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He J, Zhang L. The journey of STING: Guiding immune signaling through membrane trafficking. Cytokine Growth Factor Rev 2024:S1359-6101(24)00046-7. [PMID: 39019665 DOI: 10.1016/j.cytogfr.2024.07.003] [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: 05/09/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024]
Abstract
Stimulator of Interferon Genes (STING) serves as a pivotal mediator in the innate immune signaling pathway, transducing signals from various DNA receptors and playing a crucial role in natural immune processes. During cellular quiescence, STING protein resides in the endoplasmic reticulum (ER), and its activation typically occurs through the cGAS-STING signaling pathway. Upon activation, STING protein is transported to the Golgi apparatus, thereby initiating downstream signaling cascades. Vesicular transport serves as the primary mechanism for STING protein trafficking between the ER and Golgi apparatus, with COPII mediating anterograde transport from the ER to Golgi apparatus, while COPI is responsible for retrograde transport. Numerous factors influence these transport processes, thereby exerting either promoting or inhibitory effects on STING protein expression. Upon reaching the Golgi apparatus, to prevent over-activation, STING protein is transported to post-Golgi compartments for degradation. In addition to the conventional lysosomal degradation pathway, ESCRT has also been identified as one of the degradation pathways for STING protein. This review summarizes the recent findings on the membrane trafficking pathways of STING, highlighting their contributions to the regulation of cytokine production, the activation of immune cells, and the coordination of immune signaling pathways.
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Affiliation(s)
- Jingyi He
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
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2
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Merz N, Hartel JC, Grösch S. How ceramides affect the development of colon cancer: from normal colon to carcinoma. Pflugers Arch 2024:10.1007/s00424-024-02960-x. [PMID: 38635059 DOI: 10.1007/s00424-024-02960-x] [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: 12/21/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
The integrity of the colon and the development of colon cancer depend on the sphingolipid balance in colon epithelial cells. In this review, we summarize the current knowledge on how ceramides and their complex derivatives influence normal colon development and colon cancer development. Ceramides, glucosylceramides and sphingomyelin are essential membrane components and, due to their biophysical properties, can influence the activation of membrane proteins, affecting protein-protein interactions and downstream signalling pathways. Here, we review the cellular mechanisms known to be affected by ceramides and their effects on colon development. We also describe which ceramides are deregulated during colorectal carcinogenesis, the molecular mechanisms involved in ceramide deregulation and how this affects carcinogenesis. Finally, we review new methods that are now state of the art for studying lipid-protein interactions in the physiological environment.
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Affiliation(s)
- Nadine Merz
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Jennifer Christina Hartel
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Sabine Grösch
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt Am Main, Germany.
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3
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Fougère L, Mongrand S, Boutté Y. The function of sphingolipids in membrane trafficking and cell signaling in plants, in comparison with yeast and animal cells. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159463. [PMID: 38281556 DOI: 10.1016/j.bbalip.2024.159463] [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: 05/16/2023] [Revised: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Sphingolipids are essential membrane components involved in a wide range of cellular, developmental and signaling processes. Sphingolipids are so essential that knock-out mutation often leads to lethality. In recent years, conditional or weak allele mutants as well as the broadening of the pharmacological catalog allowed to decipher sphingolipid function more precisely in a less invasive way. This review intends to provide a discussion and point of view on the function of sphingolipids with a main focus on endomembrane trafficking, Golgi-mediated protein sorting, cell polarity, cell-to-cell communication and cell signaling at the plasma membrane. While our main angle is the plant field research, we will constantly refer to and compare with the advances made in the yeast and animal field. In this review, we will emphasize the role of sphingolipids not only as a membrane component, but also as a key player at a center of homeostatic regulatory networks involving direct or indirect interaction with other lipids, proteins and ion fluxes.
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Affiliation(s)
- Louise Fougère
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France
| | - Sebastien Mongrand
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France.
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4
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Aguilera-Romero A, Lucena R, Sabido-Bozo S, Muñiz M. Impact of sphingolipids on protein membrane trafficking. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159334. [PMID: 37201864 DOI: 10.1016/j.bbalip.2023.159334] [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: 02/21/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Membrane trafficking is essential to maintain the spatiotemporal control of protein and lipid distribution within membrane systems of eukaryotic cells. To achieve their functional destination proteins are sorted and transported into lipid carriers that construct the secretory and endocytic pathways. It is an emerging theme that lipid diversity might exist in part to ensure the homeostasis of these pathways. Sphingolipids, a chemical diverse type of lipids with special physicochemical characteristics have been implicated in the selective transport of proteins. In this review, we will discuss current knowledge about how sphingolipids modulate protein trafficking through the endomembrane systems to guarantee that proteins reach their functional destination and the proposed underlying mechanisms.
