bims-mecosi 2026-02-15 papers

bims-mecosi

Biomed News

on Membrane contact sites

Issue of 2026–02–15
seven papers selected by
Verena Kohler, Umeå University

Tunable Chemical and Optical Control of ER-Plasma Membrane Contact Site Geometry and Dynamics with High-Fidelity Visualization.
STIM1-containing contact sites promote direct calcium flux from the endoplasmic reticulum to mitochondria.
Subcellular Lipid Trafficking and Membrane Specialization in Plants.
A2-pancortins interact with Bcl-xL and WAVE1 to promote mitochondria-ER contact sites (MERCs) and exacerbate mitochondrial calcium elevation to mediate cell death in stroke.
Subcellular proteomic analyses reveal REEP5 knockdown in the mouse heart disrupts mitochondrial networks.
The yeast peroxisomal proteome at absolute quantitative scale.
Mechanistic insights into Orai dynamics during pore opening.

bioRxiv. 2026 Jan 29. pii: 2026.01.28.701813. [Epub ahead of print]

Tunable Chemical and Optical Control of ER-Plasma Membrane Contact Site Geometry and Dynamics with High-Fidelity Visualization.

Shaoqing Zhang, Jinyu Fei, Yuanmin Zheng, Ruobo Zhou.

Endoplasmic reticulum-plasma membrane (ER-PM) contact sites are essential signaling hubs that regulate lipid transport, calcium homeostasis, and spatially organized signal transduction. Emerging evidence indicates that not only the presence but also the dynamics, stability, and geometry of ER-PM contacts critically shape cellular functions; however, tools that enable simultaneous high-fidelity visualization and reversible, quantitative control of these contacts in living cells remain limited. Here, we introduce a modular toolkit for inducible ER-PM contact-site reconstitution based on complementary chemical and optical dimerization strategies. We develop a nontoxic and reversible abscisic acid (ABA)-inducible system using the plant-derived ABIcs/PYLcs pair, and a rapidly reversible optogenetic system based on the iLID/SspB module, both of which allow robust visualization and dose-dependent control over contact-site formation kinetics, increasing contact-site density and total area fraction per cell without altering the size of individual contacts. In contrast, systematic variation of rigid α-helical linker length or inducible tether abundance selectively tunes the lateral growth, stability, and lifetime of individual contact sites, without changing their density. By combining these two orthogonal strategies, we achieve independent control of both individual contact-site size and overall contact-site density, providing complementary mechanisms to adjust total contact area per cell. This versatile platform enables quantitative dissection of ER-PM contact site structure-function relationships and offers broad utility in studies of lipid exchange, calcium signaling, membrane repair, metabolic regulation, and disease-relevant dysregulation.

DOI: https://doi.org/10.64898/2026.01.28.701813
EMBO J. 2026 Feb 11.

STIM1-containing contact sites promote direct calcium flux from the endoplasmic reticulum to mitochondria.

Yolanda Orantos-Aguilera, Irene Sanchez-Lopez, Carlos Pascual-Caro, Patricia Gómez-Suaga, Estela Area-Gomez, Eulalia Pozo-Guisado, Jorge Montesinos, Francisco Javier Martin-Romero.

  STIM1 is a transmembrane protein localized in the endoplasmic reticulum (ER), where it acts as a calcium ion sensor, activating store-operated Ca2+ entry upon ER Ca2+ depletion. Via cellular calcium influx, STIM1 is thought to indirectly affect mitochondrial calcium content. Here we show that STIM1 also interacts with mitochondrial proteins such as PTPIP51 and GRP75, suggesting its presence in mitochondria-associated ER membranes (MAMs), which are specialized ER regions that facilitate ER-mitochondria communication. Lowering STIM1 expression disrupts ER-to-mitochondria Ca2+ transfer, reduces basal mitochondrial Ca2+ levels, impairs maximal mitochondrial respiration, and reduces ATP production. The STIM1-GRP75 interaction depends on STIM1's Ca2+-sensing ability. ER Ca2+ depletion or the constitutive-open R429C mutation both reduce STIM1 binding to GRP75, suggesting that conformational changes in STIM1 play a role in this interaction. Deletion analysis revealed that the STIM1 (551-611) segment is crucial for GRP75 binding, as the peptide STIM1(551-611) binds GRP75, while STIM1(Δ551-611) shows reduced binding. These findings reveal a previously unrecognized role of STIM1 in direct inter-organelle communication.

Keywords:  Calcium; GRP75; MAM; Mitochondria; STIM1

DOI:  https://doi.org/10.1038/s44318-026-00700-8
Annu Rev Plant Biol. 2026 Feb 12.

Subcellular Lipid Trafficking and Membrane Specialization in Plants.

Cailin N Smith, Tegan M Haslam, Ivo Feussner, Rebecca L Roston.

