1
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Schuster M, Kilaru S, Wösten HAB, Steinberg G. Secretion and endocytosis in subapical cells support hyphal tip growth in the fungus Trichoderma reesei. Nat Commun 2025; 16:4402. [PMID: 40355408 PMCID: PMC12069525 DOI: 10.1038/s41467-025-59606-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Accepted: 04/24/2025] [Indexed: 05/14/2025] Open
Abstract
Filamentous fungi colonise substrates by invasive growth of multi-cellular hyphae. It is commonly accepted that hyphae expand by tip growth that is restricted to the first apical cell, where turgor pressure, exocytosis and endocytosis cooperate to expand the apex. Here we show that, contrary to expectations, subapical cells play important roles in hyphal growth in the industrial enzyme-producing fungus Trichoderma reesei. We find that the second and third cells are crucial for hyphal extension, which correlates with tip-ward cytoplasmic streaming, and the fourth-to-sixth cells support rapid growth rates. Live cell imaging reveals exocytotic and endocytic activity in both apical and subapical cells, associated with microtubule-based bi-directional transport of secretory vesicles and early endosomes across septa. Moreover, visualisation of 1,3-β-glucan synthase in subapical cells reveals that these compartments deliver cell wall-forming enzymes to the apical growth region. Thus, subapical cells are active in exocytosis and endocytosis, and deliver growth supplies and enzymes to the expanding hyphal apex.
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Affiliation(s)
- Martin Schuster
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Sreedhar Kilaru
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Han A B Wösten
- Microbiology, Department of Biology, University of Utrecht, Utrecht, The Netherlands
| | - Gero Steinberg
- Department of Biosciences, University of Exeter, Exeter, United Kingdom.
- Microbiology, Department of Biology, University of Utrecht, Utrecht, The Netherlands.
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2
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Gimeno‐Agud H, Díaz‐Osorio Y, Oyarzábal A. Biological Basis of Cell Trafficking: A General Overview. J Inherit Metab Dis 2025; 48:e12839. [PMID: 39756816 PMCID: PMC11700728 DOI: 10.1002/jimd.12839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 10/20/2024] [Accepted: 12/11/2024] [Indexed: 01/07/2025]
Abstract
Cell trafficking is a tightly regulated biological process for the exchange of signals and metabolites between cell compartments, including four main processes: membrane trafficking (transport of membrane-bound vesicles), autophagy, transport along the cytoskeleton, and membrane contact sites. These processes are cross-sectional to cellular functions, ranging from the transportation of membrane proteins, membranes, and organelles to the elimination of damaged proteins and organelles. In consequence, cell trafficking is crucial for cell survival and homeostasis, serving as a cornerstone for cellular communication and facilitating interactions both with the surrounding environment and between different organelles. Disorders of cell trafficking are clinically and pathophysiological diverse and complex and form the largest group in the recent International Classification of Inherited Metabolic Disorders (ICIMD). In this review, we explore the four categories of cell trafficking and the biological principles that drive these processes. Instead of delving profoundly into each pathway, as comprehensive reviews on those topics already exist, we offer a broad overview of the molecular mechanisms behind cell trafficking, providing a foundational understanding to ease their entry into this subject and enhance comprehension of the other articles featured in this Special Issue.
