynthesis occurs exclusively in the mitochondrial matrix via a large protein-lipid complex, the CoQ synthome, comprised of CoQ itself, late-stage CoQ-intermediates, and the polypeptides Coq3-Coq9 and Coq11. Coq11 is suggested to act as a negative modulator of CoQ synthome assembly and CoQ synthesis, as its deletion enhances Coq polypeptide content, produces an enlarged CoQ synthome, and restores respiration in mutants lacking the CoQ chaperone polypeptide, Coq10. The CoQ synthome resides in specific niches within the inner mitochondrial membrane, termed CoQ domains, that are often located adjacent to the endoplasmic reticulum-mitochondria encounter structure (ERMES). Loss of ERMES destabilizes the CoQ synthome and renders CoQ biosynthesis less efficient. Here we show that deletion of COQ11 suppresses the respiratory deficient phenotype of select ERMES mutants, results in repair and reorganization of the CoQ synthome, and enhances mitochondrial CoQ domains. Given that ER-mitochondrial contact sites coordinate CoQ biosynthesis, we used a Split-MAM (Mitochondrial Associated Membrane) artificial tether consisting of an ER-mitochondrial contact site reporter, to evaluate the effects of artificial membrane tethers on CoQ biosynthesis in both wild-type and ERMES mutant yeast strains. Overall, this work identifies the deletion of COQ11 as a novel suppressor of phenotypes associated with ERMES deletion mutants and indicates that ER-mitochondria tethers influence CoQ content and turnover, highlighting the role of membrane contact sites in regulating mitochondrial respiratory homeostasis.
    Keywords:  ER-mitochondrial encounter structure; artificial tether; coenzyme Q; mitochondria
    DOI:  https://doi.org/10.1177/25152564251316350
  3. Mol Plant Pathol. 2025 Feb;26(2): e70054
    The Wheat NLR Protein PM3b Localises to Endoplasmic Reticulum-Plasma Membrane Contact Sites and Interacts With AVRPM3b2/c2 Through Its LRR Domain.
    Jonatan Isaksson, Lukas Kunz, Simon Flückiger, Victoria Widrig, Beat Keller.
      Plant nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune receptors that directly or indirectly perceive pathogen-derived effector proteins to induce an immune response. NLRs display diverse subcellular localisations, which are associated with the capacity of the immune receptor to confer disease resistance and recognise its corresponding avirulence effector. In wheat, the NLR PM3b recognises the wheat powdery mildew effector AVRPM3b2/c2 and we examined the molecular mechanism underlying this recognition. We show that PM3b and other PM3 variants localise to endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (EPCS), while AVRPM3b2/c2 localises to the nucleocytoplasmic space. Additionally, we found that PM3b interacts in planta with AVRPM3b2/c2 through its LRR domain. We further demonstrate that full-length PM3b interaction with AVRPM3b2/c2 is considerably weaker than for the isolated PM3b LRR domain or the susceptible PM3 variant PM3CS, indicating that activation of PM3b leads to dissociation of the complex. In line with this, we observed a strong interaction between PM3b and AVRPM3b2/c2 in a P-loop mutant of PM3b that was unable to initiate a cell death response, or when an inactive variant of AVRPM3b2/c2 was used. We propose that PM3b transiently interacts with AVRPM3b2/c2 through residues in the LRR that are conserved among PM3 variants, while the amino acids necessary for full activation and cell death signalling are unique to PM3b. Our data suggests that PM3b localisation and interaction with AVRPM3b2/c2 differ from other well-studied NLRs and further highlights the mechanistic diversity in NLR-mediated responses against pathogens in plants.
    Keywords:  ER–PM contact sites; NLR; pathogen effector; plant immunity; plant–fungal interactions; powdery mildew; wheat
    DOI:  https://doi.org/10.1111/mpp.70054
  4. Curr Protoc. 2025 Feb;5(2): e70043
    Optimizing In Situ Proximity Ligation Assays for Mitochondria, ER, or MERC Markers in Skeletal Muscle Tissue and Cells.
    Amber Crabtree, Han Le, Chanel Harris, Ashton Oliver, Andy Barillas, Johnathan Moore, Desiree Ngoc-Ha Nguyen, Izabella Marie Rabago, Benjamin Rodriguez, Dominique C Stephens, Heather K Beasley, Edgar Garza-Lopez, Kit Neikirk, Margaret Mungai, Larry Vang, Zer Vue, Neng Vue, Andrea G Marshall, Kyrin Turner, Jianqiang Shao, Sandra Murray, Jennifer A Gaddy, Celestine Wanjalla, Jamaine Davis, Steven Damo, Antentor O Hinton.
      Proximity ligation assays (PLAs) use specific antibodies to detect endogenous protein-protein interactions. PLAs are a highly useful biochemical technique that allow two proteins within proximity to be visualized with fluorescent probes amplified by PCR. While this technique has gained prominence, the use of a PLA in mouse skeletal muscle (SkM) is novel. In this article, we discuss how the PLA method can be used in SkM to study the protein-protein interactions within mitochondria-endoplasmic reticulum contact sites (MERCs). © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Proximity ligation assay for skeletal muscle tissue and myoblast for MERC proteins.
