1
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Kim J, Teng LY, Shaker B, Na D, Koh HY, Kwon SS, Lee JS, Kim HD, Kang HC, Kim SH. Genotypes and phenotypes of DNM1 encephalopathy. J Med Genet 2023; 60:1076-1083. [PMID: 37248033 DOI: 10.1136/jmg-2023-109233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/30/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Variants in the dynamin-1 (DNM1) gene typically cause synaptopathy, leading to developmental and epileptic encephalopathy (DEE). We aimed to determine the genotypic and phenotypic spectrum of DNM1 encephalopathy beyond DEE. METHODS Electroclinical phenotyping and genotyping of patients with a DNM1 variant were conducted for patients undergoing next-generation sequencing at our centre, followed by a systematic review. RESULTS Six patients with heterozygous DNM1 variants were identified in our cohort. Three had a typical DEE phenotype characterised by epileptic spasms, tonic seizures and severe-to-profound intellectual disability with pathogenic variants located in the GTPase or middle domain. The other three patients had atypical phenotypes of milder cognitive impairment and focal epilepsy. Genotypically, two patients with atypical phenotypes had variants located in the GTPase domain, while the third patient had a novel variant (p.M648R) in the linker region between pleckstrin homology and GTPase effector domains. The third patient with an atypical phenotype showed normal development until he developed febrile status epilepticus. Our systematic review on 55 reported cases revealed that those with GTPase or middle domain variants had more severe intellectual disability (p<0.001) and lower functional levels of ambulation (p=0.001) or speech and language (p<0.001) than the rest. CONCLUSION DNM1-related phenotypes encompass a wide spectrum of epilepsy and neurodevelopmental disorders, with specific variants underlying different phenotypes.
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Affiliation(s)
- Jeehyun Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Lip-Yuen Teng
- Paediatric Neurology, Hospital Tunku Azizah, Kuala Lumpur, Malaysia
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Korea
| | - Hyun Yong Koh
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seodaemun-gu, Korea
| | - Joon Soo Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
- Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Seoul, Korea
- Epilepsy Research Institute, Yonsei University College of Medicine, Epilepsy Research Institute, Seoul, Korea
| | - Heung Dong Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
- Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Seoul, Korea
- Epilepsy Research Institute, Yonsei University College of Medicine, Epilepsy Research Institute, Seoul, Korea
| | - Hoon-Chul Kang
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
- Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Seoul, Korea
- Epilepsy Research Institute, Yonsei University College of Medicine, Epilepsy Research Institute, Seoul, Korea
| | - Se Hee Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
- Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Seoul, Korea
- Epilepsy Research Institute, Yonsei University College of Medicine, Epilepsy Research Institute, Seoul, Korea
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2
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Khurana H, Baratam K, Bhattacharyya S, Srivastava A, Pucadyil TJ. Mechanistic analysis of a novel membrane-interacting variable loop in the pleckstrin-homology domain critical for dynamin function. Proc Natl Acad Sci U S A 2023; 120:e2215250120. [PMID: 36888655 PMCID: PMC10089193 DOI: 10.1073/pnas.2215250120] [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: 09/06/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023] Open
Abstract
Classical dynamins are best understood for their ability to generate vesicles by membrane fission. During clathrin-mediated endocytosis (CME), dynamin is recruited to the membrane through multivalent protein and lipid interactions between its proline-rich domain (PRD) with SRC Homology 3 (SH3) domains in endocytic proteins and its pleckstrin-homology domain (PHD) with membrane lipids. Variable loops (VL) in the PHD bind lipids and partially insert into the membrane thereby anchoring the PHD to the membrane. Recent molecular dynamics (MD) simulations reveal a novel VL4 that interacts with the membrane. Importantly, a missense mutation that reduces VL4 hydrophobicity is linked to an autosomal dominant form of Charcot-Marie-Tooth (CMT) neuropathy. We analyzed the orientation and function of the VL4 to mechanistically link data from simulations with the CMT neuropathy. Structural modeling of PHDs in the cryo-electron microscopy (cryo-EM) cryoEM map of the membrane-bound dynamin polymer confirms VL4 as a membrane-interacting loop. In assays that rely solely on lipid-based membrane recruitment, VL4 mutants with reduced hydrophobicity showed an acute membrane curvature-dependent binding and a catalytic defect in fission. Remarkably, in assays that mimic a physiological multivalent lipid- and protein-based recruitment, VL4 mutants were completely defective in fission across a range of membrane curvatures. Importantly, expression of these mutants in cells inhibited CME, consistent with the autosomal dominant phenotype associated with the CMT neuropathy. Together, our results emphasize the significance of finely tuned lipid and protein interactions for efficient dynamin function.
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Affiliation(s)
- Himani Khurana
- Indian Institute of Science Education and Research, Pune411008, India
| | | | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru560012, India
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3
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Metal-Binding Propensity in the Mitochondrial Dynamin-Related Protein 1. J Membr Biol 2022; 255:143-150. [PMID: 35218392 DOI: 10.1007/s00232-022-00221-5] [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: 01/16/2022] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
Dynamin-related protein1 (Drp1) functions to divide mitochondria and peroxisomes by binding specific adaptor proteins and lipids, both of which are integral to the limiting organellar membrane. In efforts to understand how such multivalent interactions regulate Drp1 functions, in vitro reconstitution schemes rely on recruiting soluble portions of the adaptors appended with genetically encoded polyhistidine tags onto membranes containing Ni2+-bound chelator lipids. These strategies are facile and circumvent the challenge in working with membrane proteins but assume that binding is specific to proteins carrying the polyhistidine tag. Here, we find using chelator lipids and chelator beads that both native and recombinant Drp1 directly bind Ni2+ ions. Metal binding, therefore, represents a potential strategy to deplete or purify Drp1 from native tissue lysates. Importantly, high concentrations of the metal in solution inhibit GTP hydrolysis and renders Drp1 inactive in membrane fission. Together, our results emphasize a metal-binding propensity, which could significantly impact Drp1 functions.
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4
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Morciano G, Vitto VAM, Bouhamida E, Giorgi C, Pinton P. Mitochondrial Bioenergetics and Dynamism in the Failing Heart. Life (Basel) 2021; 11:436. [PMID: 34066065 PMCID: PMC8151847 DOI: 10.3390/life11050436] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The heart is responsible for pumping blood, nutrients, and oxygen from its cavities to the whole body through rhythmic and vigorous contractions. Heart function relies on a delicate balance between continuous energy consumption and generation that changes from birth to adulthood and depends on a very efficient oxidative metabolism and the ability to adapt to different conditions. In recent years, mitochondrial dysfunctions were recognized as the hallmark of the onset and development of manifold heart diseases (HDs), including heart failure (HF). HF is a severe condition for which there is currently no cure. In this condition, the failing heart is characterized by a disequilibrium in mitochondrial bioenergetics, which compromises the basal functions and includes the loss of oxygen and substrate availability, an altered metabolism, and inefficient energy production and utilization. This review concisely summarizes the bioenergetics and some other mitochondrial features in the heart with a focus on the features that become impaired in the failing heart.
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Affiliation(s)
- Giampaolo Morciano
- Maria Cecilia Hospital, GVM Care&Research, 48033 Cotignola, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (V.A.M.V.); (E.B.); (C.G.)
| | - Veronica Angela Maria Vitto
- Laboratory for Technologies of Advanced Therapies (LTTA), Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (V.A.M.V.); (E.B.); (C.G.)
| | - Esmaa Bouhamida
- Laboratory for Technologies of Advanced Therapies (LTTA), Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (V.A.M.V.); (E.B.); (C.G.)
| | - Carlotta Giorgi
- Laboratory for Technologies of Advanced Therapies (LTTA), Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (V.A.M.V.); (E.B.); (C.G.)
| | - Paolo Pinton
- Maria Cecilia Hospital, GVM Care&Research, 48033 Cotignola, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (V.A.M.V.); (E.B.); (C.G.)
