101
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Abstract
Clathrin-mediated endocytosis is an essential cellular process that involves the concerted assembly and disassembly of many different proteins at the plasma membrane. In yeast, live-cell imaging has shown that the spatiotemporal dynamics of these proteins is highly stereotypical. Recent work has focused on determining how the timing and functions of endocytic proteins are regulated. In this Cell Science at a Glance article and accompanying poster, we review our current knowledge of the timeline of endocytic site maturation and discuss recent works focusing on how phosphorylation, ubiquitylation and lipids regulate various aspects of the process.
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Affiliation(s)
- Rebecca Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yidi Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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102
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Suzuki K, Kimura T, Shinoda H, Bai G, Daniels MJ, Arai Y, Nakano M, Nagai T. Five colour variants of bright luminescent protein for real-time multicolour bioimaging. Nat Commun 2016; 7:13718. [PMID: 27966527 PMCID: PMC5171807 DOI: 10.1038/ncomms13718] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 10/26/2016] [Indexed: 12/20/2022] Open
Abstract
Luminescence imaging has gained attention as a promising bio-imaging modality in situations where fluorescence imaging cannot be applied. However, wider application to multicolour and dynamic imaging is limited by the lack of bright luminescent proteins with emissions across the visible spectrum. Here we report five new spectral variants of the bright luminescent protein, enhanced Nano-lantern (eNL), made by concatenation of the brightest luciferase, NanoLuc, with various colour hues of fluorescent proteins. eNLs allow five-colour live-cell imaging, as well as detection of single protein complexes and even single molecules. We also develop an eNL-based Ca2+ indicator with a 500% signal change, which can image spontaneous Ca2+ dynamics in cardiomyocyte and neural cell models. These eNL probes facilitate not only multicolour imaging in living cells but also sensitive imaging of a wide repertoire of proteins, even at very low expression levels.
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Affiliation(s)
- Kazushi Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Taichi Kimura
- Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Hajime Shinoda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Guirong Bai
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Matthew J Daniels
- BHF Centre for Regenerative Medicine, Division of Cardiovascular Medicine, West Wing Level 6, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Yoshiyuki Arai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Masahiro Nakano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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103
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Diagonally Scanned Light-Sheet Microscopy for Fast Volumetric Imaging of Adherent Cells. Biophys J 2016; 110:1456-65. [PMID: 27028654 PMCID: PMC4816690 DOI: 10.1016/j.bpj.2016.01.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/31/2015] [Accepted: 01/28/2016] [Indexed: 11/23/2022] Open
Abstract
In subcellular light-sheet fluorescence microscopy (LSFM) of adherent cells, glass substrates are advantageously rotated relative to the excitation and emission light paths to avoid glass-induced optical aberrations. Because cells are spread across the sample volume, three-dimensional imaging requires a light-sheet with a long propagation length, or rapid sample scanning. However, the former degrades axial resolution and/or optical sectioning, while the latter mechanically perturbs sensitive biological specimens on pliant biomimetic substrates (e.g., collagen and basement membrane). Here, we use aberration-free remote focusing to diagonally sweep a narrow light-sheet along the sample surface, enabling multicolor imaging with high spatiotemporal resolution. Further, we implement a dithered Gaussian lattice to minimize sample-induced illumination heterogeneities, significantly improving signal uniformity. Compared with mechanical sample scanning, we drastically reduce sample oscillations, allowing us to achieve volumetric imaging at speeds of up to 3.5 Hz for thousands of Z-stacks. We demonstrate the optical performance with live-cell imaging of microtubule and actin cytoskeletal dynamics, phosphoinositide signaling, clathrin-mediated endocytosis, polarized blebbing, and endocytic vesicle sorting. We achieve three-dimensional particle tracking of clathrin-associated structures with velocities up to 4.5 μm/s in a dense intracellular environment, and show that such dynamics cannot be recovered reliably at lower volumetric image acquisition rates using experimental data, numerical simulations, and theoretical modeling.
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104
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Heppert JK, Dickinson DJ, Pani AM, Higgins CD, Steward A, Ahringer J, Kuhn JR, Goldstein B. Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system. Mol Biol Cell 2016; 27:3385-3394. [PMID: 27385332 PMCID: PMC5221575 DOI: 10.1091/mbc.e16-01-0063] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 11/11/2022] Open
Abstract
Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have expedited the precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments and facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap, we quantitatively assessed fluorescent protein properties in vivo in an animal model system. We generated transgenic Caenorhabditis elegans strains expressing green, yellow, or red fluorescent proteins in embryos and imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not as bright in vivo as predicted based on in vitro data but is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imaging in vivo in C. elegans embryos and suggest good candidate fluorescent proteins to test in other animal model systems for in vivo imaging experiments.
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Affiliation(s)
- Jennifer K Heppert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daniel J Dickinson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ariel M Pani
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Christopher D Higgins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Annette Steward
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Julie Ahringer
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jeffrey R Kuhn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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105
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Multiple dynamin family members collaborate to drive mitochondrial division. Nature 2016; 540:139-143. [PMID: 27798601 PMCID: PMC5656044 DOI: 10.1038/nature20555] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 10/24/2016] [Indexed: 12/11/2022]
Abstract
Mitochondria cannot be generated de novo; they must grow, replicate their genome, and divide in order to be inherited to each daughter cell during mitosis. Mitochondrial division is a structural challenge that requires a massive remodeling of membrane morphology 1–3. Although division factors differ across organisms, the need for multiple constriction steps and a dynamin-related protein (Drp1, Dnm1 in yeast) has been conserved 4–6. In mammalian cells, mitochondrial division has been shown to proceed with at least two sequential constriction steps: 1. endoplasmic reticulum (ER) and actin collaborate to generate constrictions suitable for Drp1 assembly; 2. Drp1 further constricts membranes until fission occurs 2,7–9. However, in vitro experiments argue that Drp1 does not have the dynamic range to complete membrane fission per se7. In contrast to Drp1, the neuronal-specific classical Dynamin-1 (Dyn1) has been shown to assemble on narrower lipid profiles and facilitates spontaneous membrane fission upon GTP hydrolysis 10,11. Here we discovered that the ubiquitously-expressed classical Dynamin-2 (Dyn2) is a fundamental component of the mitochondrial division machinery. A combination of live-cell and electron microscopy reveals that Dyn2 works in concert with Drp1 to orchestrate sequential constriction events leading up to division. Our work underscores the biophysical limitations of Drp1 and positions Dyn2, which has intrinsic membrane fission properties, at the final step of mitochondrial division.