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Affiliation(s)
- Helena Gimeno‐Agud
- Department of Neurology and MetabERN; Esplugues de LlobregatSynaptic Metabolism and Personalized Therapies Lab, Institut de Recerca Sant Joan de DéuBarcelonaSpain
- Pediatric Neurometabolism + Personalized Therapies LabUniversity Abat Oliba CEUBarcelonaSpain
| | - Yaiza Díaz‐Osorio
- Department of Neurology and MetabERN; Esplugues de LlobregatSynaptic Metabolism and Personalized Therapies Lab, Institut de Recerca Sant Joan de DéuBarcelonaSpain
| | - Alfonso Oyarzábal
- Department of Neurology and MetabERN; Esplugues de LlobregatSynaptic Metabolism and Personalized Therapies Lab, Institut de Recerca Sant Joan de DéuBarcelonaSpain
- Pediatric Neurometabolism + Personalized Therapies LabUniversity Abat Oliba CEUBarcelonaSpain
- Department of Neurology, Esplugues de LlobregatNeurometabolic Unit, Hospital Sant Joan de DéuBarcelonaSpain
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3
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Sumya FT, Aragon-Ramirez WS, Lupashin VV. Comprehensive Proteomic Characterization of the Intra-Golgi Trafficking Intermediates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.25.620336. [PMID: 39484492 PMCID: PMC11527126 DOI: 10.1101/2024.10.25.620336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Intracellular trafficking relies on small vesicular intermediates, though their specific role in Golgi function is still debated. To clarify this, we induced acute dysfunction of the Conserved Oligomeric Golgi (COG) complex and analyzed vesicles from cis, medial, and trans-Golgi compartments. Proteomic analysis of Golgi-derived vesicles from wild-type cells revealed distinct molecular profiles, indicating a robust recycling system for Golgi proteins. Notably, these vesicles retained various vesicular coats, while COG depletion accelerated uncoating. The increased overlap in molecular profiles with COG depletion suggests that persistent defects in vesicle tethering disrupt intra-Golgi sorting. Our findings reveal that the entire Golgi glycosylation machinery recycles within vesicles in a COG-dependent manner, whereas secretory and ER-Golgi trafficking proteins were not enriched. These results support a model in which the COG complex orchestrates multi-step recycling of glycosylation machinery, coordinated by specific Golgi coats, tethers, Rabs, and SNAREs.
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Affiliation(s)
- Farhana Taher Sumya
- University of Arkansas for Medical Sciences, Department of Physiology and Cell Biology, Little Rock, Arkansas, US
| | - Walter S. Aragon-Ramirez
- University of Arkansas for Medical Sciences, Department of Physiology and Cell Biology, Little Rock, Arkansas, US
| | - Vladimir V Lupashin
- University of Arkansas for Medical Sciences, Department of Physiology and Cell Biology, Little Rock, Arkansas, US
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4
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Li PP, Zhou YY, Gao L, Lv JN, Xu SS, Zhao YW, Xu D, Huang R, Zhang X, Li P, Fu X, He Z. The de novo missense mutation F224S in GABRB2, identified in epileptic encephalopathy and developmental delay, impairs GABA AR function. Neuroscience 2024; 553:172-184. [PMID: 38964454 DOI: 10.1016/j.neuroscience.2024.06.029] [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: 03/01/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Genetic variants in genes encoding subunits of the γ-aminobutyric acid-A receptor (GABAAR) have been found to cause neurodevelopmental disorders and epileptic encephalopathy. In a patient with epilepsy and developmental delay, a de novo heterozygous missense mutation c.671 T > C (p.F224S) was discovered in the GABRB2 gene, which encodes the β2 subunit of GABAAR. Based on previous studies on GABRB2 variants, this new GABRB2 variant (F224S) would be pathogenic. To confirm and investigate the effects of this GABRB2 mutation on GABAAR channel function, we conducted transient expression experiments using GABAAR subunits in HEK293T cells. The GABAARs containing mutant β2 (F224S) subunit showed poor trafficking to the cell membrane, while the expression and distribution of the normal α1 and γ2 subunits were unaffected. Furthermore, the peak current amplitude of the GABAAR containing the β2 (F224S) subunit was significantly smaller compared to the wild type GABAAR. We propose that GABRB2 variant F224S is pathogenic and GABAARs containing this β2 mutant reduce response to GABA under physiological conditions, which could potentially disrupt the excitation/inhibition balance in the brain, leading to epilepsy.