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5
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Baratam K, Jha K, Srivastava A. Flexible pivoting of dynamin pleckstrin homology domain catalyzes fission: insights into molecular degrees of freedom. Mol Biol Cell 2021; 32:1306-1319. [PMID: 33979205 PMCID: PMC8351549 DOI: 10.1091/mbc.e20-12-0794] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane–localized phosphatidylinositol-4,5-bisphosphate (PIP2) through the centrally located pleckstrin homology domain (PHD). The PHD is dispensable as fission (in model membranes) can be managed, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, the absence of the PHD renders a dramatic dampening of the rate of fission. These observations suggest that the PHD-PIP2–containing membrane interaction could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches to explore PHD–membrane interactions. Our results reveal that 1) the binding of PHD to PIP2-containing membranes modulates the lipids toward fission-favoring conformations and softens the membrane, and 2) PHD associates with membrane in multiple orientations using variable loops as pivots. We identify a new loop (VL4), which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane—a mechanism that we believe may be important for high-fidelity dynamin collar assembly. Together, these insights provide a molecular-level understanding of the catalytic role of PHD in dynamin-mediated membrane fission.
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Affiliation(s)
| | - Kirtika Jha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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6
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Fujise K, Okubo M, Abe T, Yamada H, Nishino I, Noguchi S, Takei K, Takeda T. Mutant BIN1-Dynamin 2 complexes dysregulate membrane remodeling in the pathogenesis of centronuclear myopathy. J Biol Chem 2021; 296:100077. [PMID: 33187981 PMCID: PMC7949082 DOI: 10.1074/jbc.ra120.015184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 11/08/2022] Open
Abstract
Membrane remodeling is required for dynamic cellular processes such as cell division, polarization, and motility. BAR domain proteins and dynamins are key molecules in membrane remodeling that work together for membrane deformation and fission. In striated muscles, sarcolemmal invaginations termed T-tubules are required for excitation-contraction coupling. BIN1 and DNM2, which encode a BAR domain protein BIN1 and dynamin 2, respectively, have been reported to be causative genes of centronuclear myopathy (CNM), a hereditary degenerative disease of skeletal muscle, and deformation of T-tubules is often observed in the CNM patients. However, it remains unclear how BIN1 and dynamin 2 are implicated in T-tubule biogenesis and how mutations in these molecules cause CNM to develop. Here, using an in cellulo reconstitution assay, we demonstrate that dynamin 2 is required for stabilization of membranous structures equivalent to T-tubules. GTPase activity of wild-type dynamin 2 is suppressed through interaction with BIN1, whereas that of the disease-associated mutant dynamin 2 remains active due to lack of the BIN1-mediated regulation, thus causing aberrant membrane remodeling. Finally, we show that in cellulo aberrant membrane remodeling by mutant dynamin 2 variants is correlated with their enhanced membrane fission activities, and the results can explain severity of the symptoms in patients. Thus, this study provides molecular insights into dysregulated membrane remodeling triggering the pathogenesis of DNM2-related CNM.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/physiology
- Animals
- Blotting, Western
- Dynamin II/genetics
- Dynamin II/metabolism
- HEK293 Cells
- Humans
- Immunoprecipitation
- Microscopy, Fluorescence
- Muscle, Skeletal/metabolism
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/metabolism
- Nanotubes/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Kenshiro Fujise
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Mariko Okubo
- National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan; Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Tadashi Abe
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hiroshi Yamada
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Ichizo Nishino
- National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Satoru Noguchi
- National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Kohji Takei
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Tetsuya Takeda
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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7
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Kalia R, Frost A. Open and cut: allosteric motion and membrane fission by dynamin superfamily proteins. Mol Biol Cell 2020; 30:2097-2104. [PMID: 31365329 PMCID: PMC6743466 DOI: 10.1091/mbc.e16-10-0709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells have evolved diverse protein-based machinery to reshape, cut, or fuse their membrane-delimited compartments. Dynamin superfamily proteins are principal components of this machinery and use their ability to hydrolyze GTP and to polymerize into helices and rings to achieve these goals. Nucleotide-binding, hydrolysis, and exchange reactions drive significant conformational changes across the dynamin family, and these changes alter the shape and stability of supramolecular dynamin oligomers, as well as the ability of dynamins to bind receptors and membranes. Mutations that interfere with the conformational repertoire of these enzymes, and hence with membrane fission, exist in several inherited human diseases. Here, we discuss insights from new x-ray crystal structures and cryo-EM reconstructions that have enabled us to infer some of the allosteric dynamics for these proteins. Together, these studies help us to understand how dynamins perform mechanical work, as well as how specific mutants of dynamin family proteins exhibit pathogenic properties.
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Affiliation(s)
- Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132.,Chan-Zuckerberg Biohub, San Francisco, CA 94158
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8
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Tornabene BA, Varlakhanova NV, Hosford CJ, Chappie JS, Ford MGJ. Structural and functional characterization of the dominant negative P-loop lysine mutation in the dynamin superfamily protein Vps1. Protein Sci 2020; 29:1416-1428. [PMID: 31981262 DOI: 10.1002/pro.3830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Dynamin-superfamily proteins (DSPs) are large self-assembling mechanochemical GTPases that harness GTP hydrolysis to drive membrane remodeling events needed for many cellular processes. Mutation to alanine of a fully conserved lysine within the P-loop of the DSP GTPase domain results in abrogation of GTPase activity. This mutant has been widely used in the context of several DSPs as a dominant-negative to impair DSP-dependent processes. However, the precise deficit of the P-loop K to A mutation remains an open question. Here, we use biophysical, biochemical and structural approaches to characterize this mutant in the context of the endosomal DSP Vps1. We show that the Vps1 P-loop K to A mutant binds nucleotide with an affinity similar to wild type but exhibits defects in the organization of the GTPase active site that explain the lack of hydrolysis. In cells, Vps1 and Dnm1 bearing the P-loop K to A mutation are defective in disassembly. These mutants become trapped in assemblies at the typical site of action of the DSP. This work provides mechanistic insight into the widely-used DSP P-loop K to A mutation and the basis of its dominant-negative effects in the cell.
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Affiliation(s)
- Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Natalia V Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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9
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Sinha S, Manoj N. Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics. FEBS Lett 2019; 593:703-718. [PMID: 30861107 DOI: 10.1002/1873-3468.13356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/02/2019] [Accepted: 03/07/2019] [Indexed: 01/24/2023]
Abstract
Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and OPA1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.
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Affiliation(s)
- Sansrity Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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10
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Pizarro L, Leibman-Markus M, Schuster S, Bar M, Avni A. Tomato Dynamin Related Protein 2A Associates With LeEIX2 and Enhances PRR Mediated Defense by Modulating Receptor Trafficking. FRONTIERS IN PLANT SCIENCE 2019; 10:936. [PMID: 31379912 PMCID: PMC6658876 DOI: 10.3389/fpls.2019.00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/04/2019] [Indexed: 05/17/2023]
Abstract
The endocytic trafficking pathway is employed by the plant to regulate immune responses, and is often targeted by pathogen effectors to promote virulence. The model system of the tomato receptor-like protein (RLP) LeEIX2 and its ligand, the elicitor EIX, employs endocytosis to transmit receptor-mediated signals, with some of the signaling events occurring directly from endosomal compartments. Here, to explore the trafficking mechanism of LeEIX2-mediated immune signaling, we used a proteomic approach to identify LeEIX2-associating proteins. We report the identification of SlDRP2A, a dynamin related protein, as an associating partner for LeEIX2. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 in VHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune responses.
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Affiliation(s)
- Lorena Pizarro
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon, Israel
| | - Meirav Leibman-Markus
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon, Israel
| | - Silvia Schuster
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon, Israel
- *Correspondence: Maya Bar,
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- *Correspondence: Adi Avni,
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11
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Claus LAN, Savatin DV, Russinova E. The crossroads of receptor-mediated signaling and endocytosis in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:827-840. [PMID: 29877613 DOI: 10.1111/jipb.12672] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 05/20/2023]
Abstract
Plants deploy numerous plasma membrane receptors to sense and rapidly react to environmental changes. Correct localization and adequate protein levels of the cell-surface receptors are critical for signaling activation and modulation of plant development and defense against pathogens. After ligand binding, receptors are internalized for degradation and signaling attenuation. However, one emerging notion is that the ligand-induced endocytosis of receptor complexes is important for the signal duration, amplitude, and specificity. Recently, mutants of major endocytosis players, including clathrin and dynamin, have been shown to display defects in activation of a subset of signal transduction pathways, implying that signaling in plants might not be solely restricted to the plasma membrane. Here, we summarize the up-to-date knowledge of receptor complex endocytosis and its effect on the signaling outcome, in the context of plant development and immunity.