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106
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Antonny B, Burd C, De Camilli P, Chen E, Daumke O, Faelber K, Ford M, Frolov VA, Frost A, Hinshaw JE, Kirchhausen T, Kozlov MM, Lenz M, Low HH, McMahon H, Merrifield C, Pollard TD, Robinson PJ, Roux A, Schmid S. Membrane fission by dynamin: what we know and what we need to know. EMBO J 2016; 35:2270-2284. [PMID: 27670760 PMCID: PMC5090216 DOI: 10.15252/embj.201694613] [Citation(s) in RCA: 327] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/25/2016] [Indexed: 12/04/2022] Open
Abstract
The large GTPase dynamin is the first protein shown to catalyze membrane fission. Dynamin and its related proteins are essential to many cell functions, from endocytosis to organelle division and fusion, and it plays a critical role in many physiological functions such as synaptic transmission and muscle contraction. Research of the past three decades has focused on understanding how dynamin works. In this review, we present the basis for an emerging consensus on how dynamin functions. Three properties of dynamin are strongly supported by experimental data: first, dynamin oligomerizes into a helical polymer; second, dynamin oligomer constricts in the presence of GTP; and third, dynamin catalyzes membrane fission upon GTP hydrolysis. We present the two current models for fission, essentially diverging in how GTP energy is spent. We further discuss how future research might solve the remaining open questions presently under discussion.
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Affiliation(s)
- Bruno Antonny
- CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis, Valbonne, France
| | - Christopher Burd
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Pietro De Camilli
- Departments of Neuroscience and Cell Biology, Howard Hughes Medical Institute and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth Chen
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Oliver Daumke
- Department of Crystallography, Max-Delbrück Centrum für Molekulare Medizin, Berlin, Germany
| | - Katja Faelber
- Department of Crystallography, Max-Delbrück Centrum für Molekulare Medizin, Berlin, Germany
| | - Marijn Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Tom Kirchhausen
- Departments of Cell Biology and Pediatrics, Harvard Medical School, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Martin Lenz
- LPTMS, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Harry H Low
- Department of Life Sciences, Imperial College, London, UK
| | | | | | - Thomas D Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Aurélien Roux
- Department of Biochemistry and Swiss NCCR Chemical Biology, University of Geneva, Geneva 4, Switzerland
| | - Sandra Schmid
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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107
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Pucadyil TJ, Holkar SS. Comparative analysis of adaptor-mediated clathrin assembly reveals general principles for adaptor clustering. Mol Biol Cell 2016; 27:3156-3163. [PMID: 27559129 PMCID: PMC5063622 DOI: 10.1091/mbc.e16-06-0399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/19/2016] [Indexed: 11/30/2022] Open
Abstract
Clathrin-mediated endocytosis sorts the bulk of membrane proteins and is a process that starts with adaptor-induced clathrin assembly. Real-time fluorescence analysis shows that adaptor sorting is determined not by the extent of clathrin recruited or the degree of clathrin clustered but instead by the rate of clathrin assembly. Clathrin-mediated endocytosis (CME) manages the sorting and uptake of the bulk of membrane proteins (or cargo) from the plasma membrane. CME is initiated by the formation of clathrin-coated pits (CCPs), in which adaptors nucleate clathrin assembly. Clathrin adaptors display diversity in both the type and number of evolutionarily conserved clathrin-binding boxes. How this diversity relates to the process of adaptor clustering as clathrin assembles around a growing pit remains unclear. Using real-time, fluorescence microscopy–based assays, we compare the formation kinetics and distribution of clathrin assemblies on membranes that display five unique clathrin adaptors. Correlations between equilibrium and kinetic parameters of clathrin assembly to the eventual adaptor distribution indicate that adaptor clustering is determined not by the amount of clathrin recruited or the degree of clathrin clustered but instead by the rate of clathrin assembly. Together our results emphasize the need to analyze kinetics of protein interactions to better understand mechanisms that regulate CME.
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Affiliation(s)
- Thomas J Pucadyil
- Indian Institute of Science Education and Research, Pune, Maharashtra 411 008, India
| | - Sachin S Holkar
- Indian Institute of Science Education and Research, Pune, Maharashtra 411 008, India
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108
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Aguet F, Upadhyayula S, Gaudin R, Chou YY, Cocucci E, He K, Chen BC, Mosaliganti K, Pasham M, Skillern W, Legant WR, Liu TL, Findlay G, Marino E, Danuser G, Megason S, Betzig E, Kirchhausen T. Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy. Mol Biol Cell 2016; 27:3418-3435. [PMID: 27535432 PMCID: PMC5221578 DOI: 10.1091/mbc.e16-03-0164] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/03/2016] [Indexed: 12/02/2022] Open
Abstract
Lattice light-sheet microscopy is used to examine two problems in membrane dynamics—molecular events in clathrin-coated pit formation and changes in cell shape during cell division. This methodology sets a new standard for imaging membrane dynamics in single cells and multicellular assemblies. Membrane remodeling is an essential part of transferring components to and from the cell surface and membrane-bound organelles and for changes in cell shape, which are particularly critical during cell division. Earlier analyses, based on classical optical live-cell imaging and mostly restricted by technical necessity to the attached bottom surface, showed persistent formation of endocytic clathrin pits and vesicles during mitosis. Taking advantage of the resolution, speed, and noninvasive illumination of the newly developed lattice light-sheet fluorescence microscope, we reexamined their assembly dynamics over the entire cell surface and found that clathrin pits form at a lower rate during late mitosis. Full-cell imaging measurements of cell surface area and volume throughout the cell cycle of single cells in culture and in zebrafish embryos showed that the total surface increased rapidly during the transition from telophase to cytokinesis, whereas cell volume increased slightly in metaphase and was relatively constant during cytokinesis. These applications demonstrate the advantage of lattice light-sheet microscopy and enable a new standard for imaging membrane dynamics in single cells and multicellular assemblies.
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Affiliation(s)
- François Aguet
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Srigokul Upadhyayula
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Raphaël Gaudin
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Yi-Ying Chou
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Emanuele Cocucci
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Kangmin He
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Bi-Chang Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | | | - Mithun Pasham
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Wesley Skillern
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Wesley R Legant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Greg Findlay
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Eric Marino
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Sean Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 .,Departments of Cell Biology and Pediatrics, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
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109
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Brown A, Woods WS, Perez-Pinera P. Multiplexed Targeted Genome Engineering Using a Universal Nuclease-Assisted Vector Integration System. ACS Synth Biol 2016; 5:582-8. [PMID: 27159246 DOI: 10.1021/acssynbio.6b00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Engineered nucleases are capable of efficiently modifying complex genomes through introduction of targeted double-strand breaks. However, mammalian genome engineering remains limited by low efficiency of heterologous DNA integration at target sites, which is typically performed through homologous recombination, a complex, ineffective and costly process. In this study, we developed a multiplexable and universal nuclease-assisted vector integration system for rapid generation of gene knock outs using selection that does not require customized targeting vectors, thereby minimizing the cost and time frame needed for gene editing. Importantly, this system is capable of remodeling native mammalian genomes through integration of DNA, up to 50 kb, enabling rapid generation and screening of multigene knockouts from a single transfection. These results support that nuclease assisted vector integration is a robust tool for genome-scale gene editing that will facilitate diverse applications in synthetic biology and gene therapy.
