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Caruel M, Pincet F. Dual-Ring SNAREpin Machinery Tuning for Fast Synaptic Vesicle Fusion. Biomolecules 2024; 14:600. [PMID: 38786007 PMCID: PMC11117985 DOI: 10.3390/biom14050600] [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: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
During neurotransmission, neurotransmitters are released less than a millisecond after the arrival of the action potential. To achieve this ultra-fast event, the synaptic vesicle must be pre-docked to the plasma membrane. In this primed state, SNAREpins, the protein-coiled coils whose assembly provides the energy to trigger fusion, are partly zippered and clamped like a hairpin and held open and ready to snap close when the clamp is released. Recently, it was suggested that three types of regulatory factors, synaptophysin, synaptotagmins, and complexins act cooperatively to organize two concentric rings, a central and a peripheral ring, containing up to six SNAREpins each. We used a mechanical model of the SNAREpins with two separate states, half-zippered and fully zippered, and determined the energy landscape according to the number of SNAREpins in each ring. We also performed simulations to estimate the fusion time in each case. The presence of the peripheral SNAREpins generally smoothens the energy landscape and accelerates the fusion time. With the predicted physiological numbers of six central and six peripheral SNAREpins, the fusion time is accelerated at least 100 times by the presence of the peripheral SNAREpins, and fusion occurs in less than 10 μs, which is well within the physiological requirements.
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Affiliation(s)
- Matthieu Caruel
- Univ Paris Est Creteil, Univ Gustave Eiffel, CNRS, UMR 8208, MSME, F-94010 Créteil, France;
| | - Frédéric Pincet
- Laboratoire de Physique de l’École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005 Paris, France
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Taskaeva I, Shatruk A, Bgatova N, Yeremina A, Trunov A, Kononova N, Chernykh V. Autophagy and vesicular trafficking in human uveal melanoma: A histopathological study. Microsc Res Tech 2024; 87:122-132. [PMID: 37698482 DOI: 10.1002/jemt.24417] [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: 01/19/2023] [Revised: 08/04/2023] [Accepted: 09/03/2023] [Indexed: 09/13/2023]
Abstract
Uveal melanoma is an ocular tumor with a high risk of developing metastases. The endo-lysosomal system can affect the melanoma progression by accelerating and facilitating invasion or metastasis. This study aims to conduct comparative analysis of normal choroidal melanocytes and uveal melanoma cells ultrastructure with a focus on intracellular transport system, and to examine the patterns of autophagy- and vesicular trafficking-related proteins expression in a case series of uveal melanomas. Transmission electron microscopy was used to assess the ultrastructure of normal choroidal melanocytes and uveal melanoma cells. The expression levels of autophagy- and vesicular trafficking-related proteins in three histological types of uveal melanoma were analyzed by immunofluorescence staining. Electron microscopy results showed that the autophagic vacuoles were more abundant in normal choroidal melanocytes, than in uveal melanoma cells. The normal choroidal melanocytes were characterized by active intracellular vesicular trafficking; however, the proportion of caveolae was higher in uveal melanoma cells. The spindle type of tumor was characterized by a high expression levels of LC3 beta, while Rab7 and Rab11 proteins expression was significantly up-regulated in the mixed-type tumor cells. The results indicate that uveal melanoma cells probably have lower basal levels of autophagy and higher receptor-mediated endocytic trafficking-associated with caveolae than normal choroidal melanocytes. RESEARCH HIGHLIGHTS: The autophagic vacuoles are abundant in normal choroidal melanocytes. Uveal melanoma cells are characterized by a high proportion of caveolae. The high expression levels of LC3 beta were revealed in a spindle type of tumor, while Rab7 and Rab11 proteins expression was up-regulated in the mixed-type tumor cells.
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Affiliation(s)
- Iuliia Taskaeva
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia Shatruk
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nataliya Bgatova
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alena Yeremina
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Aleksander Trunov
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Natalya Kononova
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Valeriy Chernykh
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
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Guzewska MM, Witek KJ, Karnas E, Rawski M, Zuba-Surma E, Kaczmarek MM. miR-125b-5p impacts extracellular vesicle biogenesis, trafficking, and EV subpopulation release in the porcine trophoblast by regulating ESCRT-dependent pathway. FASEB J 2023; 37:e23054. [PMID: 37402070 DOI: 10.1096/fj.202300710r] [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: 04/11/2023] [Revised: 05/23/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
Intercellular communication is a critical process that ensures cooperation between distinct cell types at the embryo-maternal interface. Extracellular vesicles (EVs) are considered to be potent mediators of this communication by transferring biological information in their cargo (e.g., miRNAs) to the recipient cells. miRNAs are small non-coding RNAs that affect the function and fate of neighboring and distant cells by regulating gene expression. Focusing on the maternal side of the dialog, we recently revealed the impact of embryonic signals, including miRNAs, on EV-mediated cell-to-cell communication. In this study, we show the regulatory mechanism of the miR-125b-5p ESCRT-mediated EV biogenesis pathway and the further secretion of EVs by trophoblasts at the time when the crucial steps of implantation are taking place. To test the ability of miR-125b-5p to influence the expression of genes involved in the generation and release of EV subpopulations in porcine conceptuses, we used an ex vivo approach. Next, in silico and in vitro analyses were performed to confirm miRNA-mRNA interactions. Finally, EV trafficking and release were assessed using several imaging and particle analysis tools. Our results indicated that conceptus development and implantation are accompanied by changes in the abundance of EV biogenesis and trafficking machinery. ESCRT-dependent EV biogenesis and the further secretion of EVs were modulated by miR-125b-5p, specifically impacting the ESCRT-II complex (via VPS36) and EV trafficking in primary porcine trophoblast cells. The identified miRNA-ESCRT interplay led to the generation and secretion of specific subpopulations of EVs. miRNA present at the embryo-maternal interface governs EV-mediated communication between the mother and the developing conceptus, leading to the generation, trafficking, and release of characteristic subpopulations of EVs.
