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Srinivasan S, Álvarez D, John Peter AT, Vanni S. Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. J Cell Biol 2024; 223:e202312055. [PMID: 39105757 PMCID: PMC11303870 DOI: 10.1083/jcb.202312055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/29/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024] Open
Abstract
The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.
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Affiliation(s)
| | - Daniel Álvarez
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, España
| | - Arun T John Peter
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research Bio-inspired Materials, University of Fribourg , Fribourg, Switzerland
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2
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Wang X, Di W, Wang Z, Qi P, Liu Z, Zhao H, Ding W, Di S. Cadmium stress alleviates lipid accumulation caused by chiral penthiopyrad through regulating endoplasmic reticulum stress and mitochondrial dysfunction in zebrafish liver. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135560. [PMID: 39173367 DOI: 10.1016/j.jhazmat.2024.135560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The coexistence of cadmium (Cd) can potentiate (synergism) or reduce (antagonism) the pesticide effects on organisms, which may change with chiral pesticide enantiomers. Previous studies have reported the toxic effects of chiral penthiopyrad on lipid metabolism in zebrafish (Danio rerio) liver. The Cd effects and toxic mechanism on lipid accumulation were investigated from the perspective of endoplasmic reticulum (ER) stress and mitochondrial dysfunction. The coexistence of Cd increased the concentrations of penthiopyrad and its metabolites in zebrafish. Penthiopyrad exposure exhibited significant effects on lipid metabolism and mitochondrial function-related indicators, which were verified by lipid droplets and mitochondrial damage in subcellular structures. Moreover, penthiopyrad activated the genes of ER unfolded protein reaction (UPR) and Ca2+ permeable channels, and S-penthiopyrad exhibited more serious effects on ER stress with ER hyperplasia than R-penthiopyrad. As a mitochondrial uncoupler, the coexistence of Cd could decrease lipid accumulation by alleviating ER stress and mitochondrial dysfunction, and these effects were the most significant for R-penthiopyrad. There were antagonistic effects between Cd and penthiopyrad, which could reduce the damage caused by penthiopyrad in zebrafish, thus increasing the bioaccumulation of penthiopyrad in zebrafish. These findings highlighted the importance and necessity of evaluating the ecological risks of metal-chiral pesticide mixtures.
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Affiliation(s)
- Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Weixuan Di
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China; College of Plant Protection, Northeast agricultural university, Harbin 150030, PR China
| | - Zhiwei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Peipei Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Zhenzhen Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Huiyu Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Wei Ding
- College of Plant Protection, Northeast agricultural university, Harbin 150030, PR China
| | - Shanshan Di
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China.
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3
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Zheng T, Cai S. Recent technical advances in cellular cryo-electron tomography. Int J Biochem Cell Biol 2024; 175:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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4
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Hutchings J, Villa E. Expanding insights from in situ cryo-EM. Curr Opin Struct Biol 2024; 88:102885. [PMID: 38996624 DOI: 10.1016/j.sbi.2024.102885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/28/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or in situ. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of drug discovery. Yet regardless of resolution, structure prediction driven by artificial intelligence (AI) combined with subtomogram analysis is becoming powerful in understanding macromolecular assemblies. Automated and AI-assisted data mining is increasingly necessary to cope with the growing wealth of tomography data and to maximize the information obtained from them. Leveraging developments from AI and single-particle analysis could be essential in fulfilling the potential of in situ cryo-EM. Here, we highlight new developments for in situ cryo-EM and the emerging potential for AI in this process.
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Affiliation(s)
- Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA.
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5
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Ganesan I, Busto JV, Pfanner N, Wiedemann N. Biogenesis of mitochondrial β-barrel membrane proteins. FEBS Open Bio 2024. [PMID: 39343721 DOI: 10.1002/2211-5463.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/12/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
β-barrel membrane proteins in the mitochondrial outer membrane are crucial for mediating the metabolite exchange between the cytosol and the mitochondrial intermembrane space. In addition, the β-barrel membrane protein subunit Tom40 of the translocase of the outer membrane (TOM) is essential for the import of the vast majority of mitochondrial proteins encoded in the nucleus. The sorting and assembly machinery (SAM) in the outer membrane is required for the membrane insertion of mitochondrial β-barrel proteins. The core subunit Sam50, which has been conserved from bacteria to humans, is itself a β-barrel protein. The β-strands of β-barrel precursor proteins are assembled at the Sam50 lateral gate forming a Sam50-preprotein hybrid barrel. The assembled precursor β-barrel is finally released into the outer mitochondrial membrane by displacement of the nascent β-barrel, termed the β-barrel switching mechanism. SAM forms supercomplexes with TOM and forms a mitochondrial outer-to-inner membrane contact site with the mitochondrial contact site and cristae organizing system (MICOS) of the inner membrane. SAM shares subunits with the ER-mitochondria encounter structure (ERMES), which forms a membrane contact site between the mitochondrial outer membrane and the endoplasmic reticulum. Therefore, β-barrel membrane protein biogenesis is closely connected to general mitochondrial protein and lipid biogenesis and plays a central role in mitochondrial maintenance.