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Affiliation(s)
- Alexander Brown
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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110
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Trexler AJ, Sochacki KA, Taraska JW. Imaging the recruitment and loss of proteins and lipids at single sites of calcium-triggered exocytosis. Mol Biol Cell 2016; 27:2423-34. [PMID: 27307587 PMCID: PMC4966983 DOI: 10.1091/mbc.e16-01-0057] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022] Open
Abstract
Imaging of exocytic and endocytic proteins shows which are present at exocytic sites before, during, and after exocytosis in living cells. Rab proteins and SNARE modulators are lost, and dynamin, PIP2, and BAR-domain proteins are rapidly and transiently recruited, where they may modulate the nascent fusion pore. How and when the dozens of molecules that control exocytosis assemble in living cells to regulate the fusion of a vesicle with the plasma membrane is unknown. Here we image with two-color total internal reflection fluorescence microscopy the local changes of 27 proteins at single dense-core vesicles undergoing calcium-triggered fusion. We identify two broad dynamic behaviors of exocytic molecules. First, proteins enriched at exocytic sites are associated with DCVs long before exocytosis, and near the time of membrane fusion, they diffuse away. These proteins include Rab3 and Rab27, rabphilin3a, munc18a, tomosyn, and CAPS. Second, we observe a group of classical endocytic proteins and lipids, including dynamins, amphiphysin, syndapin, endophilin, and PIP2, which are rapidly and transiently recruited to the exocytic site near the time of membrane fusion. Dynamin mutants unable to bind amphiphysin were not recruited, indicating that amphiphysin is involved in localizing dynamin to the fusion site. Expression of mutant dynamins and knockdown of endogenous dynamin altered the rate of cargo release from single vesicles. Our data reveal the dynamics of many key proteins involved in exocytosis and identify a rapidly recruited dynamin/PIP2/BAR assembly that regulates the exocytic fusion pore of dense-core vesicles in cultured endocrine beta cells.
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Affiliation(s)
- Adam J Trexler
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kem A Sochacki
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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111
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Chamberland JP, Antonow LT, Dias Santos M, Ritter B. NECAP2 controls clathrin coat recruitment to early endosomes for fast endocytic recycling. J Cell Sci 2016; 129:2625-37. [PMID: 27206861 DOI: 10.1242/jcs.173708] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/19/2016] [Indexed: 01/04/2023] Open
Abstract
Endocytic recycling returns receptors to the plasma membrane following internalization and is essential to maintain receptor levels on the cell surface, re-sensitize cells to extracellular ligands and for continued nutrient uptake. Yet, the protein machineries and mechanisms that drive endocytic recycling remain ill-defined. Here, we establish that NECAP2 regulates the endocytic recycling of EGFR and transferrin receptor. Our analysis of the recycling dynamics revealed that NECAP2 functions in the fast recycling pathway that directly returns cargo from early endosomes to the cell surface. In contrast, NECAP2 does not regulate the clathrin-mediated endocytosis of these cargos, the degradation of EGFR or the recycling of transferrin along the slow, Rab11-dependent recycling pathway. We show that protein knockdown of NECAP2 leads to enlarged early endosomes and causes the loss of the clathrin adapter AP-1 from the organelle. Through structure-function analysis, we define the protein-binding interfaces in NECAP2 that are crucial for AP-1 recruitment to early endosomes. Together, our data identify NECAP2 as a pathway-specific regulator of clathrin coat formation on early endosomes for fast endocytic recycling.
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Affiliation(s)
- John P Chamberland
- Boston University School of Medicine, Biochemistry Department, Boston, MA 02118, USA
| | - Lauren T Antonow
- Boston University School of Medicine, Biochemistry Department, Boston, MA 02118, USA
| | - Michel Dias Santos
- Boston University School of Medicine, Biochemistry Department, Boston, MA 02118, USA
| | - Brigitte Ritter
- Boston University School of Medicine, Biochemistry Department, Boston, MA 02118, USA
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112
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Lee J, Chung JH, Kim HM, Kim DW, Kim H. Designed nucleases for targeted genome editing. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:448-62. [PMID: 26369767 DOI: 10.1111/pbi.12465] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 05/20/2023]
Abstract
Targeted genome-editing technology using designed nucleases has been evolving rapidly, and its applications are widely expanding in research, medicine and biotechnology. Using this genome-modifying technology, researchers can precisely and efficiently insert, remove or change specific sequences in various cultured cells, micro-organisms, animals and plants. This genome editing is based on the generation of double-strand breaks (DSBs), repair of which modifies the genome through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR). In addition, designed nickase-induced generation of single-strand breaks can also lead to precise genome editing through HDR, albeit at relatively lower efficiencies than that induced by nucleases. Three kinds of designed nucleases have been used for targeted DSB formation: zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system. A growing number of researchers are using genome-editing technologies, which have become more accessible and affordable since the discovery and adaptation of CRISPR-Cas9. Here, the repair mechanism and outcomes of DSBs are reviewed and the three types of designed nucleases are discussed with the hope that such understanding will facilitate applications to genome editing.
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Affiliation(s)
- Junwon Lee
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Hee Chung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Dong-Wook Kim
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hyongbum Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, Korea
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113
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Maeder ML, Gersbach CA. Genome-editing Technologies for Gene and Cell Therapy. Mol Ther 2016; 24:430-46. [PMID: 26755333 PMCID: PMC4786923 DOI: 10.1038/mt.2016.10] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders. The current challenges and future prospects for genome editing as a transformative technology for gene and cell therapy are also discussed.
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Affiliation(s)
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA
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114
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Abstract
Understanding cellular structure is key to understanding cellular regulation. New developments in super-resolution fluorescence imaging, electron microscopy, and quantitative image analysis methods are now providing some of the first three-dimensional dynamic maps of biomolecules at the nanometer scale. These new maps—comprehensive nanometer-scale cellular cartographies—will reveal how the molecular organization of cells influences their diverse and changeable activities.
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Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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115
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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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116
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Dalvai M, Loehr J, Jacquet K, Huard CC, Roques C, Herst P, Côté J, Doyon Y. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells. Cell Rep 2015; 13:621-633. [PMID: 26456817 DOI: 10.1016/j.celrep.2015.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 07/27/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022] Open
Abstract
Conventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.
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Affiliation(s)
- Mathieu Dalvai
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Karine Jacquet
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Caroline C Huard
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada
| | - Céline Roques
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Pauline Herst
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Jacques Côté
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada; St-Patrick Research Group in Basic Oncology and Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center and Faculty of Medicine, Laval University, Quebec City, QC G1V 4G2, Canada.