Membrane lipid composition underpins the structural and functional identity of all plant membranes. This review examines membrane lipid metabolism and trafficking, with an emphasis on how lipid diversity and interorganelle movement support plant cell function. We explore the biophysical and biochemical specialization of subcellular membranes, with discussion of the endoplasmic reticulum, plasma membrane, apoplastic vesicles and barriers, tonoplast, peroxisomes, mitochondria, plastids, and thylakoids. We review both vesicular and nonvesicular lipid transport pathways, including membrane contact sites. Particular attention is given to glycerolipids, including phospholipids and galactolipids, sphingolipids, sterols, and, to a lesser extent, fatty acid exchange. By focusing on mechanisms of lipid transfer and remodeling, this review synthesizes our understanding of subcellular membrane lipid composition in the context of dynamic cellular processes including cell plate expansion, environmental stress responses, and photosynthetic membrane assembly.

DOI: https://doi.org/10.1146/annurev-arplant-063025-114143
Sci Rep. 2026 Feb 12.

A2-pancortins interact with Bcl-xL and WAVE1 to promote mitochondria-ER contact sites (MERCs) and exacerbate mitochondrial calcium elevation to mediate cell death in stroke.

Qi Yang, Chen-Chi Wang, Tomohiro Matsuyama, Kazuki Kuroda, Min-Jue Xie, Misato Yasumura, Chao-Yuan Tsai, Yuichiro Oka, Hideshi Yagi, Makoto Sato.

Pancortin (PCT), a protein highly expressed in the cortex during neurodevelopment, comprises four isoforms (PCT1-4) characterized by a central B-region and N-termini (A1/A2) and C-termini (C1/C2). While PCT2, enriched in adult mouse cortex, mediates ischemic neuronal death via interactions with WAVE1 and Bcl-xL, perinatal isoforms (A2-PCTs, namely PCT3 and PCT4) remain poorly defined. Given the vulnerability of the developing brain to hypoxia-induced neurological deficits, here we asked whether A2-PCTs contribute to ischemic damage in the developing cortex. In primary cortical neurons, knockdown of PCTs mitigated cell death induced by oxygen-glucose deprivation. Consistently, using A2-PCTs knockout mice subjected to middle cerebral artery occlusion, we observed significantly reduced cortical damage in younger animals, implicating A2-PCTs as pro-death factors in hypoxic conditions. Mechanistically, A2-PCTs formed a tripartite complex with Bcl-xL and WAVE1. Overexpression of A2-PCTs in HEK293 cells resulted in elevated cell mortality, and as revealed by SPLICS (a split-GFP-based contact site sensor)-based imaging of mitochondria-ER contact sites (MERCs), increased its localization to MERCs. Furthermore, A2-PCTs interacted with GRP75, a MERCs-tethering protein, in a Bcl-xL/WAVE1-dependent manner. A2-PCTs/Bcl-xL/WAVE1 complex increased IP3R-mediated calcium transfer from the ER to mitochondria, leading to cytosolic and mitochondrial calcium overload, which was attenuated by IP3R inhibition. In Neuro2a cells subjected to oxygen-glucose deprivation, PCTs knockdown similarly suppressed pathological calcium flux. Our study identifies A2-PCTs as key regulators of MERCs-mediated calcium dysregulation in neonatal stroke, pointing to their potential as therapeutic targets for mitigating ischemic brain injury in the developing brain.

DOI: https://doi.org/10.1038/s41598-026-38928-3
Mol Cell Proteomics. 2026 Feb 09. pii: S1535-9476(26)00022-8. [Epub ahead of print] 101527

Subcellular proteomic analyses reveal REEP5 knockdown in the mouse heart disrupts mitochondrial networks.

Michelle Di Paola, Cristine J Reitz, Uros Kuzmanov, Kateleen Jia, Anthony O Gramolini.

Receptor Expression-Enhancing Protein 5 (REEP5) is a cardiac-enriched, membrane-shaping protein localized to the sarco(endo)plasmic reticulum (SR/ER), where it supports membrane network architecture and cardiomyocyte function. While REEP5 has been implicated in calcium handling and contractility, its role in regulating inter-organelle communication and mitochondrial homeostasis remains less well-understood. In this study, we used recombinant adeno-associated virus serotype 9(rAAV9)-mediated shRNA knockdown of Reep5 in mouse hearts, combined with subcellular fractionation and data-independent acquisition mass spectrometry (DIA-MS), to define proteomic remodeling across microsomal (SR/ER), mitochondrial, and cytosolic compartments. Loss of REEP5 altered the composition of SR/ER membrane-shaping proteins, including upregulation of RTN4, ATL3, and CKAP4, suggesting a partial compensatory response. Microsomal, mitochondrial and cytosolic proteomes exhibited broad reorganization, with enrichment of proteins involved in redox adaptation and proteostasis, alongside depletion of mitochondrial import machinery and antioxidant enzymes. Imaging of isolated cardiomyocytes confirmed fragmented mitochondrial networks and increased reactive oxygen species (ROS), consistent with proteomic signatures of disrupted mitochondrial dynamics and oxidative stress. Gene ontology enrichment across all fractions highlighted widespread dysregulation in organelle-specific processes, including translation, protein localization, and metabolic remodeling. Notably, several altered pathways converged on mitochondria-associated membranes (MAMs), suggesting that REEP5 may support SR/ER-mitochondria tethering and functional crosstalk. These findings position REEP5 as a key regulator of organelle homeostasis in the heart and underscore how its loss disrupts mitochondrial integrity and inter-organelle communication across cellular compartments.