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Affiliation(s)
- Ping-Ping Li
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yue-Yuan Zhou
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Li Gao
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jia-Nan Lv
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Shi-Shi Xu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yan-Wen Zhao
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Di Xu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Ruoke Huang
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xiong Zhang
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Peijun Li
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117 Jinan, Shandong, China
| | - Xiaoqin Fu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117 Jinan, Shandong, China
| | - Zhiyong He
- Department of Pediatric Rehabilitation, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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5
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Sherman DJ, Liu L, Mamrosh JL, Xie J, Ferbas J, Lomenick B, Ladinsky MS, Verma R, Rulifson IC, Deshaies RJ. The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics. Proc Natl Acad Sci U S A 2024; 121:e2318619121. [PMID: 38657050 PMCID: PMC11067037 DOI: 10.1073/pnas.2318619121] [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: 10/25/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024] Open
Abstract
Nonalcoholic fatty liver disease, recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery 20 y ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
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Affiliation(s)
| | - Lei Liu
- Amgen Research, South San Francisco, CA94080
| | | | | | | | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
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6
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Tyagi K, Venkatesh V. Emerging potential approaches in alkaline phosphatase (ALP) activatable cancer theranostics. RSC Med Chem 2024; 15:1148-1160. [PMID: 38665831 PMCID: PMC11042160 DOI: 10.1039/d3md00565h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/09/2024] [Indexed: 04/28/2024] Open
Abstract
Alkaline phosphatase (ALP) is known as one of the most crucial members of the phosphatase family and encompasses the enormous ability to hydrolyze the phosphate group in various biomolecules; by this, it regulates several events in the pool of biological medium. Owing to its overexpression in various cancer cells, recently, its potential has evolved as a prominent biomarker in cancer research. In this article, we have underlined the recent advances (2019 onwards) of alkaline phosphatase in the arena of emerging cancer theranostics. Herein, we mainly focused on phosphate-locked molecular systems such as peptides, prodrugs, and aggregation-induced emission (AIE)-based molecules. When these theranostics encounter cancer cell-overexpressed ALP, it results in the hydrolysis of the phosphate group, which leads to the release of highly cytotoxic agents along with turn-on fluorophore/pre-existing fluorophore.
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Affiliation(s)
- Kartikay Tyagi
- Laboratory of Chemical Biology and Medicinal Chemistry, Department of Chemistry, Indian Institute of Technology Roorkee Uttarakhand-247667 India
| | - V Venkatesh
- Laboratory of Chemical Biology and Medicinal Chemistry, Department of Chemistry, Indian Institute of Technology Roorkee Uttarakhand-247667 India
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7
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Kava E, Garbelotti CV, Lopes JLS, Costa-Filho AJ. Myristoylated GRASP55 dimerizes in the presence of model membranes. J Biomol Struct Dyn 2024:1-12. [PMID: 38361284 DOI: 10.1080/07391102.2024.2317973] [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: 10/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
The Golgi Reassembly and Stacking Proteins (GRASPs) are engaged in various functions within the cell, both in unconventional secretion mechanisms and structuring and organizing the Golgi apparatus. Understanding their specific role in each situation still requires more structural and functional data at the molecular level. GRASP55 is one of the GRASP members in mammals, anchored to the membrane via the myristoylation of a Gly residue at its N-terminus. Therefore, co-translational modifications, such as myristoylation, are fundamental when considering a strategy to obtain detailed information on the interactions between GRASP55 and membranes. Despite its functional relevance, the N-terminal myristoylation has been underappreciated in the studies reported to date, compromising the previously proposed models for GRASP-membrane interactions. Here, we investigated the synergy between the presence of the membrane and the formation of oligomeric structures of myristoylated GRASP55, using a series of biophysical techniques to perform the structural characterization of the lipidated GRASP55 and its interaction with biological lipid model membranes. Our data fulfill an unexplored gap: the adequate evaluation of the presence of lipidations and lipid membranes on the structure-function dyad of GRASPs.