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117
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Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
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Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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118
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Fan F, Ji C, Wu Y, Ferguson SM, Tamarina N, Philipson LH, Lou X. Dynamin 2 regulates biphasic insulin secretion and plasma glucose homeostasis. J Clin Invest 2015; 125:4026-41. [PMID: 26413867 DOI: 10.1172/jci80652] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/20/2015] [Indexed: 12/18/2022] Open
Abstract
Alterations in insulin granule exocytosis and endocytosis are paramount to pancreatic β cell dysfunction in diabetes mellitus. Here, using temporally controlled gene ablation specifically in β cells in mice, we identified an essential role of dynamin 2 GTPase in preserving normal biphasic insulin secretion and blood glucose homeostasis. Dynamin 2 deletion in β cells caused glucose intolerance and substantial reduction of the second phase of glucose-stimulated insulin secretion (GSIS); however, mutant β cells still maintained abundant insulin granules, with no signs of cell surface expansion. Compared with control β cells, real-time capacitance measurements demonstrated that exocytosis-endocytosis coupling was less efficient but not abolished; clathrin-mediated endocytosis (CME) was severely impaired at the step of membrane fission, which resulted in accumulation of clathrin-coated endocytic intermediates on the plasma membrane. Moreover, dynamin 2 ablation in β cells led to striking reorganization and enhancement of actin filaments, and insulin granule recruitment and mobilization were impaired at the later stage of GSIS. Together, our results demonstrate that dynamin 2 regulates insulin secretory capacity and dynamics in vivo through a mechanism depending on CME and F-actin remodeling. Moreover, this study indicates a potential pathophysiological link between endocytosis and diabetes mellitus.
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119
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Hong SH, Cortesio CL, Drubin DG. Machine-Learning-Based Analysis in Genome-Edited Cells Reveals the Efficiency of Clathrin-Mediated Endocytosis. Cell Rep 2015; 12:2121-30. [PMID: 26387943 DOI: 10.1016/j.celrep.2015.08.048] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/05/2015] [Accepted: 08/17/2015] [Indexed: 12/30/2022] Open
Abstract
Cells internalize various molecules through clathrin-mediated endocytosis (CME). Previous live-cell imaging studies suggested that CME is inefficient, with about half of the events terminated. These CME efficiency estimates may have been confounded by overexpression of fluorescently tagged proteins and inability to filter out false CME sites. Here, we employed genome editing and machine learning to identify and analyze authentic CME sites. We examined CME dynamics in cells that express fluorescent fusions of two defining CME proteins, AP2 and clathrin. Support vector machine classifiers were built to identify and analyze authentic CME sites. From inception until disappearance, authentic CME sites contain both AP2 and clathrin, have the same degree of limited mobility, continue to accumulate AP2 and clathrin over lifetimes >∼20 s, and almost always form vesicles as assessed by dynamin2 recruitment. Sites that contain only clathrin or AP2 show distinct dynamics, suggesting they are not part of the CME pathway.
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Affiliation(s)
- Sun Hae Hong
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Christa L Cortesio
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
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120
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Aranda JF, Canfrán-Duque A, Goedeke L, Suárez Y, Fernández-Hernando C. The miR-199-dynamin regulatory axis controls receptor-mediated endocytosis. J Cell Sci 2015; 128:3197-209. [PMID: 26163491 DOI: 10.1242/jcs.165233] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 07/02/2015] [Indexed: 12/19/2022] Open
Abstract
Small non-coding RNAs (microRNAs) are important regulators of gene expression that modulate many physiological processes; however, their role in regulating intracellular transport remains largely unknown. Intriguingly, we found that the dynamin (DNM) genes, a GTPase family of proteins responsible for endocytosis in eukaryotic cells, encode the conserved miR-199a and miR-199b family of miRNAs within their intronic sequences. Here, we demonstrate that miR-199a and miR-199b regulate endocytic transport by controlling the expression of important mediators of endocytosis such as clathrin heavy chain (CLTC), Rab5A, low-density lipoprotein receptor (LDLR) and caveolin-1 (Cav-1). Importantly, miR-199a-5p and miR-199b-5p overexpression markedly inhibits CLTC, Rab5A, LDLR and Cav-1 expression, thus preventing receptor-mediated endocytosis in human cell lines (Huh7 and HeLa). Of note, miR-199a-5p inhibition increases target gene expression and receptor-mediated endocytosis. Taken together, our work identifies a new mechanism by which microRNAs regulate intracellular trafficking. In particular, we demonstrate that the DNM, miR-199a-5p and miR-199b-5p genes act as a bifunctional locus that regulates endocytosis, thus adding an unexpected layer of complexity in the regulation of intracellular trafficking.
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Affiliation(s)
- Juan F Aranda
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alberto Canfrán-Duque
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Leigh Goedeke
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yajaira Suárez
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carlos Fernández-Hernando
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
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121
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Reis CR, Chen PH, Srinivasan S, Aguet F, Mettlen M, Schmid SL. Crosstalk between Akt/GSK3β signaling and dynamin-1 regulates clathrin-mediated endocytosis. EMBO J 2015; 34:2132-46. [PMID: 26139537 DOI: 10.15252/embj.201591518] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/10/2015] [Indexed: 12/20/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) regulates signaling from the plasma membrane. Analysis of clathrin-coated pit (CCP) dynamics led us to propose the existence of a rate-limiting, regulatory step(s) that monitor the fidelity of early stages in CCP maturation. Here we show that nascent endocytic vesicles formed in mutant cells displaying rapid, dysregulated CME are defective in early endosomal trafficking, maturation and acidification, confirming the importance of this "checkpoint." Dysregulated CME also alters EGF receptor signaling and leads to constitutive activation of the protein kinase Akt. Dynamin-1, which was thought to be neuron specific, is activated by the Akt/GSK3β signaling cascade in non-neuronal cells to trigger rapid, dysregulated CME. Acute activation of dynamin-1 in RPE cells by inhibition of GSK3β accelerates CME, alters CCP dynamics and, unexpectedly, increases the rate of CCP initiation. CRISPR-Cas9n-mediated knockout and reconstitution studies establish that dynamin-1 is activated by Akt/GSK3β signaling in H1299 non-small lung cancer cells. These findings provide direct evidence for an isoform-specific role for dynamin in regulating CME and reveal a feed-forward pathway that could link signaling from cell surface receptors to the regulation of CME.
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Affiliation(s)
- Carlos R Reis
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ping-Hung Chen
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - François Aguet
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marcel Mettlen
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sandra L Schmid
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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122
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Avinoam O, Schorb M, Beese CJ, Briggs JAG, Kaksonen M. Endocytic sites mature by continuous bending and remodeling of the clathrin coat. Science 2015; 348:1369-72. [DOI: 10.1126/science.aaa9555] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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123
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Zou B, Mittal R, Grati M, Lu Z, Shu Y, Tao Y, Feng Y, Xie D, Kong W, Yang S, Chen ZY, Liu X. The application of genome editing in studying hearing loss. Hear Res 2015; 327:102-8. [PMID: 25987504 DOI: 10.1016/j.heares.2015.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/06/2015] [Accepted: 04/29/2015] [Indexed: 12/26/2022]
Abstract
Targeted genome editing mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) technology has emerged as one of the most powerful tools to study gene functions, and with potential to treat genetic disorders. Hearing loss is one of the most common sensory disorders, affecting approximately 1 in 500 newborns with no treatment. Mutations of inner ear genes contribute to the largest portion of genetic deafness. The simplicity and robustness of CRISPR/Cas9-directed genome editing in human cells and model organisms such as zebrafish, mice and primates make it a promising technology in hearing research. With CRISPR/Cas9 technology, functions of inner ear genes can be studied efficiently by the disruption of normal gene alleles through non-homologous-end-joining (NHEJ) mechanism. For genetic hearing loss, CRISPR/Cas9 has potential to repair gene mutations by homology-directed-repair (HDR) or to disrupt dominant mutations by NHEJ, which could restore hearing. Our recent work has shown CRISPR/Cas9-mediated genome editing can be efficiently performed in the mammalian inner ear in vivo. Thus, application of CRISPR/Cas9 in hearing research will open up new avenues for understanding the pathology of genetic hearing loss and provide new routes in the development of treatment to restore hearing. In this review, we describe major methodologies currently used for genome editing. We will highlight applications of these technologies in studies of genetic disorders and discuss issues pertaining to applications of CRISPR/Cas9 in auditory systems implicated in genetic hearing loss.