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Affiliation(s)
- Lucas Alves Neubus Claus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniel V Savatin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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12
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Varlakhanova NV, Alvarez FJD, Brady TM, Tornabene BA, Hosford CJ, Chappie JS, Zhang P, Ford MGJ. Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture. J Cell Biol 2018; 217:3608-3624. [PMID: 30087125 PMCID: PMC6168280 DOI: 10.1083/jcb.201712021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/26/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
How specific dynamin-related proteins (DRPs) are tailored to their cellular targets is an open question. Varlakhanova et al. present structures of the fungal DRP Vps1, which functions at the endosomal compartment. The crystal and cryoEM structures reveal a unique DRP architecture that highlights structural flexibilities of DRP self-assembly. Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to their cellular targets remains unclear. We demonstrate that the fungal DRP Vps1 primarily localizes to and functions at the endosomal compartment. We present crystal structures of a Vps1 GTPase–bundle signaling element (BSE) fusion in different nucleotide states to capture GTP hydrolysis intermediates and concomitant conformational changes. Using cryoEM, we determined the structure of full-length GMPPCP-bound Vps1. The Vps1 helix is more open and flexible than that of dynamin. This is due to further opening of the BSEs away from the GTPase domains. A novel interface between adjacent GTPase domains forms in Vps1 instead of the contacts between the BSE and adjacent stalks and GTPase domains as seen in dynamin. Disruption of this interface abolishes Vps1 function in vivo. Hence, Vps1 exhibits a unique helical architecture, highlighting structural flexibilities of DRP self-assembly.
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Affiliation(s)
| | - Frances J D Alvarez
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Tyler M Brady
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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13
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Makaraci P, Kim K. trans-Golgi network-bound cargo traffic. Eur J Cell Biol 2018; 97:137-149. [PMID: 29398202 DOI: 10.1016/j.ejcb.2018.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
Cargo following the retrograde trafficking are sorted at endosomes to be targeted the trans-Golgi network (TGN), a central receiving organelle. Though molecular requirements and their interaction networks have been somewhat established, the complete understanding of the intricate nature of their action mechanisms in every step of the retrograde traffic pathway remains unachieved. This review focuses on elucidating known functions of key regulators, including scission factors at the endosome and tethering/fusion mediators at the receiving dock, TGN, as well as a diverse range of cargo.
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Affiliation(s)
- Pelin Makaraci
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA.
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14
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O'Donnell JP, Byrnes LJ, Cooley RB, Sondermann H. A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core. J Biol Chem 2017; 293:687-700. [PMID: 29180453 DOI: 10.1074/jbc.ra117.000380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/17/2017] [Indexed: 11/06/2022] Open
Abstract
The dynamin-related GTPase atlastin (ATL) catalyzes membrane fusion of the endoplasmic reticulum and thus establishes a network of branched membrane tubules. When ATL function is compromised, the morphology of the endoplasmic reticulum deteriorates, and these defects can result in neurological disorders such as hereditary spastic paraplegia and hereditary sensory neuropathy. ATLs harness the energy of GTP hydrolysis to initiate a series of conformational changes that enable homodimerization and subsequent membrane fusion. Disease-associated amino acid substitutions cluster in regions adjacent to ATL's catalytic site, but the consequences for the GTPase's molecular mechanism are often poorly understood. Here, we elucidate structural and functional defects of an atypical hereditary spastic paraplegia mutant, ATL1-F151S, that is impaired in its nucleotide-hydrolysis cycle but can still adopt a high-affinity homodimer when bound to a transition-state analog. Crystal structures of mutant proteins yielded models of the monomeric pre- and post-hydrolysis states of ATL. Together, these findings define a mechanism for allosteric coupling in which Phe151 is the central residue in a hydrophobic interaction network connecting the active site to an interdomain interface responsible for nucleotide loading.
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Affiliation(s)
- John P O'Donnell
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Laura J Byrnes
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Richard B Cooley
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Holger Sondermann
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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15
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von Spiczak S, Helbig KL, Shinde DN, Huether R, Pendziwiat M, Lourenço C, Nunes ME, Sarco DP, Kaplan RA, Dlugos DJ, Kirsch H, Slavotinek A, Cilio MR, Cervenka MC, Cohen JS, McClellan R, Fatemi A, Yuen A, Sagawa Y, Littlejohn R, McLean SD, Hernandez-Hernandez L, Maher B, Møller RS, Palmer E, Lawson JA, Campbell CA, Joshi CN, Kolbe DL, Hollingsworth G, Neubauer BA, Muhle H, Stephani U, Scheffer IE, Pena SDJ, Sisodiya SM, Helbig I. DNM1 encephalopathy: A new disease of vesicle fission. Neurology 2017; 89:385-394. [PMID: 28667181 PMCID: PMC5574673 DOI: 10.1212/wnl.0000000000004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To evaluate the phenotypic spectrum caused by mutations in dynamin 1 (DNM1), encoding the presynaptic protein DNM1, and to investigate possible genotype-phenotype correlations and predicted functional consequences based on structural modeling. METHODS We reviewed phenotypic data of 21 patients (7 previously published) with DNM1 mutations. We compared mutation data to known functional data and undertook biomolecular modeling to assess the effect of the mutations on protein function. RESULTS We identified 19 patients with de novo mutations in DNM1 and a sibling pair who had an inherited mutation from a mosaic parent. Seven patients (33.3%) carried the recurrent p.Arg237Trp mutation. A common phenotype emerged that included severe to profound intellectual disability and muscular hypotonia in all patients and an epilepsy characterized by infantile spasms in 16 of 21 patients, frequently evolving into Lennox-Gastaut syndrome. Two patients had profound global developmental delay without seizures. In addition, we describe a single patient with normal development before the onset of a catastrophic epilepsy, consistent with febrile infection-related epilepsy syndrome at 4 years. All mutations cluster within the GTPase or middle domains, and structural modeling and existing functional data suggest a dominant-negative effect on DMN1 function. CONCLUSIONS The phenotypic spectrum of DNM1-related encephalopathy is relatively homogeneous, in contrast to many other genetic epilepsies. Up to one-third of patients carry the recurrent p.Arg237Trp variant, which is now one of the most common recurrent variants in epileptic encephalopathies identified to date. Given the predicted dominant-negative mechanism of this mutation, this variant presents a prime target for therapeutic intervention.
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Affiliation(s)
| | | | | | - Robert Huether
- Author affiliations are provided at the end of the article
| | | | | | - Mark E Nunes
- Author affiliations are provided at the end of the article
| | - Dean P Sarco
- Author affiliations are provided at the end of the article
| | | | | | - Heidi Kirsch
- Author affiliations are provided at the end of the article
| | | | - Maria R Cilio
- Author affiliations are provided at the end of the article
| | | | - Julie S Cohen
- Author affiliations are provided at the end of the article
| | | | - Ali Fatemi
- Author affiliations are provided at the end of the article
| | - Amy Yuen
- Author affiliations are provided at the end of the article
| | - Yoshimi Sagawa
- Author affiliations are provided at the end of the article
| | | | - Scott D McLean
- Author affiliations are provided at the end of the article
| | | | - Bridget Maher
- Author affiliations are provided at the end of the article
| | - Rikke S Møller
- Author affiliations are provided at the end of the article
| | | | - John A Lawson
- Author affiliations are provided at the end of the article
| | | | | | - Diana L Kolbe
- Author affiliations are provided at the end of the article
| | | | | | - Hiltrud Muhle
- Author affiliations are provided at the end of the article
| | | | | | | | | | - Ingo Helbig
- Author affiliations are provided at the end of the article.