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Affiliation(s)
- Maria M Guzewska
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Krzysztof J Witek
- Cell and Tissue Analysis and Imaging Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Elżbieta Karnas
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Ewa Zuba-Surma
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Monika M Kaczmarek
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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Le Naour J, Sztupinszki Z, Carbonnier V, Casiraghi O, Marty V, Galluzzi L, Szallasi Z, Kroemer G, Vacchelli E. A loss-of-function polymorphism in ATG16L1 compromises therapeutic outcome in head and neck carcinoma patients. Oncoimmunology 2022; 11:2059878. [PMID: 35481288 PMCID: PMC9037530 DOI: 10.1080/2162402x.2022.2059878] [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] [Indexed: 11/25/2022] Open
Abstract
The anticancer immune response is shaped by immunogenic cell stress and death pathways. Thus, cancer cells can release danger-associated molecular patterns that act on pattern recognition receptors expressed by dendritic cells and their precursors to elicit an antitumor immune response. Here, we investigated the impact of single nucleotide polymorphisms (SNPs) in genes affecting this cancer-immunity dialogue in the context of head and neck squamous cell carcinoma (HNSCC). We observed that homozygosity for a loss-of-function SNP (rs2241880, leading to the substitution of a threonine residue in position 300 by an alanine) affecting autophagy related 16 like 1 (ATG16L1) is coupled to poor progression-free survival in platinum-treated HNSCC patients. This result was obtained on a cohort of patients enrolled at the Gustave Roussy Cancer Campus and was validated on an independent cohort of The Cancer Genome Atlas (TCGA). Homozygosity in rs2241880 is well known to predispose to Crohn’s disease, and epidemiological associations between Crohn’s disease and HNSCC have been reported at the levels of cancer incidence and prognosis. We speculate that rs2241880 might be partially responsible for this association.
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Affiliation(s)
- Julie Le Naour
- Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris Sud, Paris Saclay, Faculty of Medicine Kremlin Bicêtre, France
| | - Zsofia Sztupinszki
- Computational Health Informatics Program (CHIP), Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Vincent Carbonnier
- Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris Sud, Paris Saclay, Faculty of Medicine Kremlin Bicêtre, France
| | - Odile Casiraghi
- Department of Head and Neck Surgical and Medical Oncology, Gustave Roussy Cancer Campus, Paris-Saclay University, Villejuif, France
| | - Virginie Marty
- Experimental and Translational Pathology Platform (PETRA), AMMICa Inserm US23/UMS CNRS3655, Gustave Roussy Cancer Campus, Villejuif, France
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Guido Kroemer
- Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Institut du Cancer Paris CARPEMAP-HP, Hôpital Européen Georges Pompidou, Pôle de Biologie, Paris, France
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Erika Vacchelli
- Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
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Taskaeva I, Bgatova N. Microvasculature in hepatocellular carcinoma: An ultrastructural study. Microvasc Res 2021; 133:104094. [PMID: 33011171 DOI: 10.1016/j.mvr.2020.104094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/18/2020] [Accepted: 09/28/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most vascularized tumor types, and is characterized by development of heterogeneous immature vessels with increased permeability. Here, we analyzed morphology and vascular permeability-related structures in endothelial cells of HCC microvessels. METHODS Small (Type I) and large (Type II) peritumoral blood microvessels were assessed in HCC-bearing mice. By transmission electron microscopy, endothelial cell cytoplasm area, free transport vesicles, vesiculo-vacuolar organelles and clathrin-coated vesicles were measured. RESULTS The phenotypic changes in the HCC microvessels included presence of sinusoidal capillarization, numerous luminal microprocesses and abnormal luminal channels, irregular dilatations of interendothelial junctions, local detachment of basement membranes and widened extracellular space. Endothelial cells Type I microvessels showed increased vesicular trafficking-related structures. CONCLUSION Ultrastructural characteristics of microvessels Type I can associate with HCC new-formed microvessels. The morphological changes observed in HCC microvessels might explain the increased transcellular and paracellular permeability in HCC endothelial cells.