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Affiliation(s)
- Bing Zou
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - M'hamed Grati
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Zhongmin Lu
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | - Yilai Shu
- Department of Otology and Laryngology, Harvard Medical School and Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston 02114, USA; Department of Otology and Skull Base Surgery, Eye, Ear, Nose and Throat Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong Tao
- Department of Otology and Laryngology, Harvard Medical School and Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston 02114, USA; Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Youg Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dinghua Xie
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Weijia Kong
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiming Yang
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
| | - Zheng-Yi Chen
- Department of Otology and Laryngology, Harvard Medical School and Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston 02114, USA.
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital Central South University, Changsha, Hunan, China; Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.
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124
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Peng Y, Grassart A, Lu R, Wong CCL, Yates J, Barnes G, Drubin DG. Casein kinase 1 promotes initiation of clathrin-mediated endocytosis. Dev Cell 2015; 32:231-40. [PMID: 25625208 DOI: 10.1016/j.devcel.2014.11.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 06/11/2014] [Accepted: 11/10/2014] [Indexed: 12/22/2022]
Abstract
In budding yeast, over 60 proteins functioning in at least five modules are recruited to endocytic sites with predictable order and timing. However, how sites of clathrin-mediated endocytosis are initiated and stabilized is not well understood. Here, the casein kinase 1 (CK1) Hrr25 is shown to be an endocytic protein and to be among the earliest proteins to appear at endocytic sites. Hrr25 absence or overexpression decreases or increases the rate of endocytic site initiation, respectively. Ede1, an early endocytic Eps15-like protein important for endocytic initiation, is an Hrr25 target and is required for Hrr25 recruitment to endocytic sites. Hrr25 phosphorylation of Ede1 is required for Hrr25-Ede1 interaction and promotes efficient initiation of endocytic sites. These observations indicate that Hrr25 kinase and Ede1 cooperate to initiate and stabilize endocytic sites. Analysis of the mammalian homologs CK1δ/ε suggests a conserved role for these protein kinases in endocytic site initiation and stabilization.
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Affiliation(s)
- Yutian Peng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Grassart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Catherine C L Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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125
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Shvets E, Bitsikas V, Howard G, Hansen CG, Nichols BJ. Dynamic caveolae exclude bulk membrane proteins and are required for sorting of excess glycosphingolipids. Nat Commun 2015; 6:6867. [PMID: 25897946 PMCID: PMC4410672 DOI: 10.1038/ncomms7867] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/06/2015] [Indexed: 12/19/2022] Open
Abstract
Caveolae have long been implicated in endocytosis. Recent data question this link, and in the absence of specific cargoes the potential cellular function of caveolar endocytosis remains unclear. Here we develop new tools, including doubly genome-edited cell lines, to assay the subcellular dynamics of caveolae using tagged proteins expressed at endogenous levels. We find that around 5% of the cellular pool of caveolae is present on dynamic endosomes, and is delivered to endosomes in a clathrin-independent manner. Furthermore, we show that caveolae are indeed likely to bud directly from the plasma membrane. Using a genetically encoded tag for electron microscopy and ratiometric light microscopy, we go on to show that bulk membrane proteins are depleted within caveolae. Although caveolae are likely to account for only a small proportion of total endocytosis, cells lacking caveolae show fundamentally altered patterns of membrane traffic when loaded with excess glycosphingolipid. Altogether, these observations support the hypothesis that caveolar endocytosis is specialized for transport of membrane lipid.
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Affiliation(s)
- Elena Shvets
- MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Carsten Gram Hansen
- Sanford Consortium for Regenerative Medicine UCSD, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037, USA
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126
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DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum. Microbiol Mol Biol Rev 2015; 78:469-86. [PMID: 25184562 DOI: 10.1128/mmbr.00059-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Research into the complex genetic underpinnings of the malaria parasite Plasmodium falciparum is entering a new era with the arrival of site-specific genome engineering. Previously restricted only to model systems but now expanded to most laboratory organisms, and even to humans for experimental gene therapy studies, this technology allows researchers to rapidly generate previously unattainable genetic modifications. This technological advance is dependent on DNA double-strand break repair (DSBR), specifically homologous recombination in the case of Plasmodium. Our understanding of DSBR in malaria parasites, however, is based largely on assumptions and knowledge taken from other model systems, which do not always hold true in Plasmodium. Here we describe the causes of double-strand breaks, the mechanisms of DSBR, and the differences between model systems and P. falciparum. These mechanisms drive basic parasite functions, such as meiosis, antigen diversification, and copy number variation, and allow the parasite to continually evolve in the contexts of host immune pressure and drug selection. Finally, we discuss the new technologies that leverage DSBR mechanisms to accelerate genetic investigations into this global infectious pathogen.
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127
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Feliciano D, Tolsma TO, Farrell KB, Aradi A, Di Pietro SM. A second Las17 monomeric actin-binding motif functions in Arp2/3-dependent actin polymerization during endocytosis. Traffic 2015; 16:379-97. [PMID: 25615019 DOI: 10.1111/tra.12259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/03/2015] [Accepted: 01/05/2015] [Indexed: 12/16/2022]
Abstract
During clathrin-mediated endocytosis (CME), actin assembly provides force to drive vesicle internalization. Members of the Wiskott-Aldrich syndrome protein (WASP) family play a fundamental role stimulating actin assembly. WASP family proteins contain a WH2 motif that binds globular actin (G-actin) and a central-acidic motif that binds the Arp2/3 complex, thus promoting the formation of branched actin filaments. Yeast WASP (Las17) is the strongest of five factors promoting Arp2/3-dependent actin polymerization during CME. It was suggested that this strong activity may be caused by a putative second G-actin-binding motif in Las17. Here, we describe the in vitro and in vivo characterization of such Las17 G-actin-binding motif (LGM) and its dependence on a group of conserved arginine residues. Using the yeast two-hybrid system, GST-pulldown, fluorescence polarization and pyrene-actin polymerization assays, we show that LGM binds G-actin and is necessary for normal Arp2/3-mediated actin polymerization in vitro. Live-cell fluorescence microscopy experiments demonstrate that LGM is required for normal dynamics of actin polymerization during CME. Further, LGM is necessary for normal dynamics of endocytic machinery components that are recruited at early, intermediate and late stages of endocytosis, as well as for optimal endocytosis of native CME cargo. Both in vitro and in vivo experiments show that LGM has relatively lower potency compared to the previously known Las17 G-actin-binding motif, WH2. These results establish a second G-actin-binding motif in Las17 and advance our knowledge on the mechanism of actin assembly during CME.