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Affiliation(s)
- Emanuel Kava
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Carolina V Garbelotti
- Laboratório de Fisiologia Ecológica de Plantas, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Luiz S Lopes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - 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, Brazil
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8
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Stalder D, Yakunin I, Pereira C, Eden J, Gershlick DC. Recruitment of PI4KIIIβ to the Golgi by ACBD3 is dependent on an upstream pathway of a SNARE complex and golgins. Mol Biol Cell 2024; 35:ar20. [PMID: 38134218 PMCID: PMC7615549 DOI: 10.1091/mbc.e23-09-0376] [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: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
ACBD3 is a protein localised to the Golgi apparatus and recruits other proteins, such as PI4KIIIβ, to the Golgi. However, the mechanism through which ACBD3 itself is recruited to the Golgi is poorly understood. This study demonstrates there are two mechanisms for ACBD3 recruitment to the Golgi. First, we identified that an MWT374-376 motif in the unique region upstream of the GOLD domain in ACBD3 is essential for Golgi localization. Second, we use unbiased proteomics to demonstrate that ACBD3 interacts with SCFD1, a Sec1/Munc-18 (SM) protein, and a SNARE protein, SEC22B. CRISPR-KO of SCFD1 causes ACBD3 to become cytosolic. We also found that ACBD3 is redundantly recruited to the Golgi apparatus by two golgins: golgin-45 and giantin, which bind to ACBD3 through interaction with the MWT374-376 motif. Taken together, our results suggest that ACBD3 is recruited to the Golgi in a two-step sequential process, with the SCFD1-mediated interaction occurring upstream of the interaction with the golgins.
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Affiliation(s)
- Danièle Stalder
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Igor Yakunin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Jessica Eden
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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Launhardt L, Uhlenberg J, Stellmach H, Schomburg M, Hause B, Heilmann I, Heilmann M. Association of the Arabidopsis oleoyl Δ12-desaturase FAD2 with pre-cis-Golgi stacks at endoplasmic reticulum-Golgi-exit sites. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:242-263. [PMID: 37805827 DOI: 10.1111/tpj.16492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/26/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
The unsaturation of phospholipids influences the function of membranes. In Arabidopsis thaliana, the oleoyl Δ12-desaturase FAD2 converts oleic (18:1Δ9 ) to linoleic acid (18:2Δ9,12 ) and influences phospholipid unsaturation in different cellular membranes. Despite its importance, the precise localization of Arabidopsis FAD2 has not been unambiguously described. As FAD2 is thought to modify phospholipid-associated fatty acids at the endoplasmic reticulum (ER), from where unsaturates are distributed to other cellular sites, we hypothesized that FAD2 locates to ER subdomains enabling trafficking of lipid intermediates through the secretory pathway. Fluorescent FAD2 fusions used to test this hypothesis were first assessed for functionality by heterologous expression in yeast (Saccharomyces cerevisiae), and in planta by Arabidopsis fad2 mutant rescue upon ectopic expression from an intrinsic FAD2 promoter fragment. Light sheet fluorescence, laser scanning confocal or spinning disc microscopy of roots, leaves, or mesophyll protoplasts showed the functional fluorescence-tagged FAD2 variants in flattened donut-shaped structures of ~0.5-1 μm diameter, in a pattern not resembling mere ER association. High-resolution imaging of coexpressed organellar markers showed fluorescence-tagged FAD2 in a ring-shaped pattern surrounding ER-proximal Golgi particles, colocalizing with pre-cis-Golgi markers. This localization required the unusual C-terminal retention signal of FAD2, and deletion or substitutions in this protein region resulted in relaxed distribution and diffuse association with the ER. The distinct association of FAD2 with pre-cis-Golgi stacks in Arabidopsis root and leaf tissue is consistent with a contribution of FAD2 to membrane lipid homeostasis through the secretory pathway, as verified by an increased plasma membrane liquid phase order in the fad2 mutant.