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Affiliation(s)
- Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
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6
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Novales NA, Feustel KJ, He KL, Chanfreau GF, Clarke CF. Nonfunctional coq10 mutants maintain the ERMES complex and reveal true phenotypes associated with the loss of the coenzyme Q chaperone protein Coq10. J Biol Chem 2024:107820. [PMID: 39343004 DOI: 10.1016/j.jbc.2024.107820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 09/11/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024] Open
Abstract
Coenzyme Q (CoQ) is a redox-active lipid molecule that acts as an electron carrier in the mitochondrial electron transport chain. In Saccharomyces cerevisiae, CoQ is synthesized in the mitochondrial matrix by a multi-subunit protein-lipid complex termed the CoQ synthome, the spatial positioning of which is coordinated by the Endoplasmic Reticulum-Mitochondria Encounter Structure (ERMES). The MDM12 gene encoding the cytosolic subunit of ERMES, is co-expressed with COQ10, which encodes the putative CoQ chaperone Coq10, via a shared bidirectional promoter. Deletion of COQ10 results in respiratory deficiency, impaired CoQ biosynthesis, and reduced spatial coordination between ERMES and the CoQ Synthome. While Coq10 protein content is maintained upon deletion of MDM12, we show that deletion of COQ10 by replacement with a HIS3 marker results in diminished Mdm12 protein content. Since deletion of individual ERMES subunits prevents ERMES formation, we asked whether some or all of the phenotypes associated with COQ10 deletion result from ERMES dysfunction. To identify the phenotypes resulting solely due to the loss of Coq10, we constructed strains expressing a functionally impaired (coq10-L96S) or truncated (coq10-R147*) Coq10 isoform using CRISPR-Cas9. We show that both coq10 mutants preserve Mdm12 protein content and exhibit impaired respiratory capacity like the coq10Δ mutant, indicating that Coq10's function is vital for respiration regardless of ERMES integrity. Moreover, the maintenance of CoQ synthome stability and efficient CoQ biosynthesis observed for the coq10-R147* mutant suggests these deleterious phenotypes in the coq10Δ mutant result from ERMES disruption. Overall, this study clarifies the role of Coq10 in modulating CoQ biosynthesis.
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Affiliation(s)
- Noelle Alexa Novales
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Kelsey J Feustel
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Kevin L He
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Guillaume F Chanfreau
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Catherine F Clarke
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569.
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7
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Hamaï A, Drin G. Specificity of lipid transfer proteins: an in vitro story. Biochimie 2024:S0300-9084(24)00217-7. [PMID: 39304019 DOI: 10.1016/j.biochi.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/06/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORP, Sec14, PITP, STARD, Ups/PRELI, StART-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.
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Affiliation(s)
- Amazigh Hamaï
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560 Valbonne, France Sophia Antipolis France
| | - Guillaume Drin
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560 Valbonne, France Sophia Antipolis France.
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8
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Aram L, de Haan D, Varsano N, Gilchrist JB, Heintze C, Rotkopf R, Rechav K, Elad N, Kröger N, Gal A. Intracellular morphogenesis of diatom silica is guided by local variations in membrane curvature. Nat Commun 2024; 15:7888. [PMID: 39251596 PMCID: PMC11385223 DOI: 10.1038/s41467-024-52211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/28/2024] [Indexed: 09/11/2024] Open
Abstract
Silica cell-wall formation in diatoms is a showcase for the ability of organisms to control inorganic mineralization. The process of silicification by these unicellular algae is tightly regulated within a membrane-bound organelle, the silica deposition vesicle (SDV). Two opposing scenarios were proposed to explain the tight regulation of this intracellular process: a template-mediated process that relies on preformed scaffolds, or a template-independent self-assembly process. The present work points to a third scenario, where the SDV membrane is a dynamic mold that shapes the forming silica. We use in-cell cryo-electron tomography to visualize the silicification process in situ, in its native-state, and with a nanometer-scale resolution. This reveals that the plasma membrane interacts with the SDV membrane via physical tethering at membrane contact sites, where the curvature of the tethered side of the SDV membrane mirrors the intricate silica topography. We propose that silica growth and morphogenesis result from the biophysical properties of the SDV and plasma membranes.
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Affiliation(s)
- Lior Aram
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Diede de Haan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - James B Gilchrist
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Christoph Heintze
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Ron Rotkopf
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Nils Kröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Huang Q, Zhou Y, Bartesaghi A. MiLoPYP: self-supervised molecular pattern mining and particle localization in situ. Nat Methods 2024:10.1038/s41592-024-02403-6. [PMID: 39251798 DOI: 10.1038/s41592-024-02403-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 08/05/2024] [Indexed: 09/11/2024]
Abstract
Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules within their native environment. Two outstanding challenges associated with cryo-electron tomography/single-particle tomography are the automatic identification and localization of proteins, tasks that are hindered by the molecular crowding inside cells, imaging distortions characteristic of cryo-electron tomography tomograms and the sheer size of tomographic datasets. Current methods suffer from low accuracy, demand extensive and time-consuming manual labeling or are limited to the detection of specific types of proteins. Here, we present MiLoPYP, a two-step dataset-specific contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. MiLoPYP's ability to effectively detect and localize a wide range of targets including globular and tubular complexes as well as large membrane proteins, will contribute to streamline and broaden the applicability of high-resolution workflows for in situ structure determination.