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Affiliation(s)
- Daniel Feliciano
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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128
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Simunovic M, Bassereau P. Reshaping biological membranes in endocytosis: crossing the configurational space of membrane-protein interactions. Biol Chem 2015; 395:275-83. [PMID: 24353142 DOI: 10.1515/hsz-2013-0242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/16/2013] [Indexed: 11/15/2022]
Abstract
Lipid membranes are highly dynamic. Over several decades, physicists and biologists have uncovered a number of ways they can change the shape of membranes or alter their phase behavior. In cells, the intricate action of membrane proteins drives these processes. Considering the highly complex ways proteins interact with biological membranes, molecular mechanisms of membrane remodeling still remain unclear. When studying membrane remodeling phenomena, researchers often observe different results, leading them to disparate conclusions on the physiological course of such processes. Here we discuss how combining research methodologies and various experimental conditions contributes to the understanding of the entire phase space of membrane-protein interactions. Using the example of clathrin-mediated endocytosis we try to distinguish the question 'how can proteins remodel the membrane?' from 'how do proteins remodel the membrane in the cell?' In particular, we consider how altering physical parameters may affect the way membrane is remodeled. Uncovering the full range of physical conditions under which membrane phenomena take place is key in understanding the way cells take advantage of membrane properties in carrying out their vital tasks.
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129
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Chiba K, Hockemeyer D. Genome editing in human pluripotent stem cells using site-specific nucleases. Methods Mol Biol 2015; 1239:267-80. [PMID: 25408412 DOI: 10.1007/978-1-4939-1862-1_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) (Thomson, Science 282:1145-1147, 1998; Takahashi et al. Cell 131:861-872, 2007), collectively referred to as pluripotent stem cells (hPSCs), are currently used in disease modeling to address questions specific to humans and to complement our insight gained from model organisms (Soldner et al. Cell 146:318-331, 2011; Soldner and Jaenisch, Science 338:1155-1156, 2012). Recently, genetic engineering using site-specific nucleases has been established in hPSCs (Hockemeyer et al. Nat Biotechnol 27:851-857, 2009; Hockemeyer et al., Nat Biotechnol 29:731-734, 2011; Zou et al., Cell Stem Cell 5:97-110, 2011; Yusa et al., Nature 478:391-394, 2011; DeKelver et al., Genome Res 20:1133-1142, 2010), allowing a level of genetic control previously limited to model systems. Thus, we can now perform targeted gene knockouts, generate tissue-specific cell lineage reporters, overexpress genes from a defined locus, and introduce and repair single point mutations in hPSCs. This ability to genetically engineer pluripotent stem cells will significantly facilitate the study of human disease in a defined genetic context. Here we outline protocols for efficient gene targeting in hPSCs.
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Affiliation(s)
- Kunitoshi Chiba
- Department of Molecular and Cell Biology, University of California, Berkeley, 400B Li Ka Shing Center, Berkeley, CA, 94720-3370, USA
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130
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Abstract
Systems biology has recently achieved significant success in the understanding of complex interconnected phenomena such as cell polarity and migration. In this context, the definition of systems biology has come to encompass the integration of quantitative measurements with sophisticated modeling approaches. This article will review recent progress in live cell imaging technologies that have expanded the possibilities of quantitative in vivo measurements, particularly in regards to molecule counting and quantitative measurements of protein concentration and dynamics. These methods have gained and continue to gain popularity with the biological community. In general, we will discuss three broad categories: protein interactions, protein quantitation, and protein dynamics.
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Affiliation(s)
- Sarah E Smith
- a Stowers Institute for Medical Research ; Kansas City , MO USA
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131
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Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J 2014; 462:397-413. [PMID: 25145439 DOI: 10.1042/bj20140400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.
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132
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Masedunskas A, Appaduray M, Hardeman EC, Gunning PW. What makes a model system great? INTRAVITAL 2014. [DOI: 10.4161/intv.26287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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133
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Soohoo AL, Bowersox SL, Puthenveedu MA. Visualizing clathrin-mediated endocytosis of G protein-coupled receptors at single-event resolution via TIRF microscopy. J Vis Exp 2014:e51805. [PMID: 25350161 DOI: 10.3791/51805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Many important signaling receptors are internalized through the well-studied process of clathrin-mediated endocytosis (CME). Traditional cell biological assays, measuring global changes in endocytosis, have identified over 30 known components participating in CME, and biochemical studies have generated an interaction map of many of these components. It is becoming increasingly clear, however, that CME is a highly dynamic process whose regulation is complex and delicate. In this manuscript, we describe the use of Total Internal Reflection Fluorescence (TIRF) microscopy to directly visualize the dynamics of components of the clathrin-mediated endocytic machinery, in real time in living cells, at the level of individual events that mediate this process. This approach is essential to elucidate the subtle changes that can alter endocytosis without globally blocking it, as is seen with physiological regulation. We will focus on using this technique to analyze an area of emerging interest, the role of cargo composition in modulating the dynamics of distinct clathrin-coated pits (CCPs). This protocol is compatible with a variety of widely available fluorescence probes, and may be applied to visualizing the dynamics of many cargo molecules that are internalized from the cell surface.
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Affiliation(s)
- Amanda L Soohoo
- Department of Biological Sciences, Carnegie Mellon University
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134
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Fürthauer M, Smythe E. Systems dynamics in endocytosis. Traffic 2014; 15:338-46. [PMID: 24405722 DOI: 10.1111/tra.12147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/22/2013] [Accepted: 01/09/2014] [Indexed: 11/28/2022]
Abstract
The endocytic system acts at the crossroads of different cellular activities to play a central role in the regulation of cell signaling and membrane dynamics. An European Molecular Biology Organization (EMBO) conference held in October 2013 in Villars-sur-Ollon gathered researchers from all over the world to present their latest findings on the endolysosomal system and identify major challenges for the future. The conference covered the entire spectrum of research in this rapidly evolving field ranging from the cellular mechanics of endocytosis to the role of proteins and lipids in the biogenesis and function of endolysosomal organelles and the analysis of higher order system properties in multicellular contexts. In particular, the meeting highlighted current efforts to complement the insights that can be gained by biochemical and cell biological approaches with the use of quantitative biophysics, systems biology and animal model systems to achieve an integrated view of the properties of the endomembrane system and its role in cellular information processing.
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Affiliation(s)
- Maximilian Fürthauer
- Institut de Biologie Valrose, CNRS UMR7277, INSERM 1091, University of Nice Sophia-Antipolis, Nice, France
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135
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Merrifield CJ, Kaksonen M. Endocytic accessory factors and regulation of clathrin-mediated endocytosis. Cold Spring Harb Perspect Biol 2014; 6:a016733. [PMID: 25280766 DOI: 10.1101/cshperspect.a016733] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Up to 60 different proteins are recruited to the site of clathrin-mediated endocytosis in an ordered sequence. These accessory proteins have roles during all the different stages of clathrin-mediated endocytosis. First, they participate in the initiation of the endocytic event, thereby determining when and where endocytic vesicles are made; later they are involved in the maturation of the clathrin coat, recruitment of specific cargo molecules, bending of the membrane, and finally in scission and uncoating of the nascent vesicle. In addition, many of the accessory components are involved in regulating and coupling the actin cytoskeleton to the endocytic membrane. We will discuss the different accessory components and their various roles. Most of the data comes from studies performed with cultured mammalian cells or yeast cells. The process of endocytosis is well conserved between these different organisms, but there are also many interesting differences that may shed light on the mechanistic principles of endocytosis.