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Affiliation(s)
- Iuliia Taskaeva
- Laboratory of Ultrastructural research, Research Institute of Clinical and Experimental Lymphology, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Laboratory of Boron-Neutron Capture Therapy, Department of Physics, Novosibirsk State University, Novosibirsk, Russia.
| | - Nataliya Bgatova
- Laboratory of Ultrastructural research, Research Institute of Clinical and Experimental Lymphology, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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de Oliveira RC, Tye G, Sampaio LP, Shiju TM, DeDreu J, Menko AS, Santhiago MR, Wilson SE. TGFβ1 and TGFβ2 proteins in corneas with and without stromal fibrosis: Delayed regeneration of apical epithelial growth factor barrier and the epithelial basement membrane in corneas with stromal fibrosis. Exp Eye Res 2021; 202:108325. [PMID: 33263285 PMCID: PMC7856119 DOI: 10.1016/j.exer.2020.108325] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 12/17/2022]
Abstract
The purpose of this study was to investigate the expression and localization of transforming growth factor (TGF) β1 and TGFβ2 in rabbit corneas that healed with and without stromal fibrosis, and to further study defective perlecan incorporation in the epithelial basement membrane (EBM) in corneas with scarring fibrosis. A total of 120 female rabbits had no surgery, -4.5D PRK, or -9D PRK. Immunohistochemistry (IHC) was performed at time points from unwounded to eight weeks after surgery, with four corneas at each time point in each group. Multiplex IHC was performed for TGFβ1 or TGFβ2, with Image-J quantitation, and keratocan, vimentin, alpha-smooth muscle actin (SMA), perlecan, laminin-alpha 5, nidogen-1 or CD11b. Corneas at the four-week peak for myofibroblast and fibrosis development were evaluated using Imaris 3D analysis. Delayed regeneration of both an apical epithelial growth factor barrier and EBM barrier function, including defective EBM perlecan incorporation, was greater in high injury -9D PRK corneas compared to -4.5D PRK corneas without fibrosis. Defective apical epithelial growth factor barrier and EBM allowed epithelial and tear TGFβ1 and tear TGFβ2 to enter the corneal stroma to drive myofibroblast generation in the anterior stroma from vimentin-positive corneal fibroblasts, and likely fibrocytes. Vimentin-positive cells and unidentified vimentin-negative, CD11b-negative cells also produce TGFβ1 and/or TGFβ2 in the stroma in some corneas. TGFβ1 and TGFβ2 were at higher levels in the anterior stroma in the weeks preceding myofibroblast development in the -9D group. All -9D corneas (beginning two to three weeks after surgery), and four -4.5D PRK corneas developed significant SMA + myofibroblasts and stromal fibrosis. Both the apical epithelial growth factor barrier and/or EBM barrier functions tended to regenerate weeks earlier in -4.5D PRK corneas without fibrosis, compared to -4.5D or -9D PRK corneas with fibrosis. SMA-positive myofibroblasts were markedly reduced in most corneas by eight weeks after surgery. The apical epithelial growth factor barrier and EBM barrier limit TGFβ1 and TGFβ2 entry into the corneal stroma to modulate corneal fibroblast and myofibroblast development associated with scarring stromal fibrosis. Delayed regeneration of these barriers in corneas with more severe injuries promotes myofibroblast development, prolongs myofibroblast viability and triggers stromal scarring fibrosis.
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Affiliation(s)
| | - George Tye
- The Cole Eye Institute, The Cleveland Clinic, Cleveland, OH, USA
| | | | | | - JodiRae DeDreu
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - A Sue Menko
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Marcony R Santhiago
- Department of Ophthalmology, University of São Paulo, Sao Paulo, Brazil and, University of Southern California Roski Eye Institute, Los Angeles, CA, USA
| | - Steven E Wilson
- The Cole Eye Institute, The Cleveland Clinic, Cleveland, OH, USA.
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Castillo-Badillo JA, Bandi AC, Harlalka S, Gautam N. SRRF-Stream Imaging of Optogenetically Controlled Furrow Formation Shows Localized and Coordinated Endocytosis and Exocytosis Mediating Membrane Remodeling. ACS Synth Biol 2020; 9:902-919. [PMID: 32155337 DOI: 10.1021/acssynbio.9b00521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cleavage furrow formation during cytokinesis involves extensive membrane remodeling. In the absence of methods to exert dynamic control over these processes, it has been a challenge to examine the basis of this remodeling. Here we used a subcellular optogenetic approach to induce this at will and found that furrow formation is mediated by actomyosin contractility, retrograde plasma membrane flow, localized decrease in membrane tension, and endocytosis. FRAP, 4-D imaging, and inhibition or upregulation of endocytosis or exocytosis show that ARF6 and Exo70 dependent localized exocytosis supports a potential model for intercellular bridge elongation. TIRF and Super Resolution Radial Fluctuation (SRRF) stream microscopy show localized VAMP2-mediated exocytosis and incorporation of membrane lipids from vesicles into the plasma membrane at the front edge of the nascent daughter cell. Thus, spatially separated but coordinated plasma membrane depletion and addition are likely contributors to membrane remodeling during cytokinetic processes.
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Characterizing Oligonucleotide Uptake in Cultured Cells: A Case Study Using AS1411 Aptamer. Methods Mol Biol 2020; 2036:173-186. [PMID: 31410797 DOI: 10.1007/978-1-4939-9670-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oligonucleotides can be designed or evolved to bind to specific DNA, RNA, protein, or small molecule targets and thereby alter the biological function of the target. The therapeutic potential of oligonucleotides targeted to intracellular molecules will depend largely on their ability to be taken up by the cells of interest, as well as their subsequent subcellular distribution. Here we describe methods to characterize the extent and mechanism of cellular uptake of AS1411, an aptamer oligonucleotide that has progressed to human clinical trials and which is also widely used by researchers as a cancer-targeting ligand.
