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458 Pages·2015·17.952 MB·English
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Methods in Molecular Biology 1270 Bor Luen Tang Editor Membrane Traffi cking Second Edition M M B ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: h ttp://www.springer.com/series/7651 Membrane Trafficking Second Edition Edited by Bor Luen Tang Department of Biochemistry, National University of Singapore, Singapore Editor Bor Luen Tang Department of Biochemistry National University of Singapore Singapore ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-4939-2308-3 ISBN 978-1-4939-2309-0 (eBook) DOI 10.1007/978-1-4939-2309-0 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2014959097 © Springer Science+Business Media New York 2 015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Cover illustration: A431 cells transiently transfected with RFP-Rab5 (red), fi xed after a 30 min pulse-chase with EGF- FITC (green) and co-labeled for early endosome antigen 1 (pseudo-colored magenta). Nuclei are visualized with Hoechst 33342 (blue). Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Prefa ce The term “membrane traffi cking” broadly describes selective transfer of proteins and lipids between membranous structures in both prokaryotes and eukaryotes. In principle this entails two different processes. The fi rst is a myriad of membrane traversing events mediating the translocation of proteins a cross membranes. The other refers to vesicle/membranous carrier- mediated transport b etween eukaryotic organelles in the exocytic/secretory and endocytic pathways (the endoplasmic reticulum, Golgi apparatus, plasma membrane, endosome, and lysosome) as well as other membranous structures such as the nucleus and peroxisomes. Membrane traffi cking research has been at the frontier of cell and molecular biology for the past 30–40 years, with easily recognized groundbreaking discoveries and top accolades to its researchers. One of the early greats, George Palade (Nobel Prize in Physiology and Medicine, 1974), had used electron microscopy to morphologically map the secretory pathway. Gunther Blobel (Nobel Prize in Physiology and Medicine, 1999) founded the concept of signal sequences in membrane targeting and transport. Membrane traffi cking research in the past 20 years has also witnessed a remarkable convergence and synergism from information gained using genetic approaches in yeast cells and biochemical and molecular approaches in mammalian cells. As a result, the principle molecular components mediating membrane traf- fi cking were identifi ed, with the Lasker in 2002 jointly awarded to Randy Schekman and James Rothman and the Nobel in 2013 to Randy Schekman, James Rothman, and Thomas Südhof. Foundations laid down by studies in membrane traffi cking have also aided advances of other fi elds, for example in understanding of disease conditions such as familial hypercho- lesterolemia and neurodegenerative diseases. In 2008, an excellent volume in the Methods in Molecular Biology series on M embrane Traffi cking was brought together by volume editor Ales Vancura and series editor John Walker. It included a compendium of articles describing the state-of-art methods and cutting-e dge techniques to study macromolecular transport across and between mem- branes. The past few years have, however, witnessed many new directions, and importantly, new approaches, in membrane traffi cking research. These include the discovery of novel, unconventional traffi cking pathways as well as the intersections between the classical exo- cytic and endocytic pathways with other key cellular processes that are membrane-a ssociated (such as autophagy). The advent of Omics-based technologies to perform genome-wide screens or correlative studies, expression profi ling, and array-based interrogation of the genome or the functional transcriptome (e.g., sh/siRNA-based screens) has opened up new analytical dimensions that would allow clearer defi nition of components and deeper understanding of regulatory networks in membrane traffi cking. Finally, technological advances in imaging and microscopy have now provided far greater resolution in space and time and facilitated observations in live cells, in ways that were not possible before. All these new advances, in both the science and the technologies, warrant the production of a new volume on M embrane Traffi cking . This new volume, with updates of previous chapters and the inclusion of a large n umber of new chapters, is divided into three parts. Part I includes biochemical and molecular genetics approaches and methods used in analyzing membrane traffi c in both yeast and v vi Preface mammalian cell models. Part II focuses on imaging and microscopy approaches and tech- niques, while Part III highlights the Omics-type approaches. We hope that this new volume of M embrane Traffi cking will be a useful desk reference for both experienced researchers and graduate students/junior scientists in the fi eld of membrane traffi cking. Furthermore, we hope the wide coverage of the chapters would also be helpful to researchers in other fi elds who wish to make an excursion into looking at aspects of membrane traffi cking as well as those simply wanting to familiarize themselves with the frontiers of this exciting fi eld. Bor Luen Tang Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x i 1 Intracellular Parcel Service: Current Issues in Intracellular Membrane Trafficking. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Johannes M. Herrmann and A nne Spang PART I BIOCHEMICAL AND MOLECULAR GENETICS APPROACHES 2 I n Vitro Analysis of the Mitochondrial Preprotein Import Machinery Using Recombinant Precursor Polypeptides . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Dorothea Becker and Wolfgang V oos 3 I mport of Proteins into Isolated Yeast Mitochondria. . . . . . . . . . . . . . . . . . . . 37 Valentina P eleh , Ajay R amesh , and Johannes M . Herrmann 4 E valuation of Unconventional Protein Secretion in Saccharomyces cerevisiae. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Natsuko Miura and Mitsuyoshi U eda 5 Fractionation of Plasmodium-Infected Human Red Blood Cells to Study Protein Trafficking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1 Simone K ülzer , V erena B ittl , and Jude M. Przyborski 6 Investigating Signaling Processes in Membrane Trafficking . . . . . . . . . . . . . . . 8 1 Laura J. Sharpe and A ndrew J . B rown 7 Recruitment of Coat Proteins to Liposomes and Peptidoliposomes . . . . . . . . . 9 1 Sonja H user , G regor S uri , P ascal C rottet , and Martin Spiess 8 A β-Lactamase Based Assay to Measure Surface Expression of Membrane Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Pieter Beerepoot , Vincent M. L am , and Ali Salahpour 9 C ell-Free Reconstitution of Multivesicular Body (MVB) Cargo Sorting. . . . . . 1 15 Monica Gireud , Natalie S irisaengtaksin , S usan Tsunoda , and Andrew J . B ean 10 A nalysis of Biogenesis of Lipid Droplets by Examining Rab40c Associating with Lipid Droplets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Ran Tan , X iaohui Xu , Wanjin H ong , and Tuanlao Wang 11 A nalysis of Conventional and Unconventional Trafficking of CFTR and Other Membrane Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Heon Yung G ee , J oo Young Kim , and Min Goo Lee 12 Assessing Mammalian Autophagy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 55 Sharon A . Tooze , Hannah C. D ooley , H arold B . J. Jefferies , Justin Joachim , Delphine J udith , Christopher A. L amb , M inoo R azi , and Martina W irth vii viii Contents 13 Expression of Functional Myc-Tagged Conserved Oligomeric Golgi (COG) Subcomplexes in Mammalian Cells . . . . . . . . . . . . . . . . . . . . . . 1 67 Rose A. Willett , Tetyana A . Kudlyk , and V ladimir V. Lupashin 14 Molecular and Cellular Characterization of GCC185: A Tethering Protein of the Trans-Golgi Network . . . . . . . . . . . . . . . . . . . . . . 1 79 Pak-yan P atricia C heung and Suzanne R . Pfeffer 15 V isualizing Toll-Like Receptor-Dependent Phagosomal Dynamics in Murine Dendritic Cells Using Live Cell Microscopy . . . . . . . . . . . . . . . . . . 191 Adriana R . Mantegazza and M ichael S . M arks 16 U nderstanding of Complex Protein Interactions with Respect to Anchorage Independence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 05 Jill M. T ham , Sofie C . V an Huffel , and Wanjin H ong 17 Application of Flow Cytometry to Analyze Intracellular Location and Trafficking of Cargo in Cell Populations. . . . . . . . . . . . . . . . . . . . . . . . . . 227 W ei H ong Toh , F iona J . H oughton , Pei Zhi Cheryl Chia , Yasmin M. Ramdzan , D anny M . Hatters , and Paul A. Gleeson 18 Approaches to Analyze the Role of Rab GTPases in Endocytic Trafficking of Epidermal Growth Factor Receptor (EGFR). . . . . . . . . . . . . . . . . . . . . . . . 239 Christelle En L in Chua , Angeline Yim K iat Lim , and Bor L uen Tang PART II MICROSCOPY METHODS AND IMAGING APPROACHES 19 D oes Super-Resolution Fluorescence Microscopy Obsolete Previous Microscopic Approaches to Protein Co-localization? . . . . . . . . . . . . . 255 Laura MacDonald , Giulia B aldini , and Brian S torrie 20 Bimolecular Fluorescence Complementation (BiFC) Technique in Yeast Saccharomyces cerevisiae and Mammalian Cells . . . . . . . . . . . . . . . . . . 2 77 Marion Weber-Boyvat , S hiqian L i , Kari-Pekka Skarp , V esa M . Olkkonen , Daoguang Y an , and Jussi J äntti 21 Microscopic and Spectroscopic Techniques to Investigate Lipid Droplet Formation and Turnover in Yeast. . . . . . . . . . . . . . . . . . . . . . . . . . . . 289 Heimo Wolinski and Sepp D . Kohlwein 22 Image-Based Identification of Nuclear Export Inhibitors from Natural Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 07 Bastien C autain , Nuria d e Pedro , F ernando Reyes , and Wolfgang Link 2 3 Correlative Video-Light–Electron Microscopy of Mobile Organelles. . . . . . . . 3 21 Galina V. Beznoussenko and Alexander A. M ironov 24 L ive Cell Imaging of Endosomal Trafficking in Fungi . . . . . . . . . . . . . . . . . . . 3 47 Sebastian B aumann , N orio T akeshita , N . Grün , R einhard F ischer , and Michael F eldbrügge 25 Quantitative Analysis of Transferrin Cycling by Automated Fluorescence Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365 David T . Hirschmann , C hristoph A. K asper , and Martin S piess Contents ix PART III OMICS APPROACHES 26 Identification of Factors Regulating MET Receptor Endocytosis by High-Throughput siRNA Screening. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381 Ivana Gaziova , Robert A. D avey , and Lisa A. Elferink 27 L arge-Scale Analysis of Membrane Transport in Yeast Using Invertase Reporters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395 Lauren Dalton , M ichael D avey , and Elizabeth Conibear 28 R NAi Screens for Genes Involved in Golgi Glycosylation. . . . . . . . . . . . . . . . . 4 11 Germaine Y . Goh and Frederic A . Bard 29 P roteomic Analyses of a Bi-Lobed Structure in Trypanosoma brucei. . . . . . . . . 427 Ladan Gheiratmand and C ynthia Y . H e 30 Application of the Proximity-Dependent Assay and Fluorescence Imaging Approaches to Study Viral Entry Pathways. . . . . . . 437 Alex L ipovsky , Wei Z hang , Akiko I wasaki , and Daniel DiMaio Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 53

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