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Affiliation(s)
- Christien J Merrifield
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique UPR3082, 91198 Gif-sur-Yvette, France
| | - Marko Kaksonen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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136
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Mahen R, Koch B, Wachsmuth M, Politi AZ, Perez-Gonzalez A, Mergenthaler J, Cai Y, Ellenberg J. Comparative assessment of fluorescent transgene methods for quantitative imaging in human cells. Mol Biol Cell 2014; 25:3610-8. [PMID: 25232003 PMCID: PMC4230620 DOI: 10.1091/mbc.e14-06-1091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite widespread use the extent to which different mammalian transgene methods report on the properties of endogenous proteins has not been systematically compared. This study shows that the choice of fluorescence-tagging method fundamentally influences the ability to image the activity of the mitotic kinase Aurora B. Fluorescence tagging of proteins is a widely used tool to study protein function and dynamics in live cells. However, the extent to which different mammalian transgene methods faithfully report on the properties of endogenous proteins has not been studied comparatively. Here we use quantitative live-cell imaging and single-molecule spectroscopy to analyze how different transgene systems affect imaging of the functional properties of the mitotic kinase Aurora B. We show that the transgene method fundamentally influences level and variability of expression and can severely compromise the ability to report on endogenous binding and localization parameters, providing a guide for quantitative imaging studies in mammalian cells.
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Affiliation(s)
- Robert Mahen
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Birgit Koch
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Malte Wachsmuth
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Antonio Z Politi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | | | - Yin Cai
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jan Ellenberg
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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137
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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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138
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Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. Nat Commun 2014; 5:4767. [PMID: 25182477 DOI: 10.1038/ncomms5767] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/21/2014] [Indexed: 12/15/2022] Open
Abstract
The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.
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139
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Mettlen M, Danuser G. Imaging and modeling the dynamics of clathrin-mediated endocytosis. Cold Spring Harb Perspect Biol 2014; 6:a017038. [PMID: 25167858 DOI: 10.1101/cshperspect.a017038] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clathrin-mediated endocytosis (CME) plays a central role in cellular homeostasis and is mediated by clathrin-coated pits (CCPs). Live-cell imaging has revealed a remarkable heterogeneity in CCP assembly kinetics, which can be used as an intrinsic source of mechanistic information on CCP regulation but also poses several major problems for unbiased analysis of CME dynamics. The backbone of unveiling the molecular control of CME is an imaging-based inventory of the full diversity of individual CCP behaviors, which requires detection and tracking of structural fiduciaries and regulatory proteins with an accuracy of >99.9%, despite very low signals. This level of confidence can only be achieved by combining appropriate imaging modalities with self-diagnostic computational algorithms for image analysis and data mining.
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Affiliation(s)
- Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75235-9039
| | - Gaudenz Danuser
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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140
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141
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Poking cells for efficient vector-free intracellular delivery. Nat Commun 2014; 5:4466. [DOI: 10.1038/ncomms5466] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 06/19/2014] [Indexed: 02/07/2023] Open
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142
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Grassart A, Cheng AT, Hong SH, Zhang F, Zenzer N, Feng Y, Briner DM, Davis GD, Malkov D, Drubin DG. Actin and dynamin2 dynamics and interplay during clathrin-mediated endocytosis. ACTA ACUST UNITED AC 2014; 205:721-35. [PMID: 24891602 PMCID: PMC4050722 DOI: 10.1083/jcb.201403041] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Actin assembly influences the precise temporal and quantitative recruitment of dynamin2 to sites of clathrin-mediated endocytosis. Clathrin-mediated endocytosis (CME) involves the recruitment of numerous proteins to sites on the plasma membrane with prescribed timing to mediate specific stages of the process. However, how choreographed recruitment and function of specific proteins during CME is achieved remains unclear. Using genome editing to express fluorescent fusion proteins at native levels and live-cell imaging with single-molecule sensitivity, we explored dynamin2 stoichiometry, dynamics, and functional interdependency with actin. Our quantitative analyses revealed heterogeneity in the timing of the early phase of CME, with transient recruitment of 2–4 molecules of dynamin2. In contrast, considerable regularity characterized the final 20 s of CME, during which ∼26 molecules of dynamin2, sufficient to make one ring around the vesicle neck, were typically recruited. Actin assembly generally preceded dynamin2 recruitment during the late phases of CME, and promoted dynamin recruitment. Collectively, our results demonstrate precise temporal and quantitative regulation of the dynamin2 recruitment influenced by actin polymerization.
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Affiliation(s)
- Alexandre Grassart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Aaron T Cheng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Sun Hae Hong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Fan Zhang
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - Nathan Zenzer
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - Yongmei Feng
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - David M Briner
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - Gregory D Davis
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - Dmitry Malkov
- Cell-Based Assays/Reporter Cell Lines, Sigma-Aldrich Research Biotech, St. Louis, MO 63103
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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143
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Abstract
There are many pathways of endocytosis at the cell surface that apparently operate at the same time. With the advent of new molecular genetic and imaging tools, an understanding of the different ways by which a cell may endocytose cargo is increasing by leaps and bounds. In this review we explore pathways of endocytosis that occur in the absence of clathrin. These are referred to as clathrin-independent endocytosis (CIE). Here we primarily focus on those pathways that function at the small scale in which some have distinct coats (caveolae) and others function in the absence of specific coated intermediates. We follow the trafficking itineraries of the material endocytosed by these pathways and finally discuss the functional roles that these pathways play in cell and tissue physiology. It is likely that these pathways will play key roles in the regulation of plasma membrane area and tension and also control the availability of membrane during cell migration.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, and Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, Queensland 4072, Brisbane, Australia
| | - Julie G Donaldson
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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144
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Liberali P, Snijder B, Pelkmans L. A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking. Cell 2014; 157:1473-1487. [DOI: 10.1016/j.cell.2014.04.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/30/2014] [Accepted: 04/10/2014] [Indexed: 11/29/2022]
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145
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Greene AC, Lord SJ, Tian A, Rhodes C, Kai H, Groves JT. Spatial organization of EphA2 at the cell-cell interface modulates trans-endocytosis of ephrinA1. Biophys J 2014; 106:2196-205. [PMID: 24853748 PMCID: PMC4052362 DOI: 10.1016/j.bpj.2014.03.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
Abstract
EphA2 is a receptor tyrosine kinase (RTK) that is sensitive to spatial and mechanical aspects of the cell's microenvironment. Misregulation of EphA2 occurs in many aggressive cancers. Although its juxtacrine signaling geometry (EphA2's cognate ligand ephrinA1 is expressed on the surface of an apposing cell) provides a mechanism by which the receptor may experience extracellular forces, this also renders the system challenging to decode. By depositing living cells on synthetic supported lipid membranes displaying ephrinA1, we have reconstituted key features of the juxtacrine EphA2-ephrinA1 signaling system while maintaining the ability to perturb the spatial and mechanical properties of the membrane-cell interface with precision. In addition, we developed a trans-endocytosis assay to monitor internalization of ephrinA1 from a supported membrane into the apposing cell using a quantitative three-dimensional fluorescence microscopy assay. Using this experimental platform to mimic a cell-cell junction, we found that the signaling complex is not efficiently internalized when lateral reorganization at the membrane-cell contact sites is physically hindered. This suggests that EphA2-ephrinA1 trans-endocytosis is sensitive to the mechanical properties of a cell's microenvironment and may have implications in physical aspects of tumor biology.