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Affiliation(s)
- Larissa Launhardt
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Johanna Uhlenberg
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Hagen Stellmach
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Marie Schomburg
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Ingo Heilmann
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Mareike Heilmann
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
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Krasnova O, Kovaleva A, Saveleva A, Kulakova K, Bystrova O, Martynova M, Domnina A, Sopova J, Neganova I. Mesenchymal stem cells lose the senescent phenotype under 3D cultivation. Stem Cell Res Ther 2023; 14:373. [PMID: 38111010 PMCID: PMC10729581 DOI: 10.1186/s13287-023-03599-8] [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: 08/03/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Three-dimensional (3D) cell culture is widely used in various fields of cell biology. In comparison to conventional two-dimensional (2D) cell culture, 3D cell culture facilitates a more accurate replication of the in vivo microenvironment, which is essential for obtaining more relevant results. The application of 3D cell culture techniques in regenerative medicine, particularly in mesenchymal stem cell (MSC)-based research, has been extensively studied. Many of these studies focus on the enhanced paracrine activity of MSCs cultured in 3D environments. However, few focus on the cellular processes that occur during 3D cultivation. METHODS In this work, we studied the changes occurring within 3D-cultured MSCs (3D-MSCs). Specifically, we examined the expression of numerous senescent-associated markers, the actin cytoskeleton structure, the architecture of the Golgi apparatus and the localization of mTOR, one of the main positive regulators of replicative senescence. In addition, we assessed whether the selective elimination of senescent cells occurs upon 3D culturing by using cell sorting based on autofluorescence. RESULTS Our findings indicate that 3D-MSCs were able to lose replicative senescence markers under 3D cell culture conditions. We observed changes in actin cytoskeleton structure, Golgi apparatus architecture and revealed that 3D cultivation leads to the nuclear localization of mTOR, resulting in a decrease in its active cytoplasmic form. Additionally, our findings provide evidence that 3D cell culture promotes the phenotypic reversion of senescent cell phenotype rather than their removal from the bulk population. CONCLUSION These novel insights into the biology of 3D-MSCs can be applied to research in regenerative medicine to overcome replicative senescence and MSC heterogeneity as they often pose significant concerns regarding safety and effectiveness for therapeutic purposes.
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Affiliation(s)
- O Krasnova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia.
| | - A Kovaleva
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - A Saveleva
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - K Kulakova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - O Bystrova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - M Martynova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - A Domnina
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - J Sopova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - I Neganova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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11
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Novák LVF, Treitli SC, Pyrih J, Hałakuc P, Pipaliya SV, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V. Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria. PLoS Genet 2023; 19:e1011050. [PMID: 38060519 PMCID: PMC10703272 DOI: 10.1371/journal.pgen.1011050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.
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Affiliation(s)
- Lukáš V. F. Novák
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- Université de Bretagne Occidentale, CNRS, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Sebastian C. Treitli
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Pyrih
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Shweta V. Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vojtěch Vacek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Ondřej Brzoň
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Petr Soukal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Laura Eme
- Ecology, Systematics, and Evolution Unit, Université Paris-Saclay, CNRS, Orsay, France
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Ostrava, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
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12
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Chen M, Xu L, Wu Y, Soba P, Hu C. The organization and function of the Golgi apparatus in dendrite development and neurological disorders. Genes Dis 2023; 10:2425-2442. [PMID: 37554209 PMCID: PMC10404969 DOI: 10.1016/j.gendis.2022.11.009] [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: 07/04/2022] [Revised: 09/13/2022] [Accepted: 11/05/2022] [Indexed: 12/24/2022] Open
Abstract
Dendrites are specialized neuronal compartments that sense, integrate and transfer information in the neural network. Their development is tightly controlled and abnormal dendrite morphogenesis is strongly linked to neurological disorders. While dendritic morphology ranges from relatively simple to extremely complex for a specified neuron, either requires a functional secretory pathway to continually replenish proteins and lipids to meet dendritic growth demands. The Golgi apparatus occupies the center of the secretory pathway and is regulating posttranslational modifications, sorting, transport, and signal transduction, as well as acting as a non-centrosomal microtubule organization center. The neuronal Golgi apparatus shares common features with Golgi in other eukaryotic cell types but also forms distinct structures known as Golgi outposts that specifically localize in dendrites. However, the organization and function of Golgi in dendrite development and its impact on neurological disorders is just emerging and so far lacks a systematic summary. We describe the organization of the Golgi apparatus in neurons, review the current understanding of Golgi function in dendritic morphogenesis, and discuss the current challenges and future directions.