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Affiliation(s)
- Qinwen Huang
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
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Ren L, Wan J, Li X, Yao J, Ma Y, Meng F, Zheng S, Han W, Wang H. Mitochondrial rewiring with small-molecule drug-free nanoassemblies unleashes anticancer immunity. Nat Commun 2024; 15:7664. [PMID: 39227567 PMCID: PMC11372058 DOI: 10.1038/s41467-024-51945-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
The immunosuppressive tumor microenvironment (TME) remains a major obstacle to tumor control and causes suboptimal responses to immune checkpoint blockade (ICB) therapy. Thus, developing feasible therapeutic strategies that trigger inflammatory responses in the TME could improve the ICB efficacy. Mitochondria play an essential role in inflammation regulation and tumor immunogenicity induction. Herein, we report the discovery and characterization of a class of small molecules that can recapitulate aqueous self-assembly behavior, specifically target cellular organelles (e.g., mitochondria), and invigorate tumor cell immunogenicity. Mechanistically, this nanoassembly platform dynamically rewires mitochondria, induces endoplasmic reticulum stress, and causes apoptosis/paraptosis-associated immunogenic cell death. After treatment, stressed and dying tumor cells can act as prophylactic or therapeutic cancer vaccines. In preclinical mouse models of cancers with intrinsic or acquired resistance to PD-1 blockade, the local administration of nanoassemblies inflames the immunologically silent TME and synergizes with ICB therapy, generating potent antitumor immunity. This chemically programmed small-molecule immune enhancer acts distinctly from regular cytotoxic therapeutics and offers a promising strategy for synchronous and dynamic tailoring of innate immunity to achieve traceless cancer therapy and overcome immunosuppression in cancers.
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Affiliation(s)
- Lulu Ren
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, PR China
| | - Jianqin Wan
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
| | - Xiaoyan Li
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
- Department of Chemical Engineering, Zhejiang University, Hangzhou, Zhejiang Province, PR China
| | - Jie Yao
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
- Department of Chemical Engineering, Zhejiang University, Hangzhou, Zhejiang Province, PR China
| | - Yan Ma
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
| | - Fanchao Meng
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
| | - Shusen Zheng
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China.
| | - Weidong Han
- Department of Colorectal Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, PR China.
| | - Hangxiang Wang
- The First Affiliated Hospital, NHC Key Laboratory of Combined Multi-Organ Transplantation, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, PR China.
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China.
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11
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Xu X, Zhu W, Miao M, Bai M, Fan J, Niu Y, Li Y, Zhang A, Jia Z, Wu M. Activation of LONP1 by 84-B10 alleviates aristolochic acid nephropathy via re-establishing mitochondrial and peroxisomal homeostasis. Chin J Nat Med 2024; 22:808-821. [PMID: 39326975 DOI: 10.1016/s1875-5364(24)60608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Indexed: 09/28/2024]
Abstract
Pharmaceutical formulations derived from Aristolochiaceae herbs, which contain aristolochic acids (AAs), are widely used for medicinal purposes. However, exposure to these plants and isolated AAs is linked to renal toxicity, known as AA nephropathy (AAN). Currently, the mechanisms underlying AAN are not fully understood, leading to unsatisfactory treatment strategies. In this study, we explored the protective role of 84-B10 (5-[[2-(4-methoxyphenoxy)-5-(trifluoromethyl) phenyl] amino]-5-oxo-3-phenylpentanoic acid) against AAN. RNA-seq analysis revealed that the mitochondrion and peroxisome were the most affected cellular components following 84-B10 treatment in AAN mice. Consistently, 84-B10 treatment preserved mitochondrial ultrastructure, restored mitochondrial respiration, enhanced the expression of key transporters (carnitine palmitoyltransferase 2) and enzymes (acyl-Coenzyme A dehydrogenase, medium chain) involved in mitochondrial fatty acid β-oxidation, and reduced mitochondrial ROS generation in both aristolochic acid I (AAI)-challenged mice kidneys and cultured proximal tubular epithelial cells. Additionally, 84-B10 treatment increased the expression of key transporters (ATP binding cassette subfamily D) and rate-limiting enzymes (acyl-CoA oxidase 1) involved in peroxisomal fatty acid β-oxidation and restored peroxisomal redox balance. Knocking down LONP1 expression diminished the protective effects of 84-B10 against AAN, suggesting LONP1-dependent protection. In conclusion, our study provides evidence that AAN is associated with significant disturbances in both mitochondrial and peroxisomal functions. The LONP1 activator 84-B10 demonstrates therapeutic potential against AAN, likely by maintaining homeostasis in both mitochondria and peroxisomes.
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Affiliation(s)
- Xinyue Xu
- School of Medicine, Southeast University, Nanjing 210009, China; Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Wenping Zhu
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Mengqiu Miao
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Mi Bai
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Jiaojiao Fan
- School of Medicine, Southeast University, Nanjing 210009, China; Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Yujia Niu
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Yuting Li
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China
| | - Aihua Zhang
- School of Medicine, Southeast University, Nanjing 210009, China; Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China.
| | - Zhanjun Jia
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China.
| | - Mengqiu Wu
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing 210008, China; Jiangsu Key Laboratory of Early Development and Chronic Diseases Prevention in Children, Nanjing Medical University, Nanjing 210029, China.
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12
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Xiao P, Wu S, Wang Z, Shen G, Shi X. Biotoxicity of paraquat to lung cells mediated by endoplasmic reticulum-mitochondria interaction. J Mol Histol 2024:10.1007/s10735-024-10249-7. [PMID: 39215928 DOI: 10.1007/s10735-024-10249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
The high lethality caused by paraquat (PQ) poisoning has attracted much attention in public and human health due to its high toxicity and lethality. However, the understanding of the mechanism of PQ-induced apoptosis from the perspective of organelles, especially inter-organelle interactions, is still scarce. Exploring the linkage of multiple organelles during PQ poisoning and the molecular mechanisms of PQ poisoning under its mediation will help to gain insight into the mode of PQ poisoning at the organelle level. In this study, we observed that a certain dose of PQ gavage induced oxidative stress, mitochondrial dysfunction and endoplasmic reticulum stress in rat lung tissue cells. PQ toxicity led to the occurrence of Ca2+ overload in the endoplasmic reticulum, and the activated BIP and CHOP pathways directly/indirectly led to the expression of apoptogenic factors Caspase family factors. In addition, PQ promoted Ca2+ release from the endoplasmic reticulum and Ca2+ uptake by mitochondria, which induced the disruption of Bax/Bcl-2 channel proteins in response to the IP3R/RyR/VDAC1&2/MCU Ca2+ axis thereby leading to the release of CytoC, which ultimately induced endoplasmic reticulum stress and apoptotic cell death. In addition, 10 differential proteins were screened and validated by proteomics that may act as upstream and downstream active factors of mitochondria-endoplasmic reticulum interaction-mediated biotoxicity. Our findings provide new perspectives for researchers to explore the toxicity mechanisms of PQ to reduce their adverse effects.