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Affiliation(s)
- Auxiliadora Aguilera-Romero
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain.
| | - Rafael Lucena
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain
| | - Susana Sabido-Bozo
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain
| | - Manuel Muñiz
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain.
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5
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Li J, Satyshur KA, Guo LW, Ruoho AE. Sphingoid Bases Regulate the Sigma-1 Receptor-Sphingosine and N, N'-Dimethylsphingosine Are Endogenous Agonists. Int J Mol Sci 2023; 24:3103. [PMID: 36834510 PMCID: PMC9962145 DOI: 10.3390/ijms24043103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Both bioactive sphingolipids and Sigma-1 receptor (S1R) chaperones occur ubiquitously in mammalian cell membranes. Endogenous compounds that regulate the S1R are important for controlling S1R responses to cellular stress. Herein, we interrogated the S1R in intact Retinal Pigment Epithelial cells (ARPE-19) with the bioactive sphingoid base, sphingosine (SPH), or the pain-provoking dimethylated SPH derivative, N,N'-dimethylsphingosine (DMS). As informed by a modified native gel approach, the basal and antagonist (BD-1047)-stabilized S1R oligomers dissociated to protomeric forms in the presence of SPH or DMS (PRE-084 as control). We, thus, posited that SPH and DMS are endogenous S1R agonists. Consistently, in silico docking of SPH and DMS to the S1R protomer showed strong associations with Asp126 and Glu172 in the cupin beta barrel and extensive van der Waals interactions of the C18 alkyl chains with the binding site including residues in helices 4 and 5. Mean docking free energies were 8.73-8.93 kcal/mol for SPH and 8.56-8.15 kcal/mol for DMS, and calculated binding constants were ~40 nM for SPH and ~120 nM for DMS. We hypothesize that SPH, DMS, and similar sphingoid bases access the S1R beta barrel via a membrane bilayer pathway. We further propose that the enzymatic control of ceramide concentrations in intracellular membranes as the primary sources of SPH dictates availability of endogenous SPH and DMS to the S1R and the subsequent control of S1R activity within the same cell and/or in cellular environments.
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Affiliation(s)
- Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Kenneth A. Satyshur
- Small Molecule Screening Facility, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Arnold E. Ruoho
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
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Roberts BS, Satpute-Krishnan P. The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis. Front Cell Dev Biol 2023; 10:1096899. [PMID: 36733337 PMCID: PMC9888432 DOI: 10.3389/fcell.2022.1096899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.
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Yano Y. Effects of Membrane Cholesterol on Stability of Transmembrane Helix Associations. Chem Pharm Bull (Tokyo) 2022; 70:514-518. [DOI: 10.1248/cpb.c22-00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yoshiaki Yano
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Woman’s University
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Scrima S, Tiberti M, Campo A, Corcelle-Termeau E, Judith D, Foged MM, Clemmensen KKB, Tooze SA, Jäättelä M, Maeda K, Lambrughi M, Papaleo E. Unraveling membrane properties at the organelle-level with LipidDyn. Comput Struct Biotechnol J 2022; 20:3604-3614. [PMID: 35860415 PMCID: PMC9283888 DOI: 10.1016/j.csbj.2022.06.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/22/2022] Open
Abstract
Lipidomics of organelles could be used to design models for molecular simulations. The bottleneck is the analysis and rationalization of the data from simulations. LipidDyn is an automated pipeline to streamline the analyses of lipid bilayers. LipidDyn allows to collect analysis in a non-time-consuming and reproducible manner. We applied LipidDyn to different case studies to illustrate its potential.
Cellular membranes are formed from different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and its alterations are linked to several diseases. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins. Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and resolutions. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data. In this context, we developed LipidDyn, a Python-based pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, order parameters, diffusion motions, lipid density, and lipid enrichment/depletion. The calculations exploit parallelization, and the pipeline includes graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.