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16
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Ince S, Kutsch M, Shydlovskyi S, Herrmann C. The human guanylate-binding proteins hGBP-1 and hGBP-5 cycle between monomers and dimers only. FEBS J 2017; 284:2284-2301. [PMID: 28580591 DOI: 10.1111/febs.14126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/18/2017] [Accepted: 06/01/2017] [Indexed: 12/11/2022]
Abstract
Belonging to the dynamin superfamily of large GTPases, human guanylate-binding proteins (hGBPs) comprise a family of seven isoforms (hGBP-1 to hGBP-7) that are strongly upregulated in response to interferon-γ and other cytokines. Accordingly, several hGBPs are found to exhibit various cellular functions encompassing inhibitory effects on cell proliferation, tumor suppression as well as antiviral and antibacterial activity; however, their mechanism of action is only poorly understood. Often, cellular functions of dynamin-related proteins are closely linked to their ability to form nucleotide-dependent oligomers, a feature that also applies to hGBP-1 and hGBP-5. hGBPs are described as monomers, dimers, tetramers, and higher oligomeric species, the function of which is not clearly established. Therefore, this work focused on the oligomerization capability of hGBP-1 and hGBP-5, which are reported to assemble to homodimers and homotetramers. Employing independent methods such as size-exclusion chromatography, which relies on the hydrodynamic radius, and multiangle light scattering, which relies on the mass of the protein, revealed that previous interpretations regarding the size of the proteins and their complexes have to be revised. Additional studies using inter- and intramolecular Förster resonance energy transfer demonstrated that nucleotide-triggered intramolecular structural changes lead to a more extended shape of hGBP-1 being responsible for the appearance of larger oligomeric species. Thus, previously reported tetrameric and dimeric species of hGBP-1 and hGBP-5 were unmasked as dimers and monomers, respectively, with their shapes depending on both the bound nucleotide and the ionic strength of the solution.
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Affiliation(s)
- Semra Ince
- Physical Chemistry I, Ruhr-University Bochum, Germany
| | - Miriam Kutsch
- Physical Chemistry I, Ruhr-University Bochum, Germany
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17
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Zala D, Schlattner U, Desvignes T, Bobe J, Roux A, Chavrier P, Boissan M. The advantage of channeling nucleotides for very processive functions. F1000Res 2017; 6:724. [PMID: 28663786 PMCID: PMC5473427 DOI: 10.12688/f1000research.11561.2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 12/26/2022] Open
Abstract
Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.
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Affiliation(s)
- Diana Zala
- ESPCI - Paris, PSL Research University, Paris, F-75005, France.,CNRS, UMR8249, Paris, F-75005, France
| | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), and SFR Environmental and Systems Biology (BEeSy), U1055, University Grenoble Alpes, Grenoble, 38058, France.,Inserm-U1055, Grenoble, F-38058, France
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97401, USA
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, F-35000, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, CH-1211, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, CH-1211, Switzerland
| | - Philippe Chavrier
- Institut Curie, Paris, F-75248, France.,PSL Research University, Paris, F-75005, France.,CNRS, UMR144, Paris, F-75248, France
| | - Mathieu Boissan
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMRS938, Saint-Antoine Research Center, Paris, F-75012, France.,AP-HP, Hospital Tenon, Service de Biochimie et Hormonologie, Paris, F-75020, France
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18
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Zala D, Schlattner U, Desvignes T, Bobe J, Roux A, Chavrier P, Boissan M. The advantage of channeling nucleotides for very processive functions. F1000Res 2017; 6:724. [PMID: 28663786 DOI: 10.12688/f1000research.11561.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/15/2017] [Indexed: 01/01/2023] Open
Abstract
Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.
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Affiliation(s)
- Diana Zala
- ESPCI - Paris, PSL Research University, Paris, F-75005, France.,CNRS, UMR8249, Paris, F-75005, France
| | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), and SFR Environmental and Systems Biology (BEeSy), U1055, University Grenoble Alpes, Grenoble, 38058, France.,Inserm-U1055, Grenoble, F-38058, France
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97401, USA
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, F-35000, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, CH-1211, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, CH-1211, Switzerland
| | - Philippe Chavrier
- Institut Curie, Paris, F-75248, France.,PSL Research University, Paris, F-75005, France.,CNRS, UMR144, Paris, F-75248, France
| | - Mathieu Boissan
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMRS938, Saint-Antoine Research Center, Paris, F-75012, France.,AP-HP, Hospital Tenon, Service de Biochimie et Hormonologie, Paris, F-75020, France
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19
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Dar S, Pucadyil TJ. The pleckstrin-homology domain of dynamin is dispensable for membrane constriction and fission. Mol Biol Cell 2016; 28:152-160. [PMID: 28035046 PMCID: PMC5221619 DOI: 10.1091/mbc.e16-09-0640] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022] Open
Abstract
Classical dynamins engage in rapid vesicle release during synaptic vesicle recycling and contain a lipid-binding domain called the pleckstrin-homology domain (PHD). An analysis of a reengineered dynamin construct lacking the PHD shows that the PHD acts as a catalyst to enhance the rates of dynamin-induced membrane fission. Classical dynamins bind the plasma membrane–localized phosphatidylinositol-4,5-bisphosphate using the pleckstrin-homology domain (PHD) and engage in rapid membrane fission during synaptic vesicle recycling. This domain is conspicuously absent among extant bacterial and mitochondrial dynamins, however, where loop regions manage membrane recruitment. Inspired by the core design of bacterial and mitochondrial dynamins, we reengineered the classical dynamin by replacing its PHD with a polyhistidine or polylysine linker. Remarkably, when recruited via chelator or anionic lipids, respectively, the reengineered dynamin displayed the capacity to constrict and sever membrane tubes. However, when analyzed at single-event resolution, the tube-severing process displayed long-lived, highly constricted prefission intermediates that contributed to 10-fold reduction in bulk rates of membrane fission. Our results indicate that the PHD acts as a catalyst in dynamin-induced membrane fission and rationalize its adoption to meet the physiologic requirement of a fast-acting membrane fission apparatus.
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Affiliation(s)
- Srishti Dar
- Indian Institute of Science Education and Research, Pashan, Pune Maharashtra 411008, India
| | - Thomas J Pucadyil
- Indian Institute of Science Education and Research, Pashan, Pune Maharashtra 411008, India
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20
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MoDnm1 Dynamin Mediating Peroxisomal and Mitochondrial Fission in Complex with MoFis1 and MoMdv1 Is Important for Development of Functional Appressorium in Magnaporthe oryzae. PLoS Pathog 2016; 12:e1005823. [PMID: 27556292 PMCID: PMC4996533 DOI: 10.1371/journal.ppat.1005823] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/22/2016] [Indexed: 11/24/2022] Open
Abstract
Dynamins are large superfamily GTPase proteins that are involved in various cellular processes including budding of transport vesicles, division of organelles, cytokinesis, and pathogen resistance. Here, we characterized several dynamin-related proteins from the rice blast fungus Magnaporthe oryzae and found that MoDnm1 is required for normal functions, including vegetative growth, conidiogenesis, and full pathogenicity. In addition, we found that MoDnm1 co-localizes with peroxisomes and mitochondria, which is consistent with the conserved role of dynamin proteins. Importantly, MoDnm1-dependent peroxisomal and mitochondrial fission involves functions of mitochondrial fission protein MoFis1 and WD-40 repeat protein MoMdv1. These two proteins display similar cellular functions and subcellular localizations as MoDnm1, and are also required for full pathogenicity. Further studies showed that MoDnm1, MoFis1 and MoMdv1 are in complex to regulate not only peroxisomal and mitochondrial fission, pexophagy and mitophagy progression, but also appressorium function and host penetration. In summary, our studies provide new insights into how MoDnm1 interacts with its partner proteins to mediate peroxisomal and mitochondrial functions and how such regulatory events may link to differentiation and pathogenicity in the rice blast fungus. Dynamin superfamily members are involved in budding of transport vesicles and division of organelles in eukaryotic cells. To further understand how dynamins function in phytopathogenic fungi, we characterized several dynamin-related proteins from the rice blast fungus M. oryzae. In addition to revealing major conserved dynamin functions, we described how MoDnm1 interacts with mitochondrial fission protein MoFis1 and WD repeat adaptor protein MoMdv1 to mediate peroxisomal and mitochondrial fission, pexophagy and mitophagy. Importantly, we provided evidence to demonstrate that MoDnm1-, MoFis1- and MoMdv1-dependent peroxisomal and mitochondrial functions are linked to differentiation and pathogenicity of the rice blast fungus.