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Affiliation(s)
- Ping Xiao
- Clinical Laboratory, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Shaohua Wu
- Clinical Laboratory, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Zhiyong Wang
- Department of Emergency, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Guoqiang Shen
- Department of Emergency, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Xiaofeng Shi
- Department of Emergency, Tianjin First Central Hospital, Tianjin, 300192, China.
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13
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Hanada K. Metabolic channeling of lipids via the contact zones between different organelles. Bioessays 2024; 46:e2400045. [PMID: 38932642 DOI: 10.1002/bies.202400045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
Various lipid transfer proteins (LTPs) mediate the inter-organelle transport of lipids. By working at membrane contact zones between donor and acceptor organelles, LTPs achieve rapid and accurate inter-organelle transfer of lipids. This article will describe the emerging paradigm that the action of LTPs at organelle contact zones generates metabolic channeling events in lipid metabolism, mainly referring to how ceramide synthesized in the endoplasmic reticulum is preferentially metabolized to sphingomyelin in the distal Golgi region, how cholesterol and phospholipids receive specific metabolic reactions in mitochondria, and how the hijacking of host LTPs by intracellular pathogens may generate new channeling-like events. In addition, the article will discuss how the function of LTPs is regulated, exemplified by a few representative LTP systems, and will briefly touch on experiments that will be necessary to establish the paradigm that LTP-mediated inter-organelle transport of lipids is one of the mechanisms of compartmentalization-based metabolic channeling events.
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Affiliation(s)
- Kentaro Hanada
- Center for Quality Management Systems, National Institute of Infectious Diseases, Tokyo, Japan
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14
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Hu X, Hoffmann DS, Wang M, Schuhmacher L, Stroe MC, Schreckenberger B, Elstner M, Fischer R. GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting. Nat Microbiol 2024; 9:1752-1763. [PMID: 38877225 PMCID: PMC11222155 DOI: 10.1038/s41564-024-01731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 05/14/2024] [Indexed: 06/16/2024]
Abstract
Initiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A. flagrans develops adhesive traps and recognizes its prey, Caenorhabditis elegans, through nematode-specific pheromones (ascarosides). Gene-expression analyses revealed that ascarosides activate the fungal GPCR, GprC, at the plasma membrane and together with the G-protein alpha subunit GasA, reprograms the cell. However, GprC and GasA also reside in mitochondria and boost respiration. This dual localization of GprC in A. flagrans resembles the localization of the cannabinoid receptor CB1 in humans. The C. elegans ascaroside-sensing GPCR, SRBC66 and GPCRs of many fungi are also predicted for dual localization, suggesting broad evolutionary conservation. An SRBC64/66-GprC chimaeric protein was functional in A. flagrans, and C. elegans SRBC64/66 and DAF38 share ascaroside-binding sites with the fungal GprC receptor, suggesting 400-million-year convergent evolution.
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Affiliation(s)
- Xiaodi Hu
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - David S Hoffmann
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Mai Wang
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Lars Schuhmacher
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Maria C Stroe
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Birgit Schreckenberger
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany.
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15
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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16
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Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S. The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. EMBO Rep 2024; 25:3137-3159. [PMID: 38877171 PMCID: PMC11239909 DOI: 10.1038/s44319-024-00175-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024] Open
Abstract
Junctions between the endoplasmic reticulum (ER) and the outer membrane of the nuclear envelope (NE) physically connect both organelles. These ER-NE junctions are essential for supplying the NE with lipids and proteins synthesized in the ER. However, little is known about the structure of these ER-NE junctions. Here, we systematically study the ultrastructure of ER-NE junctions in cryo-fixed mammalian cells staged in anaphase, telophase, and interphase by correlating live cell imaging with three-dimensional electron microscopy. Our results show that ER-NE junctions in interphase cells have a pronounced hourglass shape with a constricted neck of 7-20 nm width. This morphology is significantly distinct from that of junctions within the ER network, and their morphology emerges as early as telophase. The highly constricted ER-NE junctions are seen in several mammalian cell types, but not in budding yeast. We speculate that the unique and highly constricted ER-NE junctions are regulated via novel mechanisms that contribute to ER-to-NE lipid and protein traffic in higher eukaryotes.
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Affiliation(s)
- Helena Bragulat-Teixidor
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria.
| | - Keisuke Ishihara
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gréta Martina Szücs
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria
| | - Shotaro Otsuka
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
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17
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Keller J, Fernández-Busnadiego R. In situ studies of membrane biology by cryo-electron tomography. Curr Opin Cell Biol 2024; 88:102363. [PMID: 38677049 DOI: 10.1016/j.ceb.2024.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Cryo-electron tomography (cryo-ET) allows high resolution 3D imaging of biological samples in near-native environments. Thus, cryo-ET has become the method of choice to analyze the unperturbed organization of cellular membranes. Here, we briefly discuss current cryo-ET workflows and their application to study membrane biology in situ, under basal and pathological conditions.
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Affiliation(s)
- Jenny Keller
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, 37077, Germany; Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Göttingen, Germany.
| | - Rubén Fernández-Busnadiego
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, 37077, Germany; Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, 37077, Germany; Faculty of Physics, University of Göttingen, Göttingen, 37077, Germany.