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Affiliation(s)
- Meilan Chen
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education Institute for Brain, Science and Rehabilitation, South China Normal University, Guangzhou, Guangdong 510631, China
- Department of Ophthalmology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510320, China
| | - Lu Xu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education Institute for Brain, Science and Rehabilitation, South China Normal University, Guangzhou, Guangdong 510631, China
| | - Yi Wu
- Department of Ophthalmology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510320, China
| | - Peter Soba
- LIMES Institute, Department of Molecular Brain Physiology and Behavior, University of Bonn, Bonn 53115, Germany
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Chun Hu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education Institute for Brain, Science and Rehabilitation, South China Normal University, Guangzhou, Guangdong 510631, China
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13
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Sherman DJ, Liu L, Mamrosh JL, Xie J, Ferbas J, Lomenick B, Ladinsky MS, Verma R, Rulifson IC, Deshaies RJ. The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562302. [PMID: 37873239 PMCID: PMC10592801 DOI: 10.1101/2023.10.13.562302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD to date. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
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Affiliation(s)
| | - Lei Liu
- Amgen Research, South San Francisco, CA 94080, USA
| | | | | | - John Ferbas
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rati Verma
- Amgen Research, Thousand Oaks, CA 91320, USA
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14
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Petzoldt AG. Presynaptic Precursor Vesicles-Cargo, Biogenesis, and Kinesin-Based Transport across Species. Cells 2023; 12:2248. [PMID: 37759474 PMCID: PMC10527734 DOI: 10.3390/cells12182248] [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: 07/06/2023] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The faithful formation and, consequently, function of a synapse requires continuous and tightly controlled delivery of synaptic material. At the presynapse, a variety of proteins with unequal molecular properties are indispensable to compose and control the molecular machinery concerting neurotransmitter release through synaptic vesicle fusion with the presynaptic membrane. As presynaptic proteins are produced mainly in the neuronal soma, they are obliged to traffic along microtubules through the axon to reach the consuming presynapse. This anterograde transport is performed by highly specialised and diverse presynaptic precursor vesicles, membranous organelles able to transport as different proteins such as synaptic vesicle membrane and membrane-associated proteins, cytosolic active zone proteins, ion-channels, and presynaptic membrane proteins, coordinating synaptic vesicle exo- and endocytosis. This review aims to summarise and categorise the diverse and numerous findings describing presynaptic precursor cargo, mode of trafficking, kinesin-based axonal transport and the molecular mechanisms of presynaptic precursor vesicles biogenesis in both vertebrate and invertebrate model systems.
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Affiliation(s)
- Astrid G Petzoldt
- Institute for Biology and Genetics, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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15
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Sun Y, Lee SM, Ku BJ, Moon MJ. Fine structural aspects on the web glue production in the golden orb-web spider Trichonephila clavata. Anim Cells Syst (Seoul) 2023; 27:10-18. [PMID: 36733495 PMCID: PMC9888464 DOI: 10.1080/19768354.2023.2168753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The water-soluble glue substance of the capture threads in Trichonephila clavata is solely produced from two pairs of aggregate silk glands. During the web glue production, secretory vesicles were synthesized via the extensive rough endoplasmic reticulum of epithelial cells. Unlike the clearly described fibrous web production in spiders, the process of aqueous web glue production appears to involve either a condensing or a packaging step by the Golgi complex. In particular, the fine structure of secretory vesicles varies from cell to cell and may represent the secretory cycle. The electron-dense multivesicular bodies were clearly visible as discrete droplets, and the mature secretory product in the glandular epithelium appeared as a spherical vacuole grown by fusion with surrounding small vesicles. Our fine structural observation reveals that the secretion occurs when the release of secreted material involves the loss of part of the cytoplasm. The bleb along the luminal surface of the secretory cells and membrane-bound extracellular vesicles which pinched off from the cell suggests that the secretory product is released by the mechanism of apocrine secretion.
