bims-mecosi 2025-06-08 papers

bims-mecosi

Biomed News

on Membrane contact sites

Issue of 2025–06–08
eight papers selected by
Verena Kohler, Umeå University

Identification of ER:Melanosome Membrane Contact Sites in the Retinal Pigment Epithelium.
ATG9A and ARFIP2 cooperate to control PI4P levels for lysosomal repair.
Concerted transport and phosphorylation of diacylglycerol at ER-PM contact sites regulate phospholipid dynamics during stress.
Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice.
Thymoquinone alleviates myocardial ischemia/reperfusion injury by stabilizing mitochondria-associated membrane homeostasis via targeting ATAD3A.
Identification and Validation of Key Genes Involved in the Coupling of Mitochondria-Associated Endoplasmic Reticulum Membrane in Hemorrhoidal Disease.
METTL3-mediated m6A modification of FUNDC1/IP3R2 pathway facilitates cardiac hypertrophy in obesity hypertension.
Plant NETWORKED and VAP27 Proteins Work in Complexes to Regulate Membrane-Based Functions.

Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251340949

Identification of ER:Melanosome Membrane Contact Sites in the Retinal Pigment Epithelium.

Burgoyne T, Doncheva D, Eden E R.

  The retinal pigment epithelium (RPE) forms a monolayer of cells at the blood:retina interface that plays important roles for photoreceptor renewal and function and is central to retinal health. RPE pigment is provided by melanin-containing melanosomes which offer protection against light and oxidative stress. Melanosome migration into the apical processes of the RPE following light onset is thought to contribute to preventing retinal degeneration with age, though the mechanism is not yet clear. Melanosomes are transported along microtubules to the apical surface where they are transferred to actin filaments within the apical processes. Melanosomes are lysosome-related organelles derived from endosomes and endosome transport along microtubules is heavily influenced by the endoplasmic reticulum (ER) through ER:endosome contact sites. Here we describe extensive connection between the ER and melanosomes in the RPE. We further show, in skin melanocytes, that the ER forms contact sites with all stages of melanosome maturation, but ER contact is reduced as melanosomes mature. Finally, we identify tripartite contact sites between the ER, melanosomes and mitochondria in both RPE tissue and cellular models, suggesting that the ER may influence melanosome biogenesis, maturation and interaction with mitochondria.

Keywords:  RPE; contact sites; electron microscopy; endoplasmic reticulum; melanosomes

DOI:  https://doi.org/10.1177/25152564251340949
Dev Cell. 2025 May 27. pii: S1534-5807(25)00318-1. [Epub ahead of print]

ATG9A and ARFIP2 cooperate to control PI4P levels for lysosomal repair.

Stefano De Tito, Eugenia Almacellas, Daniel Dai Yu, Emily Millard, Wenxin Zhang, Cecilia de Heus, Christophe Queval, Javier H Hervás, Enrica Pellegrino, Ioanna Panagi, Ditte Fogde, Teresa L M Thurston, Judith Klumperman, Maximiliano Gutierrez, Sharon A Tooze.

  Lysosome damage activates multiple pathways to prevent lysosome-dependent cell death, including a repair mechanism involving endoplasmic reticulum (ER)-lysosome membrane contact sites, phosphatidylinositol 4-kinase-2a (PI4K2A), phosphatidylinositol-4 phosphate (PI4P), and oxysterol-binding protein-like proteins (OSBPLs) lipid transfer proteins. PI4K2A localizes to the trans-Golgi network and endosomes, yet how it is delivered to damaged lysosomes remains unknown. During acute sterile damage and damage caused by intracellular bacteria, we show that ATG9A-containing vesicles perform a critical role in delivering PI4K2A to damaged lysosomes. ADP ribosylation factor interacting protein 2 (ARFIP2), a component of ATG9A vesicles, binds and sequesters PI4P on lysosomes, balancing OSBPL-dependent lipid transfer and promoting the retrieval of ATG9A vesicles through the recruitment of the adaptor protein complex-3 (AP-3). Our results identify a role for mobilized ATG9A vesicles and ARFIP2 in lysosome homeostasis after damage and bacterial infection.

Keywords:  AP-3; ARFIP2; ATG9A; PI4K2A; PI4P; autophagy; lysosomal damage; lysosome; membrane trafficking

DOI:  https://doi.org/10.1016/j.devcel.2025.05.007
Proc Natl Acad Sci U S A. 2025 Jun 10. 122(23): e2421334122

Concerted transport and phosphorylation of diacylglycerol at ER-PM contact sites regulate phospholipid dynamics during stress.