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Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Alessia Campo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elisabeth Corcelle-Termeau
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Delphine Judith
- Institut Cochin, Inserm U1016-CNRS, UMR8104, Université de Paris, Paris, France
| | - Mads Møller Foged
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | | | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
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9
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Mendes LFS, Costa-Filho AJ. A gold revision of the Golgi Dynamics (GOLD) domain structure and associated cell functionalities. FEBS Lett 2022; 596:973-990. [PMID: 35099811 DOI: 10.1002/1873-3468.14300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/04/2022] [Accepted: 01/20/2022] [Indexed: 11/06/2022]
Abstract
The classical secretory pathway is the key membrane-based delivery system in eukaryotic cells. Several families of proteins involved in the secretory pathway, with functionalities going from cargo sorting receptors to the maintenance and dynamics of secretory organelles, share soluble globular domains predicted to mediate protein-protein interactions. One of them is "Golgi Dynamics" (GOLD) domain, named after its strong association with the Golgi apparatus. There are many GOLD-containing protein families, such as the Transmembrane emp24 domain-containing proteins (TMED/p24 family), animal SEC14-like proteins, Human Golgi resident protein ACBD3, a splice variant of TICAM2 called TRAM with GOLD domain and FYCO1. Here, we critically review the state-of-the-art knowledge of the structures and functions of the main representatives of GOLD-containing proteins in vertebrates. We provide the first unified description of the GOLD domain structure across different families since the first high-resolution structure was determined. With a brand-new update on the definition of the GOLD domain, we also discuss how its tertiary structure fits the β-sandwich-like fold map and give exciting new directions for forthcoming studies.
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Affiliation(s)
- Luis Felipe S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
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Nihei CI, Nakanishi M. Cargo selection in the early secretory pathway of African trypanosomes. Parasitol Int 2021; 84:102379. [PMID: 34000424 DOI: 10.1016/j.parint.2021.102379] [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: 12/21/2020] [Revised: 03/30/2021] [Accepted: 05/06/2021] [Indexed: 11/25/2022]
Abstract
Membrane and secretory proteins are synthesized by ribosomes and then enter the endoplasmic reticulum (ER) where they undergo glycosylation and quality control for proper folding. Subsequently, proteins are transported to the Golgi apparatus and then sorted to the plasma membrane or intracellular organelles. Transport vesicles are formed at ER-exit sites (ERES) on the ER with several coat protein complexes. Cargo proteins loaded into the vesicles are selected by specific interactions with cargo receptors and/or adaptors during vesicle formation. p24 family and intracellular lectin ERGIC-53-membrane proteins are the known cargo receptors acting in the early secretory pathway (ER-Golgi). Oligomerization of the cargo receptors have been suggested to play an important role in cargo selection and sorting via posttranslational modifications in fungi and metazoans. On the other hand, the mechanisms involved in the early secretory pathway in protozoa remain unclear. In this review, we focus on Trypanosoma brucei as a representative of protozoan and discuss differences and commonalities in the molecular mechanisms of its early secretory pathway compared with other organisms.
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Affiliation(s)
- Coh-Ichi Nihei
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (BIKAKEN), 3-14-23, Kamiosaki, Shinagawa-ku, Tokyo 141-0023, Japan.
| | - Masayuki Nakanishi
- Laboratory of Biochemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.
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Dingjan T, Futerman AH. The fine-tuning of cell membrane lipid bilayers accentuates their compositional complexity. Bioessays 2021; 43:e2100021. [PMID: 33656770 DOI: 10.1002/bies.202100021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/17/2023]
Abstract
Cell membranes are now emerging as finely tuned molecular systems, signifying that re-evaluation of our understanding of their structure is essential. Although the idea that cell membrane lipid bilayers do little more than give shape and form to cells and limit diffusion between cells and their environment is totally passé, the structural, compositional, and functional complexity of lipid bilayers often catches cell and molecular biologists by surprise. Models of lipid bilayer structure have developed considerably since the heyday of the fluid mosaic model, principally by the discovery of the restricted diffusion of membrane proteins and lipids within the plane of the bilayer. In reviewing this field, we now suggest that further refinement of current models is necessary and propose that describing lipid bilayers as "finely-tuned molecular assemblies" best portrays their complexity and function. Also see the video abstract here: https://www.youtube.com/watch?v=ddkP-QRZTl8.
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Affiliation(s)
- Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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