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Bernal-Conde LD, Ramos-Acevedo R, Reyes-Hernández MA, Balbuena-Olvera AJ, Morales-Moreno ID, Argüero-Sánchez R, Schüle B, Guerra-Crespo M. Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles. Front Neurosci 2020; 13:1399. [PMID: 32038126 PMCID: PMC6989544 DOI: 10.3389/fnins.2019.01399] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022] Open
Abstract
Alpha-synuclein (α-syn) is localized in cellular organelles of most neurons, but many of its physiological functions are only partially understood. α-syn accumulation is associated with Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy as well as other synucleinopathies; however, the exact pathomechanisms that underlie these neurodegenerative diseases remain elusive. In this review, we describe what is known about α-syn function and pathophysiological changes in different cellular structures and organelles, including what is known about its behavior as a prion-like protein. We summarize current knowledge of α-syn and its pathological forms, covering its effect on each organelle, including aggregation and toxicity in different model systems, with special interest on the mitochondria due to its relevance during the apoptotic process of dopaminergic neurons. Moreover, we explore the effect that α-syn exerts by interacting with chromatin remodeling proteins that add or remove histone marks, up-regulate its own expression, and resume the impairment that α-syn induces in vesicular traffic by interacting with the endoplasmic reticulum. We then recapitulate the events that lead to Golgi apparatus fragmentation, caused by the presence of α-syn. Finally, we report the recent findings about the accumulation of α-syn, indirectly produced by the endolysosomal system. In conclusion, many important steps into the understanding of α-syn have been made using in vivo and in vitro models; however, the time is right to start integrating observational studies with mechanistic models of α-syn interactions, in order to look at a more complete picture of the pathophysiological processes underlying α-synucleinopathies.
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Affiliation(s)
- Luis D. Bernal-Conde
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Ramos-Acevedo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mario A. Reyes-Hernández
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrea J. Balbuena-Olvera
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ishbelt D. Morales-Moreno
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rubén Argüero-Sánchez
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Birgitt Schüle
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, CA, United States
| | - Magdalena Guerra-Crespo
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Medicina Regenerativa, Departamento de Cirugía, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Manca F, Pincet F, Truskinovsky L, Rothman JE, Foret L, Caruel M. SNARE machinery is optimized for ultrafast fusion. Proc Natl Acad Sci U S A 2019; 116:2435-2442. [PMID: 30700546 PMCID: PMC6377469 DOI: 10.1073/pnas.1820394116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
SNARE proteins zipper to form complexes (SNAREpins) that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 s to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic vesicles much faster: in a 10th of a millisecond. We propose that, similar to the case of muscle myosins, the ultrafast fusion results from cooperative action of many SNAREpins. The coupling originates from mechanical interactions induced by confining scaffolds. Each SNAREpin is known to have enough energy to overcome the fusion barrier of 25-[Formula: see text]; however, the fusion barrier only becomes relevant when the SNAREpins are nearly completely zippered, and from this state, each SNAREpin can deliver only a small fraction of this energy as mechanical work. Therefore, they have to act cooperatively, and we show that at least three of them are needed to ensure fusion in less than a millisecond. However, to reach the prefusion state collectively, starting from the experimentally observed half-zippered metastable state, the SNAREpins have to mechanically synchronize, which takes more time as the number of SNAREpins increases. Incorporating this somewhat counterintuitive idea in a simple coarse-grained model results in the prediction that there should be an optimum number of SNAREpins for submillisecond fusion: three to six over a wide range of parameters. Interestingly, in situ cryoelectron microscope tomography has very recently shown that exactly six SNAREpins participate in the fusion of each synaptic vesicle. This number is in the range predicted by our theory.
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Affiliation(s)
- Fabio Manca
- Laboratoire de Physique de l'Ecole Normale Supérieure (LPENS), CNRS, Ecole Normale Supérieure, 75005 Paris, France
- LPENS, Sorbonne Université, 75005 Paris, France
- LPENS, Université Paris-Diderot, 75005 Paris, France
- LPENS, Université PSL, 75005 Paris, France
| | - Frederic Pincet
- Laboratoire de Physique de l'Ecole Normale Supérieure (LPENS), CNRS, Ecole Normale Supérieure, 75005 Paris, France
- LPENS, Sorbonne Université, 75005 Paris, France
- LPENS, Université Paris-Diderot, 75005 Paris, France
- LPENS, Université PSL, 75005 Paris, France
| | - Lev Truskinovsky
- Physique et Mécanique des Milieux Hétérogènes, CNRS, Ecole Supérieure de Physique et de Chimie Industrielles, Université PSL, 75231 Paris Cedex 05, France
| | - James E Rothman
- Department of Cell Biology, Yale University, New Haven, CT 06520;
- Department of Experimental Epilepsy, Institute of Neurology, University College London, London WC1E 6BT, United Kingdom
| | - Lionel Foret
- Laboratoire de Physique de l'Ecole Normale Supérieure (LPENS), CNRS, Ecole Normale Supérieure, 75005 Paris, France
- LPENS, Sorbonne Université, 75005 Paris, France
- LPENS, Université Paris-Diderot, 75005 Paris, France
- LPENS, Université PSL, 75005 Paris, France
| | - Matthieu Caruel
- Modélisation et Simulation Multi-Echelle, CNRS, Université Paris-Est Créteil, 94010 Créteil Cedex, France
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11
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Ohshima H. Oral biosciences: The annual review 2017. J Oral Biosci 2018. [DOI: 10.1016/j.job.2017.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Shitara A, Shibui T, Okayama M, Arakawa T, Mizoguchi I, Sakakura Y, Takuma T. VAMP4 and its cognate SNAREs are required for maintaining the ribbon structure of the Golgi apparatus. J Oral Biosci 2017. [DOI: 10.1016/j.job.2017.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Li N, Zhao R, Sun Y, Ye Z, He K, Fang X. Single-molecule imaging and tracking of molecular dynamics in living cells. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nww055] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Unlike the ensemble-averaging measurements, the single-molecule imaging and tracking (SMIT) in living cells provides the real-time quantitative information about the locations, kinetics, dynamics and interactions of individual molecules in their native environments with high spatiotemporal resolution and minimal perturbation. The past decade has witnessed a transforming development in the methods of SMIT with living cells, including fluorescent probes, labeling strategies, fluorescence microscopy, and detection and tracking algorithms. In this review, we will discuss these aspects with a particular focus on their recent advancements. We will then describe representative single-molecule studies to illustrate how the single-molecule approaches can be applied to monitor biomolecular interaction/reaction dynamics, and extract the molecular mechanistic information for different cellular systems.