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18
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Yao H, Xie Y, Li C, Liu W, Yi G. Mitochondria-Associated Organelle Crosstalk in Myocardial Ischemia/Reperfusion Injury. J Cardiovasc Transl Res 2024:10.1007/s12265-024-10523-9. [PMID: 38807004 DOI: 10.1007/s12265-024-10523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024]
Abstract
Organelle damage is a significant contributor to myocardial ischemia/reperfusion (I/R) injury. This damage often leads to disruption of endoplasmic reticulum protein regulatory programs and dysfunction of mitochondrial energy metabolism. Mitochondria and endoplasmic reticulum are seamlessly connected through the mitochondrial-associated endoplasmic reticulum membrane (MAM), which serves as a crucial site for the exchange of organelles and metabolites. However, there is a lack of reports regarding the communication of information and metabolites between mitochondria and related organelles, which is a crucial factor in triggering myocardial I/R damage. To address this research gap, this review described the role of crosstalk between mitochondria and the correlative organelles such as endoplasmic reticulum, lysosomal and nuclei involved in reperfusion injury of the heart. In summary, this review aims to provide a comprehensive understanding of the crosstalk between organelles in myocardial I/R injury, with the ultimate goal of facilitating the development of targeted therapies based on this knowledge.
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Affiliation(s)
- Hui Yao
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, 28 Chang Sheng West Road, Hunan, 421001, China
| | - Yuxin Xie
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, 28 Chang Sheng West Road, Hunan, 421001, China
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, Hunan, China
| | - Chaoquan Li
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, 28 Chang Sheng West Road, Hunan, 421001, China
| | - Wanting Liu
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, 28 Chang Sheng West Road, Hunan, 421001, China
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, Hunan, China
| | - Guanghui Yi
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, 28 Chang Sheng West Road, Hunan, 421001, China.
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, 421001, Hunan, China.
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19
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Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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20
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Saukko-Paavola AJ, Klemm RW. Remodelling of mitochondrial function by import of specific lipids at multiple membrane-contact sites. FEBS Lett 2024; 598:1274-1291. [PMID: 38311340 DOI: 10.1002/1873-3468.14813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Organelles form physical and functional contact between each other to exchange information, metabolic intermediates, and signaling molecules. Tethering factors and contact site complexes bring partnering organelles into close spatial proximity to establish membrane contact sites (MCSs), which specialize in unique functions like lipid transport or Ca2+ signaling. Here, we discuss how MCSs form dynamic platforms that are important for lipid metabolism. We provide a perspective on how import of specific lipids from the ER and other organelles may contribute to remodeling of mitochondria during nutrient starvation. We speculate that mitochondrial adaptation is achieved by connecting several compartments into a highly dynamic organelle network. The lipid droplet appears to be a central hub in coordinating the function of these organelle neighborhoods.
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Affiliation(s)
| | - Robin W Klemm
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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21
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Dudka W, Salo VT, Mahamid J. Zooming into lipid droplet biology through the lens of electron microscopy. FEBS Lett 2024; 598:1127-1142. [PMID: 38726814 DOI: 10.1002/1873-3468.14899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Electron microscopy (EM), in its various flavors, has significantly contributed to our understanding of lipid droplets (LD) as central organelles in cellular metabolism. For example, EM has illuminated that LDs, in contrast to all other cellular organelles, are uniquely enclosed by a single phospholipid monolayer, revealed the architecture of LD contact sites with different organelles, and provided near-atomic resolution maps of key enzymes that regulate neutral lipid biosynthesis and LD biogenesis. In this review, we first provide a brief history of pivotal findings in LD biology unveiled through the lens of an electron microscope. We describe the main EM techniques used in the context of LD research and discuss their current capabilities and limitations, thereby providing a foundation for utilizing suitable EM methodology to address LD-related questions with sufficient level of structural preservation, detail, and resolution. Finally, we highlight examples where EM has recently been and is expected to be instrumental in expanding the frontiers of LD biology.
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Affiliation(s)
- Wioleta Dudka
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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22
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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23
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Koch C, Lenhard S, Räschle M, Prescianotto-Baschong C, Spang A, Herrmann JM. The ER-SURF pathway uses ER-mitochondria contact sites for protein targeting to mitochondria. EMBO Rep 2024; 25:2071-2096. [PMID: 38565738 PMCID: PMC11014988 DOI: 10.1038/s44319-024-00113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Most mitochondrial proteins are synthesized on cytosolic ribosomes and imported into mitochondria in a post-translational reaction. Mitochondrial precursor proteins which use the ER-SURF pathway employ the surface of the endoplasmic reticulum (ER) as an important sorting platform. How they reach the mitochondrial import machinery from the ER is not known. Here we show that mitochondrial contact sites play a crucial role in the ER-to-mitochondria transfer of precursor proteins. The ER mitochondria encounter structure (ERMES) and Tom70, together with Djp1 and Lam6, are part of two parallel and partially redundant ER-to-mitochondria delivery routes. When ER-to-mitochondria transfer is prevented by loss of these two contact sites, many precursors of mitochondrial inner membrane proteins are left stranded on the ER membrane, resulting in mitochondrial dysfunction. Our observations support an active role of the ER in mitochondrial protein biogenesis.
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Affiliation(s)
- Christian Koch
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Anne Spang
- Biozentrum, University of Basel, 4056, Basel, Switzerland
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24
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Renne MF, Ernst R. ERMES - from myths to molecules. Nat Rev Mol Cell Biol 2024; 25:161. [PMID: 37857894 DOI: 10.1038/s41580-023-00677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Affiliation(s)
- Mike F Renne
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany.