    Keywords:  MERCs; Mfn1; Mfn2; mitochondria; protein‐protein interactions; proximity ligation assays; skeletal muscles
    DOI:  https://doi.org/10.1002/cpz1.70043
  5. Proc Natl Acad Sci U S A. 2025 Feb 11. 122(6): e2416927122
    The ER-PM interaction is essential for cytokinesis and recruits the actin cytoskeleton through the SCAR/WAVE complex.
    Zhijing Xu, Jingze Zang, Xintong Zhang, Qiwei Zheng, Yifan Li, Nadine Field, Jindriska Fiserova, Bing Hua, Xiaolu Qu, Verena Kriechbaumer, Michael J Deeks, Patrick J Hussey, Pengwei Wang.
      Plant cytokinesis requires coordination between the actin cytoskeleton, microtubules, and membranes to guide division plane formation and cell plate expansion; how these regulatory factors are coordinated remains unknown. The actin cytoskeleton assembly is controlled by several actin nucleation factors, such as the SCAR/WAVE complex, which regulates actin nucleation and branching through the activation of the ARP2/3 complex. The activity of these actin regulatory proteins is likely influenced by interactions with specific membranes; however, the molecular basis and the biological relevance of SCAR-membrane interactions are also unclear. In this study, we demonstrate that the ER-PM tethering protein VAP27-1 directly interacts with SCAR2 at the ER membrane and that they colocalize to guide cell plate orientation during cell division. In the root meristem, both VAP27-1 and SCAR2 exhibit polarized localization at the cell plates, where the interaction between ER and PM is abundant. VAP27-1 recruits SCAR2 to the cell division plane, where there is a high concentration of actin filaments. In the vap27-1346 mutant, the densities of cortical ER, SCAR2, and consequently actin filaments are significantly reduced at the cell division plane, affecting cell plate orientation, cell division, and root development. A similar phenomenon is also observed in the scar1234 mutant, suggesting that VAP27 and SCAR proteins regulate cell division through a similar pathway. In conclusion, our data reveal a plant-specific function of VAP27-regulated ER-PM interaction and advance our understanding of plant ER-PM contact site and its role in cell division.
    Keywords:  ER–PM contact sites; SCAR/WAVE complex; actin cytoskeleton; cytokinesis; endoplasmic reticulum
    DOI:  https://doi.org/10.1073/pnas.2416927122
  6. J Hazard Mater. 2025 Jan 25. pii: S0304-3894(25)00286-9. [Epub ahead of print]488 137374
    Regulation of calcium signaling prevents neuronal death mediated by NIST DEP in xenoferroptotic cell death conditions.
    Leshan Zhang, Hong Yan, Mohammad Saidur Rahman, Christina Ht J Mol-van der Veen, Ana Manzano Covarrubias, Karim Rafie, Diana Pendin, Martina Schmidt, Amalia M Dolga.
      Increased calcium levels are associated with the ferroptosis pathway in neurodegenerative conditions. Recent evidence showed that exposure to particulate matter (PM) could accelerate the pathology of neurodegenerative diseases. However, the molecular mechanisms of how PM could affect brain cell pathology is not fully understood. We hypothesized that diesel exhaust particles (NIST DEP) could alter the ferroptosis pathway through calcium signaling, and therefore accelerate the cell death pathway. In this study, we used mouse hippocampal neuronal-like HT22 cells to evaluate whether exposure to NIST DEP could accelerate RSL-3-induced ferroptosis by increasing calcium deregulation, mitochondrial dysfunction and reactive oxygen species (ROS). MTT assay results showed that NIST DEP (25, 50, 75, and 100 μg/mL) did not significantly reduce the survival rate of HT22 cells, while NIST DEP significantly increased RSL-3-induced ferroptotic cell death in a concentration-dependent manner. Based on fluorescence image analysis, co-exposure to NIST DEP and RSL-3 disrupted HT22 cell mitochondrial morphology, intracellular and mitochondrial calcium levels. Combined exposure resulted in an increase in ER-mitochondria contact sites measured by proximity ligation assay (PLA) compared to control solvent group. Additionally, lipid peroxidation, mitochondrial ROS and malondialdehyde content, were increased significantly by combined exposure to NIST DEP and RSL-3. Interestingly, the calcium regulators of the mitochondrial calcium uniporter MCUi4 and positive modulation of small conductance calcium-activated potassium channels by CyPPA significantly preserved cellular metabolic activity, restored calcium homeostasis, and alleviated fragmentation of mitochondria. Consequently, targeting calcium signaling may be promising therapeutic option for xenoferroptotic conditions in which PM affect cell survival.
    Keywords:  Calcium; Diesel exhaust particle; Mitochondria; Oxidative stress; Xenoferroptosis
    DOI:  https://doi.org/10.1016/j.jhazmat.2025.137374
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