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21
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Panarella A, Bexiga MG, Galea G, O’ Neill ED, Salvati A, Dawson KA, Simpson JC. A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells. Sci Rep 2016; 6:28865. [PMID: 27374232 PMCID: PMC4931513 DOI: 10.1038/srep28865] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/06/2016] [Indexed: 12/24/2022] Open
Abstract
Synthetic nanoparticles are promising tools for imaging and drug delivery; however the molecular details of cellular internalization and trafficking await full characterization. Current knowledge suggests that following endocytosis most nanoparticles pass from endosomes to lysosomes. In order to design effective drug delivery strategies that can use the endocytic pathway, or by-pass lysosomal accumulation, a comprehensive understanding of nanoparticle uptake and trafficking mechanisms is therefore fundamental. Here we describe and apply an RNA interference-based high-content screening microscopy strategy to assess the intracellular trafficking of fluorescently-labeled polystyrene nanoparticles in HeLa cells. We screened a total of 408 genes involved in cytoskeleton and membrane function, revealing roles for myosin VI, Rab33b and OATL1 in this process. This work provides the first systematic large-scale quantitative assessment of the proteins responsible for nanoparticle trafficking in cells, paving the way for subsequent genome-wide studies.
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Affiliation(s)
- Angela Panarella
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mariana G. Bexiga
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - George Galea
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elaine D. O’ Neill
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anna Salvati
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth A. Dawson
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jeremy C. Simpson
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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22
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Rennie ML, McKelvie SA, Bulloch EMM, Kingston RL. Transient dimerization of human MxA promotes GTP hydrolysis, resulting in a mechanical power stroke. Structure 2016; 22:1433-45. [PMID: 25295396 DOI: 10.1016/j.str.2014.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/14/2014] [Accepted: 08/20/2014] [Indexed: 12/11/2022]
Abstract
Myxovirus resistance (Mx) proteins restrict replication of numerous viruses. They are closely related to membrane-remodeling fission GTPases, such as dynamin. Mx proteins can tubulate lipids and form rings or filaments that may interact directly with viral structures. GTPase domain dimerization is thought to allow crosstalk between the rungs of a tubular or helical assembly, facilitating constriction. We demonstrate that the GTPase domain of MxA dimerizes to facilitate catalysis, in a fashion analogous to dynamin. GTP binding is associated with the lever-like movement of structures adjacent to the GTPase domain, while GTP hydrolysis returns MxA to its resting state. Dimerization is not significantly promoted by substrate binding and occurs only transiently, yet is central to catalytic efficiency. Therefore, we suggest dimerization functions to coordinate the activity of spatially adjacent Mx molecules within an assembly, allowing their mechanical power strokes to be synchronized at key points in the contractile cycle.
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Affiliation(s)
- Martin L Rennie
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Siri A McKelvie
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Esther M M Bulloch
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Richard L Kingston
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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23
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Paez Valencia J, Goodman K, Otegui MS. Endocytosis and Endosomal Trafficking in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:309-35. [PMID: 27128466 DOI: 10.1146/annurev-arplant-043015-112242] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Endocytosis and endosomal trafficking are essential processes in cells that control the dynamics and turnover of plasma membrane proteins, such as receptors, transporters, and cell wall biosynthetic enzymes. Plasma membrane proteins (cargo) are internalized by endocytosis through clathrin-dependent or clathrin-independent mechanism and delivered to early endosomes. From the endosomes, cargo proteins are recycled back to the plasma membrane via different pathways, which rely on small GTPases and the retromer complex. Proteins that are targeted for degradation through ubiquitination are sorted into endosomal vesicles by the ESCRT (endosomal sorting complex required for transport) machinery for degradation in the vacuole. Endocytic and endosomal trafficking regulates many cellular, developmental, and physiological processes, including cellular polarization, hormone transport, metal ion homeostasis, cytokinesis, pathogen responses, and development. In this review, we discuss the mechanisms that mediate the recognition and sorting of endocytic and endosomal cargos, the vesiculation processes that mediate their trafficking, and their connection to cellular and physiological responses in plants.
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Affiliation(s)
- Julio Paez Valencia
- Department of Botany
- R.M. Bock Laboratories of Cell and Molecular Biology, and
| | - Kaija Goodman
- Department of Botany
- R.M. Bock Laboratories of Cell and Molecular Biology, and
| | - Marisa S Otegui
- Department of Botany
- R.M. Bock Laboratories of Cell and Molecular Biology, and
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706; , ,
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24
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Gadila SKG, Kim K. Cargo trafficking from the trans-Golgi network towards the endosome. Biol Cell 2016; 108:205-18. [DOI: 10.1111/boc.201600001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kyoungtae Kim
- Department of Biology; Missouri State University; Springfield MO 65807 USA
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25
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Srinivasan S, Dharmarajan V, Reed DK, Griffin PR, Schmid SL. Identification and function of conformational dynamics in the multidomain GTPase dynamin. EMBO J 2016; 35:443-57. [PMID: 26783363 DOI: 10.15252/embj.201593477] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/13/2023] Open
Abstract
Vesicle release upon endocytosis requires membrane fission, catalyzed by the large GTPase dynamin. Dynamin contains five domains that together orchestrate its mechanochemical activity. Hydrogen-deuterium exchange coupled with mass spectrometry revealed global nucleotide- and membrane-binding-dependent conformational changes, as well as the existence of an allosteric relay element in the α2(S) helix of the dynamin stalk domain. As predicted from structural studies, FRET analyses detect large movements of the pleckstrin homology domain (PHD) from a 'closed' conformation docked near the stalk to an 'open' conformation able to interact with membranes. We engineered dynamin constructs locked in either the closed or open state by chemical cross-linking or deletion mutagenesis and showed that PHD movements function as a conformational switch to regulate dynamin self-assembly, membrane binding, and fission. This PHD conformational switch is impaired by a centronuclear myopathy-causing disease mutation, S619L, highlighting the physiological significance of its role in regulating dynamin function. Together, these data provide new insight into coordinated conformational changes that regulate dynamin function and couple membrane binding, oligomerization, and GTPase activity during dynamin-catalyzed membrane fission.
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Affiliation(s)
| | | | - Dana Kim Reed
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA
| | - Sandra L Schmid
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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26
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Tang BL. Rab, Arf, and Arl-Regulated Membrane Traffic in Cortical Neuron Migration. J Cell Physiol 2015; 231:1417-23. [DOI: 10.1002/jcp.25261] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Bor Luen Tang
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- NUS Graduate School for Integrative Sciences and Engineering; National University of Singapore; Singapore
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27
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Peters NC, Berg CA. Dynamin-mediated endocytosis is required for tube closure, cell intercalation, and biased apical expansion during epithelial tubulogenesis in the Drosophila ovary. Dev Biol 2015; 409:39-54. [PMID: 26542010 DOI: 10.1016/j.ydbio.2015.10.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 08/09/2015] [Accepted: 10/31/2015] [Indexed: 11/28/2022]
Abstract
Most metazoans are able to grow beyond a few hundred cells and to support differentiated tissues because they elaborate multicellular, epithelial tubes that are indispensable for nutrient and gas exchange. To identify and characterize the cellular behaviors and molecular mechanisms required for the morphogenesis of epithelial tubes (i.e., tubulogenesis), we have turned to the D. melanogaster ovary. Here, epithelia surrounding the developing egg chambers first pattern, then form and extend a set of simple, paired, epithelial tubes, the dorsal appendage (DA) tubes, and they create these structures in the absence of cell division or cell death. This genetically tractable system lets us assess the relative contributions that coordinated changes in cell shape, adhesion, orientation, and migration make to basic epithelial tubulogenesis. We find that Dynamin, a conserved regulator of endocytosis and the cytoskeleton, serves a key role in DA tubulogenesis. We demonstrate that Dynamin is required for distinct aspects of DA tubulogenesis: DA-tube closure, DA-tube-cell intercalation, and biased apical-luminal cell expansion. We provide evidence that Dynamin promotes these processes by facilitating endocytosis of cell-cell and cell-matrix adhesion complexes, and we find that precise levels and sub-cellular distribution of E-Cadherin and specific Integrin subunits impact DA tubulogenesis. Thus, our studies identify novel morphogenetic roles (i.e., tube closure and biased apical expansion), and expand upon established roles (i.e., cell intercalation and adhesion remodeling), for Dynamin in tubulogenesis.