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Affiliation(s)
- Nan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi Ye
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangmin He
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Liu M, Qiu W, He X, Zheng L, Song X, Han X, Jiang J, Qiao G, Sang J, Liu M, Zhuo R. Functional Characterization of a Gene in Sedum alfredii Hance Resembling Rubber Elongation Factor Endowed with Functions Associated with Cadmium Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:965. [PMID: 27446189 PMCID: PMC4925709 DOI: 10.3389/fpls.2016.00965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/16/2016] [Indexed: 05/19/2023]
Abstract
Cadmium is a major toxic heavy-metal pollutant considering their bioaccumulation potential and persistence in the environment. The hyperaccumulating ecotype of Sedum alfredii Hance is a Zn/Cd co-hyperaccumulator inhabiting in a region of China with soils rich in Pb/Zn. Investigations into the underlying molecular regulatory mechanisms of Cd tolerance are of substantial interest. Here, library screening for genes related to cadmium tolerance identified a gene resembling the rubber elongation factor gene designated as SaREFl. The heterologous expression of SaREFl rescued the growth of a transformed Cd-sensitive strain (ycf1). Furthermore, SaREFl-expressing Arabidopsis plants were more tolerant to cadmium stress compared with wild type by measuring parameters of root length, fresh weight and physiological indexes. When under four different heavy metal treatments, we found that SaREFl responded most strongly to Cd and the root was the plant organ most sensitive to this heavy metal. Yeast two-hybrid screening of SaREFl as a bait led to the identification of five possible interacting targets in Sedum alfredii Hance. Among them, a gene annotated as prenylated Rab acceptor 1 (PRA1) domain protein was detected with a high frequency. Moreover, subcellular localization of SaREF1-GFP fusion protein revealed some patchy spots in cytosol suggesting potential association with organelles for its cellular functions. Our findings would further enrich the connotation of REF-like genes and provide theoretical assistance for the application in breeding heavy metal-tolerant plants.
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Affiliation(s)
- Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Wenming Qiu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Xuelian He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
- Biotechnology Research Center of China Three Gorges University, YichangChina
| | - Liu Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
- Biotechnology Research Center of China Three Gorges University, YichangChina
| | - Xixi Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Jian Sang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
| | - Mingqing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Vocational Secondary Specialized School of Hedong District, LinyiChina
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, BeijingChina
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangzhouChina
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15
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Beletkaia E, Fenz SF, Pomp W, Snaar-Jagalska BE, Hogendoorn PW, Schmidt T. CXCR4 signaling is controlled by immobilization at the plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:607-16. [DOI: 10.1016/j.bbamcr.2015.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 12/23/2015] [Accepted: 12/29/2015] [Indexed: 12/14/2022]
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16
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RAB7 counteracts PI3K-driven macropinocytosis activated at early stages of melanoma development. Oncotarget 2016; 6:11848-62. [PMID: 26008978 PMCID: PMC4494909 DOI: 10.18632/oncotarget.4055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022] Open
Abstract
Derailed endolysosomal trafficking is emerging as a widespread feature of aggressive neoplasms. However, the oncogenic signals that alter membrane homeostasis and their specific contribution to cancer progression remain unclear. Understanding the upstream drivers and downstream regulators of aberrant vesicular trafficking is distinctly important in melanoma. This disease is notorious for its inter- and intra-tumoral heterogeneity. Nevertheless, melanomas uniformly overexpress a cluster of endolysosomal genes, being particularly addicted to the membrane traffic regulator RAB7. Still, the underlying mechanisms and temporal determinants of this dependency have yet to be defined. Here we addressed these questions by combining electron microscopy, real time imaging and mechanistic analyses of vesicular trafficking in normal and malignant human melanocytic cells. This strategy revealed Class I PI3K as the key trigger of a hyperactive influx of macropinosomes that melanoma cells counteract via RAB7-mediated lysosomal degradation. In addition, gain- and loss-of-function in vitro studies followed by histopathological validation in clinical biopsies and genetically-engineered mouse models, traced back the requirement of RAB7 to the suppression of premature cellular senescence traits elicited in melanocytes by PI3K-inducing oncogenes. Together, these results provide new insight into the regulators and modes of action of RAB7, broadening the impact of endosomal fitness on melanoma development.