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Affiliation(s)
- Yan Sun
- Department of Biological Sciences, Dankook University, Cheonan, Korea
| | - Seung-Min Lee
- Department of Biological Sciences, Dankook University, Cheonan, Korea
| | - Bon-Jin Ku
- Department of Biological Sciences, Dankook University, Cheonan, Korea
| | - Myung-Jin Moon
- Department of Biological Sciences, Dankook University, Cheonan, Korea, Myung-Jin Moon Department of Biological Sciences, Dankook University, Cheonan31116, Korea
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16
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Sumya FT, Pokrovskaya ID, D'Souza Z, Lupashin VV. Acute COG complex inactivation unveiled its immediate impact on Golgi and illuminated the nature of intra-Golgi recycling vesicles. Traffic 2023; 24:52-75. [PMID: 36468177 PMCID: PMC9969905 DOI: 10.1111/tra.12876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022]
Abstract
Conserved Oligomeric Golgi (COG) complex controls Golgi trafficking and glycosylation, but the precise COG mechanism is unknown. The auxin-inducible acute degradation system was employed to investigate initial defects resulting from COG dysfunction. We found that acute COG inactivation caused a massive accumulation of COG-dependent (CCD) vesicles that carry the bulk of Golgi enzymes and resident proteins. v-SNAREs (GS15, GS28) and v-tethers (giantin, golgin84, and TMF1) were relocalized into CCD vesicles, while t-SNAREs (STX5, YKT6), t-tethers (GM130, p115), and most of Rab proteins remained Golgi-associated. Airyscan microscopy and velocity gradient analysis revealed that different Golgi residents are segregated into different populations of CCD vesicles. Acute COG depletion significantly affected three Golgi-based vesicular coats-COPI, AP1, and GGA, suggesting that COG uniquely orchestrates tethering of multiple types of intra-Golgi CCD vesicles produced by different coat machineries. This study provided the first detailed view of primary cellular defects associated with COG dysfunction in human cells.
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Affiliation(s)
- Farhana Taher Sumya
- Department of Physiology and Cell BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Irina D. Pokrovskaya
- Department of Physiology and Cell BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Zinia D'Souza
- Department of Physiology and Cell BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Vladimir V. Lupashin
- Department of Physiology and Cell BiologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
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17
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Banerjee P, Tan X, Russell WK, Kurie JM. Analysis of Golgi Secretory Functions in Cancer. Methods Mol Biol 2022; 2557:785-810. [PMID: 36512251 DOI: 10.1007/978-1-0716-2639-9_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer cells utilize secretory pathways for paracrine signaling and extracellular matrix remodeling to facilitate directional cell migration, invasion, and metastasis. The Golgi apparatus is a central secretory signaling hub that is often deregulated in cancer. Here we described technologies that utilize microscopic, biochemical, and proteomic approaches to analyze Golgi secretory functions in genetically heterogeneous cancer cell lines.
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Affiliation(s)
- Priyam Banerjee
- Frits and Rita Markus Bio-Imaging Resource Center, The Rockefeller University, New York, NY, USA
| | - Xiaochao Tan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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18
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Khakurel A, Kudlyk T, Pokrovskaya I, D’Souza Z, Lupashin VV. GARP dysfunction results in COPI displacement, depletion of Golgi v-SNAREs and calcium homeostasis proteins. Front Cell Dev Biol 2022; 10:1066504. [PMID: 36578782 PMCID: PMC9791199 DOI: 10.3389/fcell.2022.1066504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Golgi-associated retrograde protein (GARP) is an evolutionary conserved heterotetrameric protein complex that tethers endosome-derived vesicles and is vital for Golgi glycosylation. Microscopy and proteomic approaches were employed to investigate defects in Golgi physiology in RPE1 cells depleted for the GARP complex. Both cis and trans-Golgi compartments were significantly enlarged in GARP-knock-out (KO) cells. Proteomic analysis of Golgi-enriched membranes revealed significant depletion of a subset of Golgi residents, including Ca2+ binding proteins, enzymes, and SNAREs. Validation of proteomics studies revealed that SDF4 and ATP2C1, related to Golgi calcium homeostasis, as well as intra-Golgi v-SNAREs GOSR1 and BET1L, were significantly depleted in GARP-KO cells. Finding that GARP-KO is more deleterious to Golgi physiology than deletion of GARP-sensitive v-SNAREs, prompted a detailed investigation of COPI trafficking machinery. We discovered that in GARP-KO cells COPI is significantly displaced from the Golgi and partially relocalized to the ER-Golgi intermediate compartment (ERGIC). Moreover, COPI accessory proteins GOLPH3, ARFGAP1, GBF1, and BIG1 are also relocated to off-Golgi compartments. We propose that the dysregulation of COPI machinery, along with the depletion of Golgi v-SNAREs and alteration of Golgi Ca2+ homeostasis, are the major driving factors for the depletion of Golgi resident proteins, structural alterations, and glycosylation defects in GARP deficient cells.