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Affiliation(s)
- Nathaniel C Peters
- University of Washington, Molecular and Cellular Biology Program and Department of Genome Sciences, Box 355065, Seattle, WA 98195-5065, United States
| | - Celeste A Berg
- University of Washington, Molecular and Cellular Biology Program and Department of Genome Sciences, Box 355065, Seattle, WA 98195-5065, United States.
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28
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A high-throughput platform for real-time analysis of membrane fission reactions reveals dynamin function. Nat Cell Biol 2015; 17:1588-96. [PMID: 26479317 DOI: 10.1038/ncb3254] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
Dynamin, the paradigmatic membrane fission catalyst, assembles as helical scaffolds that hydrolyse GTP to sever the tubular necks of clathrin-coated pits. Using a facile assay system of supported membrane tubes (SMrT) engineered to mimic the dimensions of necks of clathrin-coated pits, we monitor the dynamics of a dynamin-catalysed tube-severing reaction in real time using fluorescence microscopy. We find that GTP hydrolysis by an intact helical scaffold causes progressive constriction of the underlying membrane tube. On reaching a critical dimension of 7.3 nm in radius, the tube undergoes scission and concomitant splitting of the scaffold. In a constant GTP turnover scenario, scaffold assembly and GTP hydrolysis-induced tube constriction are kinetically inseparable events leading to tube-severing reactions occurring at timescales similar to the characteristic fission times seen in vivo. We anticipate SMrT templates to allow dynamic fluorescence-based detection of conformational changes occurring in self-assembling proteins that remodel membranes.
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29
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Reubold TF, Faelber K, Plattner N, Posor Y, Ketel K, Curth U, Schlegel J, Anand R, Manstein DJ, Noé F, Haucke V, Daumke O, Eschenburg S. Crystal structure of the dynamin tetramer. Nature 2015; 525:404-8. [PMID: 26302298 DOI: 10.1038/nature14880] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 08/03/2015] [Indexed: 12/21/2022]
Abstract
The mechanochemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes. Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane. Previous studies have described the architecture of dynamin dimers, but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here we present the crystal structure of the human dynamin tetramer in the nucleotide-free state. Combining structural data with mutational studies, oligomerization measurements and Markov state models of molecular dynamics simulations, we suggest a mechanism by which oligomerization of dynamin is linked to the release of intramolecular autoinhibitory interactions. We elucidate how mutations that interfere with tetramer formation and autoinhibition can lead to the congenital muscle disorders Charcot-Marie-Tooth neuropathy and centronuclear myopathy, respectively. Notably, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.
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Affiliation(s)
- Thomas F Reubold
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Katja Faelber
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Nuria Plattner
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - York Posor
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Katharina Ketel
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Ute Curth
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Forschungseinrichtung Strukturanalyse, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Jeanette Schlegel
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Roopsee Anand
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Dietmar J Manstein
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Forschungseinrichtung Strukturanalyse, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Frank Noé
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Volker Haucke
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Susanne Eschenburg
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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30
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Schroeder B, McNiven MA. Importance of endocytic pathways in liver function and disease. Compr Physiol 2015; 4:1403-17. [PMID: 25428849 DOI: 10.1002/cphy.c140001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hepatocellular endocytosis is a highly dynamic process responsible for the internalization of a variety of different receptor ligand complexes, trophic factors, lipids, and, unfortunately, many different pathogens. The uptake of these external agents has profound effects on seminal cellular processes including signaling cascades, migration, growth, and proliferation. The hepatocyte, like other well-polarized epithelial cells, possesses a host of different endocytic mechanisms and entry routes to ensure the selective internalization of cargo molecules. These pathways include receptor-mediated endocytosis, lipid raft associated endocytosis, caveolae, or fluid-phase uptake, although there are likely many others. Understanding and defining the regulatory mechanisms underlying these distinct entry routes, sorting and vesicle formation, as well as the postendocytic trafficking pathways is of high importance especially in the liver, as their mis-regulation can contribute to aberrant liver pathology and liver diseases. Further, these processes can be "hijacked" by a variety of different infectious agents and viruses. This review provides an overview of common components of the endocytic and postendocytic trafficking pathways utilized by hepatocytes. It will also discuss in more detail how these general themes apply to liver-specific processes including iron homeostasis, HBV infection, and even hepatic steatosis.
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Affiliation(s)
- Barbara Schroeder
- Department of Biochemistry and Molecular Biology, Center for Basic Research in Digestive Diseases, Mayo Clinic and Foundation, Rochester, Minnesota
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31
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Bonfim-Melo A, Zanetti BF, Ferreira ÉR, Vandoninck S, Han SW, Van Lint J, Mortara RA, Bahia D. Trypanosoma cruziextracellular amastigotes trigger the protein kinase D1-cortactin-actin pathway during cell invasion. Cell Microbiol 2015; 17:1797-810. [DOI: 10.1111/cmi.12472] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 05/31/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Alexis Bonfim-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina; Universidade Federal de São Paulo (EPM-UNIFESP); São Paulo Brazil
| | - Bianca Ferrarini Zanetti
- Interdisciplinary Center for Gene Therapy (CINTERGEN); Universidade Federal de São Paulo (UNIFESP); São Paulo Brazil
| | - Éden Ramalho Ferreira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina; Universidade Federal de São Paulo (EPM-UNIFESP); São Paulo Brazil
| | - Sandy Vandoninck
- Department of Cellular and Molecular Medicine; University of Leuven; Leuven Belgium
| | - Sang Won Han
- Interdisciplinary Center for Gene Therapy (CINTERGEN); Universidade Federal de São Paulo (UNIFESP); São Paulo Brazil
| | - Johan Van Lint
- Department of Cellular and Molecular Medicine; University of Leuven; Leuven Belgium
| | - Renato Arruda Mortara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina; Universidade Federal de São Paulo (EPM-UNIFESP); São Paulo Brazil
| | - Diana Bahia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina; Universidade Federal de São Paulo (EPM-UNIFESP); São Paulo Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais (ICB-UFMG); Belo Horizonte Brazil
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32
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Paczkowski JE, Richardson BC, Fromme JC. Cargo adaptors: structures illuminate mechanisms regulating vesicle biogenesis. Trends Cell Biol 2015; 25:408-16. [PMID: 25795254 DOI: 10.1016/j.tcb.2015.02.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/11/2015] [Accepted: 02/19/2015] [Indexed: 12/29/2022]
Abstract
Cargo adaptors sort transmembrane protein cargos into nascent vesicles by binding directly to their cytosolic domains. Recent studies have revealed previously unappreciated roles for cargo adaptors and regulatory mechanisms governing their function. The adaptor protein (AP)-1 and AP-2 clathrin adaptors switch between open and closed conformations that ensure they function at the right place at the right time. The exomer cargo adaptor has a direct role in remodeling the membrane for vesicle fission. Several different cargo adaptors functioning in distinct trafficking pathways at the Golgi are similarly regulated through bivalent binding to the ADP-ribosylation factor 1 (Arf1) GTPase, potentially enabling regulation by a threshold concentration of Arf1. Taken together, these studies highlight that cargo adaptors do more than just adapt cargos.
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Affiliation(s)
- Jon E Paczkowski
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian C Richardson
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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33
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Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ. Toxicity of an α-pore-forming toxin depends on the assembly mechanism on the target membrane as revealed by single molecule imaging. J Biol Chem 2014; 290:4856-4865. [PMID: 25525270 DOI: 10.1074/jbc.m114.600676] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-Pore-forming toxins (α-PFTs) are ubiquitous defense tools that kill cells by opening pores in the target cell membrane. Despite their relevance in host/pathogen interactions, very little is known about the pore stoichiometry and assembly pathway leading to membrane permeabilization. Equinatoxin II (EqtII) is a model α-PFT from sea anemone that oligomerizes and forms pores in sphingomyelin-containing membranes. Here, we determined the spatiotemporal organization of EqtII in living cells by single molecule imaging. Surprisingly, we found that on the cell surface EqtII did not organize into a unique oligomeric form. Instead, it existed as a mixture of oligomeric species mostly including monomers, dimers, tetramers, and hexamers. Mathematical modeling based on our data supported a new model in which toxin clustering happened in seconds and proceeded via condensation of EqtII dimer units formed upon monomer association. Furthermore, altering the pathway of EqtII assembly strongly affected its toxic activity, which highlights the relevance of the assembly mechanism on toxicity.