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17
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PPIP5K1 interacts with the exocyst complex through a C-terminal intrinsically disordered domain and regulates cell motility. Cell Signal 2016; 28:401-411. [PMID: 26854614 DOI: 10.1016/j.cellsig.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
Abstract
Cellular signaling involves coordinated regulation of many events. Scaffolding proteins are crucial regulators of cellular signaling, because they are able to affect numerous events by coordinating specific interactions among multiple protein partners in the same pathway. Scaffolding proteins often contain intrinsically disordered regions (IDR) that facilitate the formation and function of distinct protein complexes. We show that PPIP5K1 contains an unusually long and evolutionarily conserved IDR. To investigate the biological role(s) of this domain, we identified interacting proteins using affinity purification coupled with mass spectrometry. Here, we report that PPIP5K1 is associated with a network of proteins that regulate vesicle-mediated transport. We further identified exocyst complex component 1 as a direct interactor with the IDR of PPIP5K1. Additionally, we report that knockdown of PPIP5K1 decreases motility of HeLa cells in a wound-healing assay. These results suggest that PPIP5K1 might play an important role in regulating function of exocyst complex in establishing cellular polarity and directional migration of cells.
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18
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Davis BW, Seabury CM, Brashear WA, Li G, Roelke-Parker M, Murphy WJ. Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models. Mol Biol Evol 2015; 32:2534-46. [PMID: 26006188 PMCID: PMC4592343 DOI: 10.1093/molbev/msv124] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented "rule of speciation." We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the "Large X-Effect" in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation.
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Affiliation(s)
- Brian W Davis
- College of Veterinary Medicine, Texas A&M University Interdisciplinary Program in Genetics, Texas A&M University
| | - Christopher M Seabury
- College of Veterinary Medicine, Texas A&M University Interdisciplinary Program in Genetics, Texas A&M University
| | - Wesley A Brashear
- College of Veterinary Medicine, Texas A&M University Interdisciplinary Program in Genetics, Texas A&M University
| | - Gang Li
- College of Veterinary Medicine, Texas A&M University
| | - Melody Roelke-Parker
- College of Veterinary Medicine, Texas A&M University National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - William J Murphy
- College of Veterinary Medicine, Texas A&M University Interdisciplinary Program in Genetics, Texas A&M University
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19
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Khan FR, Misra SK, Bury NR, Smith BD, Rainbow PS, Luoma SN, Valsami-Jones E. Inhibition of potential uptake pathways for silver nanoparticles in the estuarine snail Peringia ulvae. Nanotoxicology 2014; 9:493-501. [DOI: 10.3109/17435390.2014.948519] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Farhan R. Khan
- Life Sciences, Natural History Museum, Cromwell Road, London, UK,
| | - Superb K. Misra
- Earth Sciences, Natural History Museum, Cromwell Road, London, UK,
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK,
| | - Nicolas R. Bury
- Nutritional Sciences Division, King's College London, Franklin-Wilkins Building, London, UK, and
| | - Brian D. Smith
- Life Sciences, Natural History Museum, Cromwell Road, London, UK,
| | | | - Samuel N. Luoma
- John Muir Institute of the Environment, University of California at Davis, Davis, CA, USA
| | - Eugenia Valsami-Jones
- Earth Sciences, Natural History Museum, Cromwell Road, London, UK,
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK,
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20
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Ivanov AI. Pharmacological inhibitors of exocytosis and endocytosis: novel bullets for old targets. Methods Mol Biol 2014; 1174:3-18. [PMID: 24947371 DOI: 10.1007/978-1-4939-0944-5_1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Pharmacological inhibitors of vesicle trafficking possess great promise as valuable analytical tools for the study of a variety of biological processes and as potential therapeutic agents to fight microbial infections and cancer. However, many commonly used trafficking inhibitors are characterized by poor selectivity that diminishes their use in solving basic problems of cell biology or drug development. Recent high-throughput chemical screens intensified the search for novel modulators of vesicle trafficking, and successfully identified a number of small molecules that inhibit exocytosis and endocytosis in different types of mammalian cells. This chapter provides a systematic overview of recently discovered inhibitors of vesicle trafficking. It describes cellular effects and mechanisms of action of novel inhibitors of exocytosis and endocytosis. Furthermore, it pays special attention to the selectivity and possible off-target effects of these inhibitors.
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Affiliation(s)
- Andrei I Ivanov
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Virginia Commonwealth University, Goodwin Laboratory, 401 College Street, 980035, Richmond, VA, 23298, USA,
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21
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Shitara A, Shibui T, Okayama M, Arakawa T, Mizoguchi I, Sakakura Y, Shakakura Y, Takuma T. VAMP4 is required to maintain the ribbon structure of the Golgi apparatus. Mol Cell Biochem 2013; 380:11-21. [PMID: 23677696 PMCID: PMC3695666 DOI: 10.1007/s11010-013-1652-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/11/2013] [Indexed: 10/31/2022]
Abstract
The Golgi apparatus forms a twisted ribbon-like network in the juxtanuclear region of vertebrate cells. Vesicle-associated membrane protein 4 (VAMP4), a v-SNARE protein expressed exclusively in the vertebrate trans-Golgi network (TGN), plays a role in retrograde trafficking from the early endosome to the TGN, although its precise function within the Golgi apparatus remains unclear. To determine whether VAMP4 plays a functional role in maintaining the structure of the Golgi apparatus, we depleted VAMP4 gene expression using RNA interference technology. Depletion of VAMP4 from HeLa cells led to fragmentation of the Golgi ribbon. These fragments were not uniformly distributed throughout the cytoplasm, but remained in the juxtanuclear area. Electron microscopy and immunohistochemistry showed that in the absence of VAMP4, the length of the Golgi stack was shortened, but Golgi stacking was normal. Anterograde trafficking was not impaired in VAMP4-depleted cells, which contained intact microtubule arrays. Depletion of the cognate SNARE partners of VAMP4, syntaxin 6, syntaxin 16, and Vti1a also disrupted the Golgi ribbon structure. Our findings suggested that the maintenance of Golgi ribbon structure requires normal retrograde trafficking from the early endosome to the TGN, which is likely to be mediated by the formation of VAMP4-containing SNARE complexes.