Selene Garcia-Hernandez, Jorge Morello-López, Richard Haslam, Vitor Amorim-Silva, José Moya-Cuevas, Rafael Catalá, Louise Michaelson, Jessica Pérez-Sancho, Vedrana Marković, Julio Salinas, Johnathan Napier, Yvon Jaillais, Noemí Ruiz-Lopez, Miguel A Botella.

  A universal response of plants to environmental stresses is the activation of plasma membrane (PM) phospholipase C, which hydrolyzes phosphoinositides to produce soluble inositol phosphate and diacylglycerol (DAG). Because of their conical shape, DAG amounts have to be tightly regulated or they can destabilize membranes. We previously showed that upon stress, Synaptotagmin1 (SYT1) transports DAG from the PM to the endoplasmic reticulum (ER) at ER-PM Contact Sites (CS). Here, we addressed the fate of the incoming DAG in the ER. We show that diacylglycerol kinases (DGKs) DGK1 and DGK2 form a module with SYT1 functionally coupling DAG transport and phosphorylation at ER-PM CS. Although SYT1 and DGK1/DGK2 do not show exclusive ER-PM CS localization, their interaction occurs specifically at ER-PM CS and the removal of ER-PM CS abolishes the interaction. Lipidomic analysis of a dgk1dgk2 double mutant supports that DGK1 and DGK2 phosphorylate DAG at the ER and transcriptomic and phenotypic analyses indicate that SYT1 and DGK1/DGK2 are functionally related. Taken together, our results highlight a mechanism at ER-PM CS that coordinates the transfer of DAG from the PM to the ER by SYT1 upon stress and the concomitant phosphorylation of DAG by DGK1 and DGK2 at the ER. These findings underscore the critical role of spatial coordination in lipid metabolism during stress-induced membrane remodeling.

Keywords:  DAG; PI cycle; abiotic stress; contact sites; signaling

DOI:  https://doi.org/10.1073/pnas.2421334122
bioRxiv. 2025 May 13. pii: 2025.05.09.653147. [Epub ahead of print]

Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice.

Peng Xu, Rubia Isler Mancuso, Marianna Leonzino, Caroline J Zeiss, Diane S Krause, Pietro De Camilli.

VPS13 is the founding member of a family of proteins that mediate lipid transfer at intracellular membrane contact sites by a bridge-like mechanism. Mammalian genomes comprise 4 VPS13 genes encoding proteins with distinct localizations and function. The gene duplication resulting in VPS13A and VPS13C is the most recent in evolution and, accordingly, these two proteins are the most similar to each other. However, they have distinct subcellular localizations and their loss of function mutations in humans are compatible with life but result in two different age-dependent neurodegenerative diseases, chorea-acanthocytosis and Parkinson's disease, respectively. Thus, it remains unclear whether these two proteins have overlapping functions. Here, we show that while Vps13a KO and Vps13c KO mice are viable, embryonic development of Vps13a/Vps13c double knockout (DKO) mice is arrested at midgestation. Prior to death, DKO embryos were smaller than controls, were anemic and had a smaller liver, the key erythropoietic site at this developmental stage. Further analyses of erythroid precursor cells showed that their differentiation was impaired and that this defect was accompanied by activation of innate immunity as revealed by upregulation of interferon stimulated genes (ISGs). Additionally, the RIG-I and MDA5 components of dsRNA triggered innate immunity were found upregulated in the DKO fetal liver. Activation of innate immunity may result from loss of integrity of the membranes of intracellular organelles, such as mitochondria and autophagic lysosomes, due to the absence of these lipid transport proteins. The surprising and striking synthetic effect resulting for the combined loss of VPS13A and VPS13C suggests that despite of the different localization of these two proteins, the lipid fluxes that they mediate are partially redundant.

DOI: https://doi.org/10.1101/2025.05.09.653147
Phytomedicine. 2025 Jun 02. pii: S0944-7113(25)00552-5. [Epub ahead of print]143 156914

Thymoquinone alleviates myocardial ischemia/reperfusion injury by stabilizing mitochondria-associated membrane homeostasis via targeting ATAD3A.

Zeyu Li, Suiqing Huang, Li Luo, Jingxuan Zhang, Ou Hu, Zhongkai Wu, Peiqing Liu.

