Membrane Trafficking: Second Edition

458 Pages·2015·17.952 MB·English

by  Bor Luen Tang (eds.)

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
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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