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Affiliation(s)
- Yamunadevi Subburaj
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany; German Cancer Research Center, Bioquant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Uris Ros
- Center for Protein Studies, Faculty of Biology, Calle 25 #455, Plaza de la Revolución, La Habana, Cuba
| | - Eduard Hermann
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany; German Cancer Research Center, Bioquant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany,; Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Rudi Tong
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Ana J García-Sáez
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany; German Cancer Research Center, Bioquant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany,; Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.
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34
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Abstract
Synaptic vesicles release their vesicular contents to the extracellular space by Ca(2+)-triggered exocytosis. The Ca(2+)-triggered exocytotic process is regulated by synaptotagmin (Syt), a vesicular Ca(2+)-binding C2 domain protein. Synaptotagmin 1 (Syt1), the most studied major isoform among 16 Syt isoforms, mediates Ca(2+)-triggered synaptic vesicle exocytosis by interacting with the target membranes and SNARE/complexin complex. In synapses of the central nervous system, synaptobrevin 2, a major vesicular SNARE protein, forms a ternary SNARE complex with the plasma membrane SNARE proteins, syntaxin 1 and SNAP25. The affinities of Ca(2+)-dependent interactions between Syt1 and its targets (i.e., SNARE complexes and membranes) are well correlated with the efficacies of the corresponding exocytotic processes. Therefore, different SNARE protein isoforms and membrane lipids, which interact with Syt1 with various affinities, are capable of regulating the efficacy of Syt1-mediated exocytosis. Otoferlin, another type of vesicular C2 domain protein that binds to the membrane in a Ca(2+)-dependent manner, is also involved in the Ca(2+)-triggered synaptic vesicle exocytosis in auditory hair cells. However, the functions of otoferlin in the exocytotic process are not well understood. In addition, at least five different types of synaptic vesicle proteins such as synaptic vesicle protein 2, cysteine string protein α, rab3, synapsin, and a group of proteins containing four transmembrane regions, which includes synaptophysin, synaptogyrin, and secretory carrier membrane protein, are involved in modulating the exocytotic process by regulating the formation and trafficking of synaptic vesicles.
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Affiliation(s)
- Ok-Ho Shin
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas
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35
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Dorn GW, Kitsis RN. The mitochondrial dynamism-mitophagy-cell death interactome: multiple roles performed by members of a mitochondrial molecular ensemble. Circ Res 2014; 116:167-82. [PMID: 25323859 DOI: 10.1161/circresaha.116.303554] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mitochondrial research is experiencing a renaissance, in part, because of the recognition that these endosymbiotic descendants of primordial protobacteria seem to be pursuing their own biological agendas. Not only is mitochondrial metabolism required to produce most of the biochemical energy that supports their eukaryotic hosts (us) but mitochondria can actively (through apoptosis and programmed necrosis) or passively (through reactive oxygen species toxicity) drive cellular dysfunction or demise. The cellular mitochondrial collective autoregulates its population through biogenic renewal and mitophagic culling; mitochondrial fission and fusion, 2 components of mitochondrial dynamism, are increasingly recognized as playing central roles as orchestrators of these processes. Mitochondrial dynamism is rare in striated muscle cells, so cardiac-specific genetic manipulation of mitochondrial fission and fusion factors has proven useful for revealing noncanonical functions of mitochondrial dynamics proteins. Here, we review newly described functions of mitochondrial fusion/fission proteins in cardiac mitochondrial quality control, cell death, calcium signaling, and cardiac development. A mechanistic conceptual paradigm is proposed in which cell death and selective organelle culling are not distinct processes, but are components of a unified and integrated quality control mechanism that exerts different effects when invoked to different degrees, depending on pathophysiological context. This offers a plausible explanation for seemingly paradoxical expression of mitochondrial dynamics and death factors in cardiomyocytes wherein mitochondrial morphometric remodeling does not normally occur and the ability to recover from cell suicide is severely limited.
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Affiliation(s)
- Gerald W Dorn
- From the Department of Internal Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO (G.W.D.); and Departments of Medicine (Cardiology) and Cell Biology and Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY (R.N.K.).
| | - Richard N Kitsis
- From the Department of Internal Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO (G.W.D.); and Departments of Medicine (Cardiology) and Cell Biology and Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY (R.N.K.)
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36
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Cocucci E, Gaudin R, Kirchhausen T. Dynamin recruitment and membrane scission at the neck of a clathrin-coated pit. Mol Biol Cell 2014; 25:3595-609. [PMID: 25232009 PMCID: PMC4230619 DOI: 10.1091/mbc.e14-07-1240] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Dynamin2 dimers are the preferred assembly units recruited to coated pits. About 26 dynamins (one helical turn of a dynamin collar) are enough for release of most coated vesicles. A circumferential twist–propagating model is proposed that requires that one complete turn of the helix reach a state in which one or more pairs of GTPase domains interact. Dynamin, the GTPase required for clathrin-mediated endocytosis, is recruited to clathrin-coated pits in two sequential phases. The first is associated with coated pit maturation; the second, with fission of the membrane neck of a coated pit. Using gene-edited cells that express dynamin2-EGFP instead of dynamin2 and live-cell TIRF imaging with single-molecule EGFP sensitivity and high temporal resolution, we detected the arrival of dynamin at coated pits and defined dynamin dimers as the preferred assembly unit. We also used live-cell spinning-disk confocal microscopy calibrated by single-molecule EGFP detection to determine the number of dynamins recruited to the coated pits. A large fraction of budding coated pits recruit between 26 and 40 dynamins (between 1 and 1.5 helical turns of a dynamin collar) during the recruitment phase associated with neck fission; 26 are enough for coated vesicle release in cells partially depleted of dynamin by RNA interference. We discuss how these results restrict models for the mechanism of dynamin-mediated membrane scission.
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Affiliation(s)
- Emanuele Cocucci
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115 Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Raphaël Gaudin
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115
| | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115 Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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37
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Srinivasan S, Mattila JP, Schmid SL. Intrapolypeptide interactions between the GTPase effector domain (GED) and the GTPase domain form the bundle signaling element in dynamin dimers. Biochemistry 2014; 53:5724-6. [PMID: 25171143 PMCID: PMC4166026 DOI: 10.1021/bi500998s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Biochemical and structural studies
of dynamin have shown that the
C-terminus of the GTPase effector domain (GED) folds back and docks
onto a platform created by the N- and C-terminal α-helices of
the GTPase domain to form a three-helix bundle. While cross-linking
studies suggested that insect cell-expressed dynamin existed as a
domain-swapped dimer, X-ray structures of protein expressed in Escherichia coli failed to detect evidence of this domain
swap. Here, by cross-linking several cysteine pair replacements and
analyzing cross-linked species by matrix-assisted laser desorption
ionization Mega time of flight, we conclude that dynamin is not domain-swapped
and that GED–GTPase domain interactions occur in cis.
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Affiliation(s)
- Saipraveen Srinivasan
- Department of Cell Biology, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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38
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Sundborger AC, Fang S, Heymann JA, Ray P, Chappie JS, Hinshaw JE. A dynamin mutant defines a superconstricted prefission state. Cell Rep 2014; 8:734-42. [PMID: 25088425 DOI: 10.1016/j.celrep.2014.06.054] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/08/2014] [Accepted: 06/25/2014] [Indexed: 11/25/2022] Open
Abstract
Dynamin is a 100 kDa GTPase that organizes into helical assemblies at the base of nascent clathrin-coated vesicles. Formation of these oligomers stimulates the intrinsic GTPase activity of dynamin, which is necessary for efficient membrane fission during endocytosis. Recent evidence suggests that the transition state of dynamin's GTP hydrolysis reaction serves as a key determinant of productive fission. Here, we present the structure of a transition-state-defective dynamin mutant K44A trapped in a prefission state at 12.5 Å resolution. This structure constricts to 3.7 nm, reaching the theoretical limit required for spontaneous membrane fission. Computational docking indicates that the ground-state conformation of the dynamin polymer is sufficient to achieve this superconstricted prefission state and reveals how a two-start helical symmetry promotes the most efficient packing of dynamin tetramers around the membrane neck. These data suggest a model for the assembly and regulation of the minimal dynamin fission machine.