   BACKGROUND: Recent research has shown that regulating the homeostasis of mitochondria-associated endoplasmic reticulum membrane (MAM) to improve ER-mitochondrial communication holds promise for treating myocardial ischemia-reperfusion injury (MI/RI).
PURPOSE: This study aims to determine whether thymoquinone (TQ), a potential ATAD3A modulator, protects against MI/RI by regulating MAM-mediated ER-mitochondrial communication via the ATAD3A-PERK axis to preserve myocardial bioenergetics and inhibit endoplasmic reticulum stress (ERS).
METHODS: Left ventricular tissues from healthy donors and heart failure patients post-MI/R were analyzed. In vivo MI/R models were established using C57BL/6 mice, with cardiac-specific ATAD3A overexpression achieved via AAV9-cTnT transduction. In vitro models included adult mouse cardiomyocytes (AMCMs) and neonatal mouse cardiomyocytes (NMCMs) subjected to hypoxia/reoxygenation (H/R). TQ-ATAD3A binding was validated by surface plasmon resonance (SPR, Kd=18.6 μM) and cellular thermal shift assay (CETSA). MAM dynamics were quantified using proximity ligation assay, MAM-SplitGFP system, and electron microscopy. Proteomic profiling via immunoprecipitation-mass spectrometry (IP-MS) identified TQ-modulated ATAD3A interactors. ATAD3A-knockout (KO) rescue experiments with L368-mutant constructs clarified the functional binding site.
RESULTS: ATAD3A overexpression attenuated cardiomyocyte apoptosis, preserved cardiac function, and suppressed remodeling in MI/R models. Mechanistically, TQ stabilized ATAD3A protein via direct binding to its C-terminal L368 residue, enhancing ATAD3A-PERK interaction at MAMs. This axis preserved MAM integrity, blunted PERK/eIF2α-mediated ER stress, and restored mitochondrial bioenergetics. TQ treatment reduced reactive oxygen species (ROS) accumulation, stabilized mtDNA, and improved mitochondrial ultrastructure. Genetic ablation of ATAD3A-L368 or pharmacological inhibition of PERK negated TQ's protective effects.
CONCLUSION: This study establishes ATAD3A as a novel therapeutic target for MI/RI. TQ, as the first identified ATAD3A agonist, confers cardioprotection by reinforcing MAM-mediated ER-mitochondrial communication through the ATAD3A-PERK axis. These findings provide a mechanistic framework for developing MAM-targeted therapies in ischemic heart disease.

Keywords:  ATAD3A; ERS; Mitochondria-associated membranes MAM; Mitochondrial malfunction; Oxidative stress; PERK

DOI:  https://doi.org/10.1016/j.phymed.2025.156914
Int J Gen Med. 2025 ;18 2781-2798

Identification and Validation of Key Genes Involved in the Coupling of Mitochondria-Associated Endoplasmic Reticulum Membrane in Hemorrhoidal Disease.

Lihua Mao, Zhiying Rao, Yanru Wang, Jun Yang, Junmei He, Zhi Zheng, Lanyu Chen.

   Background: Hemorrhoidal disease (HD) is the most prevalent rectal disorder, with various cellular processes influenced by the mitochondria-associated endoplasmic reticulum membrane (MAM). Potential therapeutic mechanisms for HD may be associated with MAM. This study aims to identify key genes linked to MAM in HD and to provide novel therapeutic targets.
Methods: Transcriptome data and MAM-related genes (MAM-RGs) were obtained from the Gene Expression Omnibus (GEO) database and relevant literature. Differential expression analysis and single-sample Gene Set Enrichment Analysis (ssGSEA) scores were initially employed to identify candidate genes. Key genes were further refined using Least Absolute Shrinkage and Selection Operator (LASSO) and Protein-Protein Interaction (PPI) networks. A nomogram based on these key genes was developed and assessed. Additionally, CIBERSORT algorithms were utilized to evaluate immune cell infiltration abundance, differences, and correlations in the samples. Finally, the expression of key genes was validated via reverse transcription-quantitative PCR (RT-qPCR).
Results: Differential expression analysis identified 956 differentially expressed genes (DEGs), and ssGSEA identified 143 differentially expressed MAM-RGs. A total of 50 candidate genes were selected through their intersection. Machine learning identified two key genes, MUC16 and DEFA5. A nomogram with strong predictive capability was constructed. Immune cell analysis revealed two types of differential immune cells-activated dendritic cells and plasma cells-where activated dendritic cells were more highly expressed in the case group, and plasma cells showed a strong positive correlation with DEFA5. Additionally, MUC16 was significantly overexpressed in patients with HD, while DEFA5 exhibited down-regulation compared to controls.
Conclusion: This study identifies MUC16 and DEFA5 as key genes associated with HD and MAM and presents a predictive nomogram with high accuracy. These findings provide novel insights into the mechanisms and potential treatment targets for HD.

Keywords:  hemorrhoidal disease; immune infiltration; mitochondria-associated endoplasmic reticulum membrane; nomogram

DOI:  https://doi.org/10.2147/IJGM.S511281
Life Sci. 2025 May 30. pii: S0024-3205(25)00415-1. [Epub ahead of print]377 123780

METTL3-mediated m6A modification of FUNDC1/IP3R2 pathway facilitates cardiac hypertrophy in obesity hypertension.