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Affiliation(s)
- Adrienne C Greene
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California; Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - Samuel J Lord
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California
| | - Aiwei Tian
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California
| | - Christopher Rhodes
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California; Department of Mechanical Engineering, University of California, Berkeley, California
| | - Hiroyuki Kai
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California
| | - Jay T Groves
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California; Mechanobiology Institute, National University of Singapore, Singapore.
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146
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Abstract
Programmable nucleases - including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and RNA-guided engineered nucleases (RGENs) derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system - enable targeted genetic modifications in cultured cells, as well as in whole animals and plants. The value of these enzymes in research, medicine and biotechnology arises from their ability to induce site-specific DNA cleavage in the genome, the repair (through endogenous mechanisms) of which allows high-precision genome editing. However, these nucleases differ in several respects, including their composition, targetable sites, specificities and mutation signatures, among other characteristics. Knowledge of nuclease-specific features, as well as of their pros and cons, is essential for researchers to choose the most appropriate tool for a range of applications.
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Affiliation(s)
- Hyongbum Kim
- Graduate School of Biomedical Science and Engineering, and College of Medicine, Hanyang University, Wangsimni-ro 222, Sungdong-gu, Seoul 133-791, South Korea
| | - Jin-Soo Kim
- 1] Center for Genome Engineering, Institute for Basic Science, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea. [2] Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea
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147
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Deen AJ, Rilla K, Oikari S, Kärnä R, Bart G, Häyrinen J, Bathina AR, Ropponen A, Makkonen K, Tammi RH, Tammi MI. Rab10-mediated endocytosis of the hyaluronan synthase HAS3 regulates hyaluronan synthesis and cell adhesion to collagen. J Biol Chem 2014; 289:8375-89. [PMID: 24509846 PMCID: PMC3961663 DOI: 10.1074/jbc.m114.552133] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Indexed: 12/17/2022] Open
Abstract
Hyaluronan synthases (HAS1-3) are unique in that they are active only when located in the plasma membrane, where they extrude the growing hyaluronan (HA) directly into cell surface and extracellular space. Therefore, traffic of HAS to/from the plasma membrane is crucial for the synthesis of HA. In this study, we have identified Rab10 GTPase as the first protein known to be involved in the control of this traffic. Rab10 colocalized with HAS3 in intracellular vesicular structures and was co-immunoprecipitated with HAS3 from isolated endosomal vesicles. Rab10 silencing increased the plasma membrane residence of HAS3, resulting in a significant increase of HA secretion and an enlarged cell surface HA coat, whereas Rab10 overexpression suppressed HA synthesis. Rab10 silencing blocked the retrograde traffic of HAS3 from the plasma membrane to early endosomes. The cell surface HA coat impaired cell adhesion to type I collagen, as indicated by recovery of adhesion following hyaluronidase treatment. The data indicate a novel function for Rab10 in reducing cell surface HAS3, suppressing HA synthesis, and facilitating cell adhesion to type I collagen. These are processes important in tissue injury, inflammation, and malignant growth.
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Affiliation(s)
| | | | - Sanna Oikari
- From the Institutes of Biomedicine
- Clinical Medicine and
| | | | | | | | | | - Antti Ropponen
- Dentistry, School of Medicine, University of Eastern Finland, Kuopio 70210, Finland
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148
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Abstract
Current technology enables the production of highly specific genome modifications with excellent efficiency and specificity. Key to this capability are targetable DNA cleavage reagents and cellular DNA repair pathways. The break made by these reagents can produce localized sequence changes through inaccurate nonhomologous end joining (NHEJ), often leading to gene inactivation. Alternatively, user-provided DNA can be used as a template for repair by homologous recombination (HR), leading to the introduction of desired sequence changes. This review describes three classes of targetable cleavage reagents: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas RNA-guided nucleases (RGNs). As a group, these reagents have been successfully used to modify genomic sequences in a wide variety of cells and organisms, including humans. This review discusses the properties, advantages, and limitations of each system, as well as the specific considerations required for their use in different biological systems.
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Affiliation(s)
- Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112;
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149
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Godlee C, Kaksonen M. Review series: From uncertain beginnings: initiation mechanisms of clathrin-mediated endocytosis. ACTA ACUST UNITED AC 2014; 203:717-25. [PMID: 24322426 PMCID: PMC3857488 DOI: 10.1083/jcb.201307100] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Clathrin-mediated endocytosis is a central and well-studied trafficking process in eukaryotic cells. How this process is initiated is likely to be a critical point in regulating endocytic activity spatially and temporally, but the underlying mechanisms are poorly understood. During the early stages of endocytosis three components—adaptor and accessory proteins, cargo, and lipids—come together at the plasma membrane to begin the formation of clathrin-coated vesicles. Although different models have been proposed, there is still no clear picture of how these three components cooperate to initiate endocytosis, which may indicate that there is some flexibility underlying this important event.
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Affiliation(s)
- Camilla Godlee
- Cell Biology and Biophysics Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
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Hecht KA, O'Donnell AF, Brodsky JL. The proteolytic landscape of the yeast vacuole. CELLULAR LOGISTICS 2014; 4:e28023. [PMID: 24843828 PMCID: PMC4022603 DOI: 10.4161/cl.28023] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 01/07/2023]
Abstract
The vacuole in the yeast Saccharomyces cerevisiae plays a number of essential roles, and to provide some of these required functions the vacuole harbors at least seven distinct proteases. These proteases exhibit a range of activities and different classifications, and they follow unique paths to arrive at their ultimate, common destination in the cell. This review will first summarize the major functions of the yeast vacuole and delineate how proteins are targeted to this organelle. We will then describe the specific trafficking itineraries and activities of the characterized vacuolar proteases, and outline select features of a new member of this protease ensemble. Finally, we will entertain the question of why so many proteases evolved and reside in the vacuole, and what future research challenges exist in the field.
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Affiliation(s)
- Karen A Hecht
- Department of Biological Sciences; University of Pittsburgh; Pittsburgh, PA USA
| | - Allyson F O'Donnell
- Department of Cell Biology; University of Pittsburgh School of Medicine; Pittsburgh, PA USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences; University of Pittsburgh; Pittsburgh, PA USA
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