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany.
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25
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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26
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Bittner E, Stehlik T, Lam J, Dimitrov L, Heimerl T, Schöck I, Harberding J, Dornes A, Heymons N, Bange G, Schuldiner M, Zalckvar E, Bölker M, Schekman R, Freitag J. Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLoS Biol 2024; 22:e3002508. [PMID: 38377076 PMCID: PMC10906886 DOI: 10.1371/journal.pbio.3002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/01/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER-mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.
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Affiliation(s)
- Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jason Lam
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Lazar Dimitrov
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Thomas Heimerl
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Isabelle Schöck
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jannik Harberding
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nikola Heymons
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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27
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Ronayne CT, Latorre-Muro P. Navigating the landscape of mitochondrial-ER communication in health and disease. Front Mol Biosci 2024; 11:1356500. [PMID: 38323074 PMCID: PMC10844478 DOI: 10.3389/fmolb.2024.1356500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
Intracellular organelle communication enables the maintenance of tissue homeostasis and health through synchronized adaptive processes triggered by environmental cues. Mitochondrial-Endoplasmic Reticulum (ER) communication sustains cellular fitness by adjusting protein synthesis and degradation, and metabolite and protein trafficking through organelle membranes. Mitochondrial-ER communication is bidirectional and requires that the ER-components of the Integrated Stress Response signal to mitochondria upon activation and, likewise, mitochondria signal to the ER under conditions of metabolite and protein overload to maintain proper functionality and ensure cellular survival. Declines in the mitochondrial-ER communication occur upon ageing and correlate with the onset of a myriad of heterogeneous age-related diseases such as obesity, type 2 diabetes, cancer, or neurodegenerative pathologies. Thus, the exploration of the molecular mechanisms of mitochondrial-ER signaling and regulation will provide insights into the most fundamental cellular adaptive processes with important therapeutical opportunities. In this review, we will discuss the pathways and mechanisms of mitochondrial-ER communication at the mitochondrial-ER interface and their implications in health and disease.
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Affiliation(s)
- Conor T. Ronayne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Pedro Latorre-Muro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
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28
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Voeltz GK, Sawyer EM, Hajnóczky G, Prinz WA. Making the connection: How membrane contact sites have changed our view of organelle biology. Cell 2024; 187:257-270. [PMID: 38242082 DOI: 10.1016/j.cell.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024]
Abstract
The view of organelles and how they operate together has changed dramatically over the last two decades. The textbook view of organelles was that they operated largely independently and were connected by vesicular trafficking and the diffusion of signals through the cytoplasm. We now know that all organelles make functional close contacts with one another, often called membrane contact sites. The study of these sites has moved to center stage in cell biology as it has become clear that they play critical roles in healthy and developing cells and during cell stress and disease states. Contact sites have important roles in intracellular signaling, lipid metabolism, motor-protein-mediated membrane dynamics, organelle division, and organelle biogenesis. Here, we summarize the major conceptual changes that have occurred in cell biology as we have come to appreciate how contact sites integrate the activities of organelles.
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Affiliation(s)
- G K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - E M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - G Hajnóczky
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - W A Prinz
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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29
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Ching C, Maufront J, di Cicco A, Lévy D, Dezi M. C ool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241231364. [PMID: 38410695 PMCID: PMC10895918 DOI: 10.1177/25152564241231364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.
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Affiliation(s)
- Cyan Ching
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Julien Maufront
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Aurélie di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
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30
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Freitag J, Stehlik T, Bange G. Mitochondria, Peroxisomes and Beyond-How Dual Targeting Regulates Organelle Tethering. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241264254. [PMID: 39364173 PMCID: PMC11447717 DOI: 10.1177/25152564241264254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/14/2024] [Accepted: 05/31/2024] [Indexed: 10/05/2024]
Abstract
Eukaryotic cells feature distinct membrane-enclosed organelles such as mitochondria and peroxisomes, each playing vital roles in cellular function and organization. These organelles are linked at membrane contact sites, facilitating interorganellar molecule and ion exchange. Most contact-forming proteins identified to date are membrane proteins or membrane-associated proteins, which can form very stable contacts. Recent findings suggest additional mechanistically distinct tethering events that arise from dual protein targeting. Proteins bearing targeting signals for multiple organelles, such as an N-terminal signal for mitochondria and a C-terminal signal for peroxisomes, function as tethers, fostering contacts by engaging targeting factors at both organelles. A number of dually targeted membrane proteins can contribute to contact site formation and transit from one organelle to the other as well. These interactions may enable the fine-tuning of organelle proximity, hence, adapting connections to meet varying physiological demands.
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Affiliation(s)
- Johannes Freitag
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Molecular Physiology of Microbes, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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31
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Hu X, Cai Y, Ji WK. Recent Advances on Synaptotagmin-Like Mitochondrial-Lipid Binding Protein Domain Containing Lipid Transfer Proteins. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241273646. [PMID: 39139576 PMCID: PMC11320393 DOI: 10.1177/25152564241273646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024]
Abstract
The Synaptotagmin-like mitochondrial-lipid binding protein (SMP) domain is found in a group of ER-resident lipid transfer proteins that are recruited to membrane contact sites (MCSs) by adaptors. Deciphering the molecular basis underlying the recruitment of SMP proteins to specific MCS sheds light not only on their cellular localization but also on their biological functions at these sites. Here we summarize recent advances in SMP domain-containing lipid transfer proteins, focusing on a recent study showing the localization, regulation and cellular function of a specific SMP protein named testis expressed protein 2 (Tex2). TMEM55, a potential PIP phosphatase on late endosome/lysosomal (LE/lys) membranes, was identified as an adaptor that enables the recruitment of Tex2 to ER- LE/lys MCS. In addition, we have summarized several important questions about the regulation and physiological functions of Tex2 that remained unanswered.