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Affiliation(s)
| | | | | | | | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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19
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Control of Unconventional Secretion By The Autophagy Machinery. CURRENT OPINION IN PHYSIOLOGY 2022. [DOI: 10.1016/j.cophys.2022.100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow. PLoS Comput Biol 2022; 18:e1010181. [PMID: 35639793 PMCID: PMC9216591 DOI: 10.1371/journal.pcbi.1010181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/22/2022] [Accepted: 05/07/2022] [Indexed: 12/03/2022] Open
Abstract
The high-level organization of the cell is embedded in indirect relationships that connect distinct cellular processes. Existing computational approaches for detecting indirect relationships between genes typically consist of propagating abstract information through network representations of the cell. However, the selection of genes to serve as the source of propagation is inherently biased by prior knowledge. Here, we sought to derive an unbiased view of the high-level organization of the cell by identifying the genes that propagate and receive information most effectively in the cell, and the indirect relationships between these genes. To this aim, we adapted a perturbation-response scanning strategy initially developed for identifying allosteric interactions within proteins. We deployed this strategy onto an elastic network model of the yeast genetic interaction profile similarity network. This network revealed a superior propensity for information propagation relative to simulated networks with similar topology. Perturbation-response scanning identified the major distributors and receivers of information in the network, named effector and sensor genes, respectively. Effectors formed dense clusters centrally integrated into the network, whereas sensors formed loosely connected antenna-shaped clusters and contained genes with previously characterized involvement in signal transduction. We propose that indirect relationships between effector and sensor clusters represent major paths of information flow between distinct cellular processes. Genetic similarity networks for fission yeast and human displayed similarly strong propensities for information propagation and clusters of effector and sensor genes, suggesting that the global architecture enabling indirect relationships is evolutionarily conserved across species. Our results demonstrate that elastic network modeling of cellular networks constitutes a promising strategy to probe the high-level organization and cooperativity in the cell.
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21
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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: 0.3] [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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22
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D’Souza Z, Sumya FT, Khakurel A, Lupashin V. Getting Sugar Coating Right! The Role of the Golgi Trafficking Machinery in Glycosylation. Cells 2021; 10:cells10123275. [PMID: 34943782 PMCID: PMC8699264 DOI: 10.3390/cells10123275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022] Open
Abstract
The Golgi is the central organelle of the secretory pathway and it houses the majority of the glycosylation machinery, which includes glycosylation enzymes and sugar transporters. Correct compartmentalization of the glycosylation machinery is achieved by retrograde vesicular trafficking as the secretory cargo moves forward by cisternal maturation. The vesicular trafficking machinery which includes vesicular coats, small GTPases, tethers and SNAREs, play a major role in coordinating the Golgi trafficking thereby achieving Golgi homeostasis. Glycosylation is a template-independent process, so its fidelity heavily relies on appropriate localization of the glycosylation machinery and Golgi homeostasis. Mutations in the glycosylation enzymes, sugar transporters, Golgi ion channels and several vesicle tethering factors cause congenital disorders of glycosylation (CDG) which encompass a group of multisystem disorders with varying severities. Here, we focus on the Golgi vesicle tethering and fusion machinery, namely, multisubunit tethering complexes and SNAREs and their role in Golgi trafficking and glycosylation. This review is a comprehensive summary of all the identified CDG causing mutations of the Golgi trafficking machinery in humans.
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