DOI: https://doi.org/10.1016/j.mcpro.2026.101527
Histochem Cell Biol. 2026 Feb 13. 164(1): 8

The yeast peroxisomal proteome at absolute quantitative scale.

Hirak Das, Silke Oeljeklaus, Renate Maier, Julian Bender, Bettina Warscheid.

  Peroxisomes are dynamic organelles vital for lipid metabolism and redox homeostasis. In Saccharomyces cerevisiae, the expression of peroxisomal proteins is tightly regulated in response to metabolic conditions. Here, we provide the first absolute quantification of the yeast peroxisomal proteome under peroxisome-inducing (oleate) and fermentative (glucose) conditions using a label-free mass spectrometry approach. We determined protein copy numbers for ~ 4500 proteins, including 99 peroxisomal and peroxisome-associated proteins. Our data reveal that the overall peroxisomal proteome is approximately threefold more abundant in oleate-grown cells, constituting 2.8% (2.01 × 106 protein copies) of the total proteome compared to 0.8% (6.67 × 105 protein copies) in glucose. Considering only peroxisomal core proteins, i.e., proteins exclusively or predominantly localized in peroxisomes, total copy numbers for peroxisomal proteins were even ninefold higher on oleate (0.9%, 6.29 × 105 protein copies) compared to glucose (0.1%, 7.78 × 104 protein copies), reflecting the necessity for peroxisomal functions such as fatty acid beta-oxidation. Enzymes of the beta-oxidation and glyoxylate cycle showed up to > 500-fold higher abundance in oleate. In contrast, core components of the peroxisomal protein import machinery (e.g., Pex5, Pex14) exhibited only moderate changes (~ 2- to 8-fold). In addition to metabolic enzymes and components of the peroxisomal protein import pathways, we provide copy number data for proteins involved in cellular stress response, peroxisome proliferation, division and organization, peroxisome-associated membrane contact sites, and metabolite transporter. Taken together, our dataset offers a quantitative framework of peroxisomal remodeling under different metabolic conditions and highlights the organelle's adaptive flexibility, providing a valuable resource for future studies on peroxisome biology.

Keywords:   Saccharomyces cerevisiae ; Absolute quantification; Mass spectrometry; Peroxisomes; Protein copy numbers; Proteomic ruler

DOI:  https://doi.org/10.1007/s00418-026-02458-w
Channels (Austin). 2026 Dec;20(1): 2624276

Mechanistic insights into Orai dynamics during pore opening.

Hadil Najjar, Veronika Aichner, Magdalena Prantl, Nora Müller, Heinrich Krobath, Isabella Derler.

  Orai channels form highly Ca2+-selective pores in the plasma membrane (PM) and represent one of the two essential components of the Ca2+ release-activated Ca2+ (CRAC) channel. The second component is the Stromal Interaction Molecule (STIM) proteins, which is located in the endoplasmic reticulum (ER). Ca2+ influx through CRAC channels serves as the primary route of Ca2+ entry into the cell, playing a critical role in downstream signaling pathways such as gene transcription and cell proliferation. Activation of Orai channels is tightly coupled to the depletion of ER Ca2+ stores, which triggers STIM proteins to oligomerize and adopt an extended conformation that spans the ER-PM junction, enabling direct interaction with and activation of Orai. Several studies have shown that Orai activation is mediated by global conformational changes across the entire channel complex. In recent years, detailed functional analyses, structural investigations, genetic code expansion techniques, and molecular dynamics simulations have further refined our understanding of the molecular mechanisms underlying Orai1 pore opening and the associated amino acid-level conformational dynamics. In this review, we highlight proposed mechanisms, dynamic features, and functionally relevant contact sites across the Orai1 channel complex that contribute to gating and ion permeation, while also summarizing outstanding questions that remain to be resolved.

Keywords:  Ion channels, SOCE; Orai1; STIM1; calcium (Ca2+), CRAC channels; inter- and intra-transmembrane domain contact sites, hydration, genetic code expansion, crosslinking; protein dynamics

DOI:  https://doi.org/10.1080/19336950.2026.2624276