Yulong Ma, Da Li, Xunjie Zhou, Xiaozhe Chen, Chunlei Hou, Yunfeng Li, Yuxiu Zhao, Mingtai Gui, Lei Yao, Jianhua Li, Mingzhu Wang, Deyu Fu, Bo Lu.

   BACKGROUND: FUNDC1-mediated mitochondria-associated endoplasmic reticulum membrane (MAM) Ca2+ conduction is crucial in cardiac hypertrophy. N6-methyladenosine (m6A) methylation, a crucial mRNA modification, is implicated in this process. We hypothesise that m6A regulation of FUNDC1-mediated MAM-associated Ca2+ overload contributes to obesity hypertension (OBH) cardiac hypertrophy.
METHODS: We investigated OBH in spontaneously hypertensive rats fed a high-fat diet, with WKY rats as controls. Assessments included blood pressure, cardiac hypertrophy, pyroptosis, protein expression of MAM-related (FUNDC1, IP3R2) and m6A-related gene (METTL3, IGF2BP2). MeRIP assay detected m6A methylation in mRNA. We also examined cardiomyocyte morphology, viability, mitochondrial function (mtROS, SOD, MDA and ATP levels), and expression of pyroptosis-related factors (IL-1β, IL-18, NLRP3, GSDMD-N and Caspase-1/p10) in vitro. Silencing and overexpression of FUNDC1 and METTL3 clarified MAM effects on cardiac hypertrophy. FUNDC1 and IP3R2 interaction was assessed by co-immunoprecipitation.
RESULTS: OBH rats exhibited significantly elevated blood pressure, cardiac hypertrophy, MAM dysfunction, elevated FUNDC1, IP3R2 and METTL3 expression, and pyroptosis. Ang II treatment in vitro upregulated FUNDC1, causing mitochondrial dysfunction, inflammation and pyroptosis in cardiomyocytes. FUNDC1 knockdown improved cardiomyocyte morphology and function, reduced mitochondrial Ca2+ concentration, enhanced mitochondrial function and attenuated pyroptosis while increasing IP3R2 ubiquitination. Mito Tempo reversed cardiomyocyte hypertrophy, mitochondrial dysfunction, inflammatory response and pyroptosis induced by FUNDC1 overexpression. Additionally silencing METTL3 and IGF2BP2 reduced m6A methylation of FUNDC1, inhibiting its expression.
CONCLUSION: METTL3 regulates FUNDC1 m6A methylation modification via IGF2BP2, thereby affecting FUNDC1 expression. FUNDC1 binding to IP3R2 regulates MAM-associated Ca2+ overload, inducing mitochondrial dysfunction and pyroptosis, leading to cardiac hypertrophy in OBH.

Keywords:  Ca(2+) overload; Cardiac hypertrophy; Mitochondria-associated endoplasmic reticulum membrane; N6-methyladenosine; Obesity hypertension; Pyroptosis

DOI:  https://doi.org/10.1016/j.lfs.2025.123780
Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251342533

Plant NETWORKED and VAP27 Proteins Work in Complexes to Regulate Membrane-Based Functions.

Patrick J Duckney, Pengwei Wang, Patrick J Hussey.

  Eukaryotic cells are subdivided into specialised organelle compartments, each with unique physiological environments and functions. Interaction and cross-talk between organelles is inherent to Eukaryotic life, and each organelle is physically interconnected to their surrounding subcellular components including the cytoskeleton and adjacent membrane compartments. In animals and yeast, the mechanisms of organelle interaction have been well characterised and are known to have fundamental importance to life. In contrast, we are only beginning to understand the mechanisms and functions of such interactions in plants. The discovery and ongoing characterisation of the NETWORKED (NET) protein family of plant actin-membrane adaptors has greatly advanced our understanding of the mechanisms of organelle-cytoskeletal interaction. Furthermore, unfolding investigation into the NET proteins has revealed their binding partner, VAMP-ASSOCIATED PROTEIN-27 (VAP27), to be a regulator of organelle tethering and interaction with previously unknown, specialised roles in plants. Research on NET and VAP27 proteins has rapidly increased our knowledge of the mechanisms regulating membrane interaction in plants, their functions in regulating cell structure and organisation, as well as their importance to plant growth, development and stress-response. Here, we discuss the discovery and characterisation of the NET and VAP27 proteins, their regulation of organelle interaction and their functions in plants.

Keywords:  NET; VAP27; actin; autophagy; contact site; cytoskeleton; endoplasmic reticulum; membrane; organelle; plant

DOI:  https://doi.org/10.1177/25152564251342533