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Affiliation(s)
- Xuewen Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Yirui Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Center; Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, China
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32
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Eskelinen EL. Novel insights into autophagosome biogenesis revealed by cryo-electron tomography. FEBS Lett 2024; 598:9-16. [PMID: 37625816 DOI: 10.1002/1873-3468.14726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Autophagosome biogenesis, from the appearance of the phagophore to elongation and closure into an autophagosome, is one of the long-lasting open questions in the autophagy field. Recent studies utilising cryo-electron tomography and detailed analysis of the image data have revealed new information on the membrane dynamics of these events, including the shape and dimensions of omegasomes, phagophores and autophagosomes, and their relationships with the organelles around them. One of the important predictions from the new results is that 60-80% of the autophagosome membrane area is delivered by direct lipid transfer or lipid synthesis. Cryo-electron tomography can be expected to provide new directions for autophagy research in the near future.
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33
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Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat Methods 2023; 20:1900-1908. [PMID: 37932397 PMCID: PMC10703698 DOI: 10.1038/s41592-023-02053-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we present a ligand-inducible labeling strategy for intracellular proteins based on fluorescent, 25-nm-sized, genetically encoded multimeric particles (GEMs). The particles exhibit recognizable structural signatures, enabling their automated detection in cryo-ET data by convolutional neural networks. The coupling of GEMs to green fluorescent protein-tagged macromolecules of interest is triggered by addition of a small-molecule ligand, allowing for time-controlled labeling to minimize disturbance to native protein function. We demonstrate the applicability of GEMs for subcellular-level localization of endogenous and overexpressed proteins across different organelles in human cells using cryo-correlative fluorescence and cryo-ET imaging. We describe means for quantifying labeling specificity and efficiency, and for systematic optimization for rare and abundant protein targets, with emphasis on assessing the potential effects of labeling on protein function.
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Affiliation(s)
- Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yuki Hayashi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anastasiia Babenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brunner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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34
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Kučerová J, Zdrha A, Shinde A, Harant K, Hrdý I, Tachezy J. The divergent ER-mitochondria encounter structures (ERMES) are conserved in parabasalids but lost in several anaerobic lineages with hydrogenosomes. BMC Biol 2023; 21:259. [PMID: 37968591 PMCID: PMC10648710 DOI: 10.1186/s12915-023-01765-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND The endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCS) are extensively studied in aerobic eukaryotes; however, little is known about MCS in anaerobes with reduced forms of mitochondria named hydrogenosomes. In several eukaryotic lineages, the direct physical tether between ER and the outer mitochondrial membrane is formed by ER-mitochondria encounter structure (ERMES). The complex consists of four core proteins (Mmm1, Mmm2, Mdm12, and Mdm10) which are involved in phospholipid trafficking. Here we investigated ERMES distribution in organisms bearing hydrogenosomes and employed Trichomonas vaginalis as a model to estimate ERMES cellular localization, structure, and function. RESULTS Homology searches revealed that Parabasalia-Anaeramoebae, anaerobic jakobids, and anaerobic fungi are lineages with hydrogenosomes that retain ERMES, while ERMES components were gradually lost in Fornicata, and are absent in Preaxostyla and Archamoebae. In T. vaginalis and other parabasalids, three ERMES components were found with the expansion of Mmm1. Immunofluorescence microscopy confirmed that Mmm1 localized in ER, while Mdm12 and Mmm2 were partially localized in hydrogenosomes. Pull-down assays and mass spectrometry of the ERMES components identified a parabasalid-specific Porin2 as a substitute for the Mdm10. ERMES modeling predicted a formation of a continuous hydrophobic tunnel of TvMmm1-TvMdm12-TvMmm2 that is anchored via Porin2 to the hydrogenosomal outer membrane. Phospholipid-ERMES docking and Mdm12-phospholipid dot-blot indicated that ERMES is involved in the transport of phosphatidylinositol phosphates. The absence of enzymes involved in hydrogenosomal phospholipid metabolism implies that ERMES is not involved in the exchange of substrates between ER and hydrogenosomes but in the unidirectional import of phospholipids into hydrogenosomal membranes. CONCLUSIONS Our investigation demonstrated that ERMES mediates ER-hydrogenosome interactions in parabasalid T. vaginalis, while the complex was lost in several other lineages with hydrogenosomes.
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Affiliation(s)
- Jitka Kučerová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Alois Zdrha
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Abhishek Shinde
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Karel Harant
- OMICS Proteomics Laboratory, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic.
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35
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Hanna M, Guillén-Samander A, De Camilli P. RBG Motif Bridge-Like Lipid Transport Proteins: Structure, Functions, and Open Questions. Annu Rev Cell Dev Biol 2023; 39:409-434. [PMID: 37406299 DOI: 10.1146/annurev-cellbio-120420-014634] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The life of eukaryotic cells requires the transport of lipids between membranes, which are separated by the aqueous environment of the cytosol. Vesicle-mediated traffic along the secretory and endocytic pathways and lipid transfer proteins (LTPs) cooperate in this transport. Until recently, known LTPs were shown to carry one or a few lipids at a time and were thought to mediate transport by shuttle-like mechanisms. Over the last few years, a new family of LTPs has been discovered that is defined by a repeating β-groove (RBG) rod-like structure with a hydrophobic channel running along their entire length. This structure and the localization of these proteins at membrane contact sites suggest a bridge-like mechanism of lipid transport. Mutations in some of these proteins result in neurodegenerative and developmental disorders. Here we review the known properties and well-established or putative physiological roles of these proteins, and we highlight the many questions that remain open about their functions.