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Affiliation(s)
- Akiko Shitara
- Division of Biochemistry, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu Hokkaido, Ishikari 061-0293, Japan.
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22
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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Ying H, Yue BYJT. Cellular and molecular biology of optineurin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 294:223-58. [PMID: 22364875 DOI: 10.1016/b978-0-12-394305-7.00005-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Optineurin is a gene linked to glaucoma, amyotrophic lateral sclerosis, other neurodegenerative diseases, and Paget's disease of bone. This review describes the characteristics of optineurin and summarizes the cellular and molecular biology investigations conducted so far on optineurin. Data from a number of laboratories indicate that optineurin is a cytosolic protein containing 577 amino acid residues. Interacting with proteins such as myosin VI, Rab8, huntingtin, transferrin receptor, and TANK-binding kinase 1, optineurin is involved in basic cellular functions including protein trafficking, maintenance of the Golgi apparatus, as well as NF-κB pathway, antiviral, and antibacteria signaling. Mutation or alteration of homeostasis of optineurin (such as overexpression or knockdown) results in adverse consequences in the cells, leading to the development of neurodegenerative diseases including glaucoma.
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Affiliation(s)
- Hongyu Ying
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, College of Medicine, Chicago, Illinois, USA
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24
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Fan JL, Wei XZ, Wan LC, Zhang LY, Zhao XQ, Liu WZ, Hao HQ, Zhang HY. Disarrangement of actin filaments and Ca²⁺ gradient by CdCl₂ alters cell wall construction in Arabidopsis thaliana root hairs by inhibiting vesicular trafficking. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1157-67. [PMID: 21497412 DOI: 10.1016/j.jplph.2011.01.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 01/03/2011] [Accepted: 01/27/2011] [Indexed: 05/08/2023]
Abstract
Cadmium (Cd), one of the most toxic heavy metals, inhibits many cellular and physiological processes in plants. Here, the involvement of cytoplasmic Ca²⁺ gradient and actin filaments (AFs) in vesicular trafficking, cell wall deposition and tip growth was investigated during root (hair) development of Arabidopsis thaliana in response to CdCl₂ treatment. Seed germination and root elongation were prevented in a dose- and time-dependent manner by CdCl₂ treatment. Fluorescence labelling and non-invasive detection showed that CdCl₂ inhibited extracellular Ca²⁺ influx, promoted intracellular Ca²⁺ efflux, and disturbed the cytoplasmic tip-focused Ca²⁺ gradient. In vivo labelling revealed that CdCl₂ modified actin organization, which subsequently contributed to vesicle trafficking. Transmission electron microscopy revealed that CdCl₂ induced cytoplasmic vacuolization and was detrimental to organelles such as mitochondria and endoplasmic reticulum (ER). Finally, immunofluorescent labelling and Fourier transform infrared (FTIR) analysis indicated that configuration/distribution of cell wall components such as pectins and cellulose was significantly altered in response to CdCl₂. Our results indicate that CdCl₂ induces disruption of Ca²⁺ gradient and AFs affects the distribution of cell wall components in root hairs by disturbing vesicular trafficking in A. thaliana.
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Affiliation(s)
- Jun-Ling Fan
- Key Laboratory of Photosynthesis and Molecular Environmental Physiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
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25
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Charrua A, Avelino A, Cruz F. Modulation of urinary bladder innervation: TRPV1 and botulinum toxin A. Handb Exp Pharmacol 2011:345-374. [PMID: 21290235 DOI: 10.1007/978-3-642-16499-6_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The persisting interest around neurotoxins such as vanilloids and botulinum toxin (BoNT) derives from their marked effect on detrusor overactivity refractory to conventional antimuscarinic treatments. In addition, both are administered by intravesical route. This offers three potential advantages. First, intravesical therapy is an easy way to provide high concentrations of pharmacological agents in the bladder tissue without causing unsuitable levels in other organs. Second, drugs effective on the bladder, but inappropriate for systemic administration, can be safely used as it is the case of vanilloids and BoNT. Third, the effects of one single treatment might be extremely longlasting, contributing to render these therapies highly attractive to patients despite the fact that the reasons to the prolonged effect are still incompletely understood. Attractive as it may be, intravesical pharmacological therapy should still be considered as a second-line treatment in patients refractory to conventional oral antimuscarinic therapy or who do not tolerate its systemic side effects. However, the increasing off-label use of these neurotoxins justifies a reappraisal of their pharmacological properties.