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Affiliation(s)
- Anna C Sundborger
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shunming Fang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jürgen A Heymann
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pampa Ray
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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39
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Yamaoka S, Hara-Nishimura I. The mitochondrial Ras-related GTPase Miro: views from inside and outside the metazoan kingdom. FRONTIERS IN PLANT SCIENCE 2014; 5:350. [PMID: 25076955 PMCID: PMC4100572 DOI: 10.3389/fpls.2014.00350] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/30/2014] [Indexed: 05/24/2023]
Abstract
Miro GTPase, a member of the Ras superfamily, consists of two GTPase domains flanking a pair of EF hand motifs and a C-terminal transmembrane domain that anchors the protein to the mitochondrial outer membrane. Since the identification of Miro in humans, a series of studies in metazoans, including mammals and fruit flies, have shown that Miro plays a role in the calcium-dependent regulation of mitochondrial transport along microtubules. However, in non-metazoans, including yeasts, slime molds, and plants, Miro is primarily involved in the maintenance of mitochondrial morphology and homeostasis. Given the high level of conservation of Miro in eukaryotes and the variation in the molecular mechanisms of mitochondrial transport between eukaryotic lineages, Miro may have a common ancestral function in mitochondria, and its roles in the regulation of mitochondrial transport may have been acquired specifically by metazoans after the evolutionary divergence of eukaryotes.
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Affiliation(s)
- Shohei Yamaoka
- Graduate School of Biostudies, Kyoto UniversityKyoto, Japan
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40
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Williams M, Kim K. From membranes to organelles: emerging roles for dynamin-like proteins in diverse cellular processes. Eur J Cell Biol 2014; 93:267-77. [PMID: 24954468 DOI: 10.1016/j.ejcb.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022] Open
Abstract
Dynamin is a GTPase mechanoenzyme most noted for its role in vesicle scission during endocytosis, and belongs to the dynamin family proteins. The dynamin family consists of classical dynamins and dynamin-like proteins (DLPs). Due to structural and functional similarities DLPs are thought to carry out membrane tubulation and scission in a similar manner to dynamin. Here, we discuss the newly emerging roles for DLPs, which include vacuole fission and fusion, peroxisome maintenance, endocytosis and intracellular trafficking. Specific focus is given to the role of DLPs in the budding yeast Saccharomyces cerevisiae because the diverse function of DLPs has been well characterized in this organism. Recent insights into DLPs may provide a better understanding of mammalian dynamin and its associated diseases.
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Affiliation(s)
- Michelle Williams
- Department of Biology, Missouri State University, 901 South National, Springfield, MO 65897, United States
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 South National, Springfield, MO 65897, United States.
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41
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Abstract
Mitochondrial fission is mediated by a dynamin-related GTPase that assembles at constricted sites on the organelle. The mechanism of action of this GTPase in fission is related to that of classical dynamin, which severs the necks of clathrin-coated pits at the plasma membrane. The scale of these membrane remodeling events differs by an order of magnitude, however, and structural studies have revealed variations in the assembly properties of classical and mitochondrial dynamins that accommodate these differences. Despite this progress, structural and mechanistic models have not yet incorporated a growing number of adaptor proteins that are required for the membrane recruitment and function of mitochondrial dynamins. Here, we review the structure and assembly properties of the yeast and mammalian mitochondrial dynamins and discuss what is known about the activities of their adaptor proteins.
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Affiliation(s)
- Huyen T Bui
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Kirchhausen T, Owen D, Harrison SC. Molecular structure, function, and dynamics of clathrin-mediated membrane traffic. Cold Spring Harb Perspect Biol 2014; 6:a016725. [PMID: 24789820 DOI: 10.1101/cshperspect.a016725] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clathrin is a molecular scaffold for vesicular uptake of cargo at the plasma membrane, where its assembly into cage-like lattices underlies the clathrin-coated pits of classical endocytosis. This review describes the structures of clathrin, major cargo adaptors, and other proteins that participate in forming a clathrin-coated pit, loading its contents, pinching off the membrane as a lattice-enclosed vesicle, and recycling the components. It integrates as much of the structural information as possible at the time of writing into a sketch of the principal steps in coated-pit and coated-vesicle formation.
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Affiliation(s)
- Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School/PCMM, Boston, Massachusetts 02115
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Mehrotra N, Nichols J, Ramachandran R. Alternate pleckstrin homology domain orientations regulate dynamin-catalyzed membrane fission. Mol Biol Cell 2014; 25:879-90. [PMID: 24478459 PMCID: PMC3952856 DOI: 10.1091/mbc.e13-09-0548] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The isolated dynamin PH domain is an assembly-independent sensor of membrane curvature but not a curvature generator. In full-length dynamin, the PH alternates between two different orientations on the membrane surface during the GTP hydrolysis cycle, causing dramatic fluctuations in the diameter of dynamin polymers. The self-assembling GTPase dynamin catalyzes endocytic vesicle scission via membrane insertion of its pleckstrin homology (PH) domain. However, the molecular mechanisms underlying PH domain–dependent membrane fission remain obscure. Membrane-curvature–sensing and membrane-curvature–generating properties have been attributed, but it remains to be seen whether the PH domain is involved in either process independent of dynamin self-assembly. Here, using multiple fluorescence spectroscopic and microscopic techniques, we demonstrate that the isolated PH domain does not act to bend membranes but instead senses high membrane curvature through hydrophobic insertion into the membrane bilayer. Furthermore, we use a complementary set of short- and long-distance Förster resonance energy transfer approaches to distinguish PH-domain orientation from proximity at the membrane surface in full-length dynamin. We reveal, in addition to the GTP-sensitive “hydrophobic mode,” the presence of an alternate, GTP-insensitive “electrostatic mode” of PH domain–membrane interactions that retains dynamin on the membrane surface during the GTP hydrolysis cycle. Stabilization of this alternate orientation produces dramatic variations in the morphology of membrane-bound dynamin spirals, indicating that the PH domain regulates membrane fission through the control of dynamin polymer dynamics.
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Affiliation(s)
- Niharika Mehrotra
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106
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Fujimoto M, Tsutsumi N. Dynamin-related proteins in plant post-Golgi traffic. FRONTIERS IN PLANT SCIENCE 2014; 5:408. [PMID: 25237312 PMCID: PMC4154393 DOI: 10.3389/fpls.2014.00408] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/31/2014] [Indexed: 05/21/2023]
Abstract
Membrane traffic between two organelles begins with the formation of transport vesicles from the donor organelle. Dynamin-related proteins (DRPs), which are large multidomain GTPases, play crucial roles in vesicle formation in post-Golgi traffic. Numerous in vivo and in vitro studies indicate that animal dynamins, which are members of DRP family, assemble into ring- or helix-shaped structures at the neck of a bud site on the donor membrane, where they constrict and sever the neck membrane in a GTP hydrolysis-dependent manner. While much is known about DRP-mediated trafficking in animal cells, little is known about it in plant cells. So far, two structurally distinct subfamilies of plant DRPs (DRP1 and DRP2) have been found to participate in various pathways of post-Golgi traffic. This review summarizes the structural and functional differences between these two DRP subfamilies, focusing on their molecular, cellular and developmental properties. We also discuss the molecular networks underlying the functional machinery centering on these two DRP subfamilies. Furthermore, we hope that this review will provide direction for future studies on the mechanisms of vesicle formation that are not only unique to plants but also common to eukaryotes.
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Affiliation(s)
- Masaru Fujimoto
- *Correspondence: Masaru Fujimoto, Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan e-mail:
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