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Affiliation(s)
- Michael Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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36
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Wang Y, Idoughi R, Rückert D, Li R, Heidrich W. Adaptive differentiable grids for cryo-electron tomography reconstruction and denoising. BIOINFORMATICS ADVANCES 2023; 3:vbad131. [PMID: 37810456 PMCID: PMC10560095 DOI: 10.1093/bioadv/vbad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
Motivation Tilt-series cryo-electron tomography is a powerful tool widely used in structural biology to study 3D structures of micro-organisms, macromolecular complexes, etc. Still, the reconstruction process remains an arduous task due to several challenges: The missing-wedge acquisition, sample misalignment and motion, the need to process large data, and, especially, a low signal-to-noise ratio. Results Inspired by the recently introduced neural representations, we propose an adaptive learning-based representation of the density field of the captured sample. This representation consists of an octree structure, where each node represents a 3D density grid optimized from the captured projections during the training process. This optimization is performed using a loss that combines a differentiable image formation model with different regularization terms: total variation, boundary consistency, and a cross-nodes non-local constraint. The final reconstruction is obtained by interpolating the learned density grid at the desired voxel positions. The evaluation of our approach using captured data of viruses and cells shows that our proposed representation is well adapted to handle missing wedges, and improves the signal-to-noise ratio of the reconstructed tomogram. The reconstruction quality is highly improved in comparison to the state-of-the-art methods, while using the lowest computing time footprint. Availability and implementation The code is available on Github at https://github.com/yuanhaowang1213/adaptivediffgrid_ex.
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Affiliation(s)
- Yuanhao Wang
- Visual Computing Center (VCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Ramzi Idoughi
- Visual Computing Center (VCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darius Rückert
- Department of Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Rui Li
- Visual Computing Center (VCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Wolfgang Heidrich
- Visual Computing Center (VCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Álvarez D, Sapia J, Vanni S. Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity. Curr Opin Cell Biol 2023; 83:102205. [PMID: 37451175 DOI: 10.1016/j.ceb.2023.102205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with recent developments in structural biology, such as cryo-electron microscopy and artificial intelligence-based structure determination, opens new, exciting possibilities for future investigations. However, the full potential of MD simulations to provide a molecular view of the complex and dynamic processes involving membrane trafficking can only be realized if certain limitations are addressed, and especially those concerning the quality of coarse-grain models, which, despite recent successes in describing large-scale systems, still suffer from far-from-ideal chemical accuracy. In this review, we will highlight recent success stories of MD simulations in the investigation of membrane trafficking processes, their implications for future research, and the challenges that lie ahead in this specific research domain.
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Affiliation(s)
- Daniel Álvarez
- Department of Biology, University of Fribourg, Switzerland; Departamento de Química Física y Analítica, Universidad de Oviedo, Spain
| | - Jennifer Sapia
- Department of Biology, University of Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland; Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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Khaddaj R, Kukulski W. Piecing together the structural organisation of lipid exchange at membrane contact sites. Curr Opin Cell Biol 2023; 83:102212. [PMID: 37515839 DOI: 10.1016/j.ceb.2023.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
Membrane contact sites (MCSs) are areas of close proximity between organelles, implicated in transport of small molecules and in organelle biogenesis. Lipid transfer proteins at MCSs facilitate the distribution of lipid species between organelle membranes. Such exchange processes rely on the apposition of two different membranes delimiting distinct compartments and a cytosolic intermembrane space. Maintaining organelle identity while transferring molecules therefore implies control over MCS architecture both on the ultrastructural and molecular levels. Factors including intermembrane distance, density of resident proteins, and contact surface area fine-tune MCS function. Furthermore, the structural arrangement of lipid transfer proteins and associated proteins underpins the molecular mechanisms of lipid fluxes at MCSs. Thus, the architecture of MCSs emerges as an essential aspect of their function.
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Affiliation(s)
- Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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Guile MD, Jain A, Anderson KA, Clarke CF. New Insights on the Uptake and Trafficking of Coenzyme Q. Antioxidants (Basel) 2023; 12:1391. [PMID: 37507930 PMCID: PMC10376127 DOI: 10.3390/antiox12071391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Coenzyme Q (CoQ) is an essential lipid with many cellular functions, such as electron transport for cellular respiration, antioxidant protection, redox homeostasis, and ferroptosis suppression. Deficiencies in CoQ due to aging, genetic disease, or medication can be ameliorated by high-dose supplementation. As such, an understanding of the uptake and transport of CoQ may inform methods of clinical use and identify how to better treat deficiency. Here, we review what is known about the cellular uptake and intracellular distribution of CoQ from yeast, mammalian cell culture, and rodent models, as well as its absorption at the organism level. We discuss the use of these model organisms to probe the mechanisms of uptake and distribution. The literature indicates that CoQ uptake and distribution are multifaceted processes likely to have redundancies in its transport, utilizing the endomembrane system and newly identified proteins that function as lipid transporters. Impairment of the trafficking of either endogenous or exogenous CoQ exerts profound effects on metabolism and stress response. This review also highlights significant gaps in our knowledge of how CoQ is distributed within the cell and suggests future directions of research to better understand this process.
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Affiliation(s)
- Michael D Guile
- Department of Chemistry & Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90059, USA
| | - Akash Jain
- Department of Chemistry & Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90059, USA
| | - Kyle A Anderson
- Department of Chemistry & Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90059, USA
| | - Catherine F Clarke
- Department of Chemistry & Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90059, USA
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