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Affiliation(s)
- Ana Charrua
- Institute of Histology and Embryology, Porto, Portugal
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26
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Kim HJ, Soyombo AA, Tjon-Kon-Sang S, So I, Muallem S. The Ca(2+) channel TRPML3 regulates membrane trafficking and autophagy. Traffic 2009; 10:1157-67. [PMID: 19522758 PMCID: PMC2993507 DOI: 10.1111/j.1600-0854.2009.00924.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
TRPML3 is an inward rectifying Ca(2+) channel that is regulated by extracytosolic H(+). Although gain-of-function mutation in TRPML3 causes the varitint-waddler phenotype, the role of TRPML3 in cellular physiology is not known. In this study, we report that TRPML3 is a prominent regulator of endocytosis, membrane trafficking and autophagy. Gradient fractionation and confocal localization reveal that TRPML3 is expressed in the plasma membrane and multiple intracellular compartments. However, expression of TRPML3 is dynamic, with accumulation of TRPML3 in the plasma membrane upon inhibition of endocytosis, and recruitment of TRPML3 to autophagosomes upon induction of autophagy. Accordingly, overexpression of TRPML3 leads to reduced constitutive and regulated endocytosis, increased autophagy and marked exacerbation of autophagy evoked by various cell stressors with nearly complete recruitment of TRPML3 into the autophagosomes. Importantly, both knockdown of TRPML3 by siRNA and expression of the channel-dead dominant negative TRPML3(D458K) have a reciprocal effect, reducing endocytosis and autophagy. These findings reveal a prominent role for TRPML3 in regulating endocytosis, membrane trafficking and autophagy, perhaps by controlling the Ca(2+) in the vicinity of cellular organelles that is necessary to regulate these cellular events.
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Affiliation(s)
- Hyun Jin Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Abigail A. Soyombo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sandra Tjon-Kon-Sang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Insuk So
- Department of Physiology and Biophysics, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Shmuel Muallem
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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27
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Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. Mol Cell Biol 2009; 29:5251-63. [PMID: 19620288 DOI: 10.1128/mcb.00495-09] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tethering factors and SNAREs control the last two steps of vesicular trafficking: the initial interaction and the fusion, respectively, of transport vesicles with target membranes. The Golgi-associated retrograde protein (GARP) complex regulates retrograde transport from endosomes to the trans-Golgi network (TGN). Although GARP has been proposed to function as a tethering factor at the TGN, direct evidence for such a role is still lacking. Herein we report novel and specific interactions of the mammalian GARP complex with SNAREs that participate in endosome-to-TGN transport, namely, syntaxin 6, syntaxin 16, and Vamp4. These interactions depend on the N-terminal regions of Vps53 and Vps54 and the SNARE motif of the SNAREs. We show that GARP functions upstream of the SNAREs, regulating their localization and assembly into SNARE complexes. However, interactions of GARP with SNAREs are insufficient to promote retrograde transport, because deletion of the C-terminal region of Vps53 precludes GARP function without affecting GARP-SNARE interactions. Finally, we present in vitro data consistent with a tethering role for GARP, which is disrupted by deletion of the Vps53 C-terminal region. These findings indicate that GARP orchestrates retrograde transport from endosomes to the TGN by promoting vesicle tethering and assembly of SNARE complexes in consecutive, independent steps.
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28
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Sudhahar C, Haney R, Xue Y, Stahelin R. Cellular membranes and lipid-binding domains as attractive targets for drug development. Curr Drug Targets 2008; 9:603-13. [PMID: 18691008 PMCID: PMC5975357 DOI: 10.2174/138945008785132420] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Interdisciplinary research focused on biological membranes has revealed them as signaling and trafficking platforms for processes fundamental to life. Biomembranes harbor receptors, ion channels, lipid domains, lipid signals, and scaffolding complexes, which function to maintain cellular growth, metabolism, and homeostasis. Moreover, abnormalities in lipid metabolism attributed to genetic changes among other causes are often associated with diseases such as cancer, arthritis and diabetes. Thus, there is a need to comprehensively understand molecular events occurring within and on membranes as a means of grasping disease etiology and identifying viable targets for drug development. A rapidly expanding field in the last decade has centered on understanding membrane recruitment of peripheral proteins. This class of proteins reversibly interacts with specific lipids in a spatial and temporal fashion in crucial biological processes. Typically, recruitment of peripheral proteins to the different cellular sites is mediated by one or more modular lipid-binding domains through specific lipid recognition. Structural, computational, and experimental studies of these lipid-binding domains have demonstrated how they specifically recognize their cognate lipids and achieve subcellular localization. However, the mechanisms by which these modular domains and their host proteins are recruited to and interact with various cell membranes often vary drastically due to differences in lipid affinity, specificity, penetration as well as protein-protein and intramolecular interactions. As there is still a paucity of predictive data for peripheral protein function, these enzymes are often rigorously studied to characterize their lipid-dependent properties. This review summarizes recent progress in our understanding of how peripheral proteins are recruited to biomembranes and highlights avenues to exploit in drug development targeted at cellular membranes and/or lipid-binding proteins.
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Affiliation(s)
- C.G. Sudhahar
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46656, USA
- Walther Center for Cancer Research, University of Notre Dame, Notre Dame, IN 46656, USA
| | - R.M. Haney
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46656, USA
| | - Y. Xue
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617
| | - R.V. Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46656, USA
- Walther Center for Cancer Research, University of Notre Dame, Notre Dame, IN 46656, USA
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