Heterologous Gene Expression in E.coli: Methods and Protocols

427 Pages·2017·11.182 MB·English

by  Nicola A. Burgess-Brown (eds.)

Methods in
Molecular Biology 1586
Nicola A. Burgess-Brown Editor
Heterologous
Gene Expression
in E. coli
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651
Heterologous Gene Expression
in E. coli
Methods and Protocols
Edited by
Nicola A. Burgess-Brown
SGC, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
Editor
Nicola A. Burgess-Brown
SGC
Nuffield Department of Clinical Medicine
University of Oxford
Oxford, UK
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6885-5 ISBN 978-1-4939-6887-9 (eBook)
DOI 10.1007/978-1-4939-6887-9
Library of Congress Control Number: 2017934051
© Springer Science+Business Media LLC 2017
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is
concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction
on microfilms 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.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not
imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and
regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to
be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty,
express or implied, with respect to the material contained herein or for any errors or omissions that may have been made.
The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Printed on acid-free paper
This Humana Press imprint is published by Springer Nature
The registered company is Springer Science+Business Media LLC
The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.
Preface
Heterologous gene expression in E. coli has been one of the most widely used methods for
generating recombinant proteins for many scientific analyses and still remains the first choice
for most laboratories around the world. The ease of use and low cost of production often
lead researchers to initially attempt to express their proteins of interest in E. coli rather than
opting for a eukaryotic host. Decades of development have seen the variety of methods for
expressing genes in E. coli broaden, with improved media and optimized conditions for
growth, a choice of promoter systems to regulate expression, fusion tags to aid solubility and
purification, and E. coli host strains to accommodate more challenging or toxic proteins.
Having worked in the area of protein production for structural genomics for the past
12 years, and also having a requirement to generate human proteins, I have seen a shift
from expression of many genes in E. coli to use of the baculovirus expression system using
insect cells and more recently to mammalian cells. This revolution from prokaryotic to
eukaryotic expression has been visible throughout the protein production field and is largely
due to the requirement to obtain specific proteins linked to disease, for functional assays as
well as structures, which may be larger, or require machinery to enable specific post-
translational modifications. It is perhaps important to note, however, that the structural
output from the SGC in Oxford today is still ~80% derived from E. coli.
This book is aimed at molecular biologists, biochemists, and structural biologists,
both from the beginning of their research careers to those in their prime, to give both an
historical and modern overview of the methods available to express their genes of interest
in this exceptional organism. The topics are largely grouped under four parts: (I) high-
throughput cloning, expression screening, and optimization of expression conditions, (II)
protein production and solubility enhancement, (III) case studies to produce challenging
proteins and specific protein families, and (IV) applications of E. coli expression. This vol-
ume provides scientists with a toolbox for designing constructs, tackling expression and
solubility issues, handling membrane proteins and protein complexes, and innovative
engineering of E. coli. It will hopefully prove valuable both in small laboratories and in
higher throughput facilities. I would like to thank all the authors for their contributions
and for making this a global effort.
Oxford, UK Nicola A. Burgess-Brown
v
Contents
Preface.......................................................... v
Contributors.......................................................... xi
Part I HIgH-tHrougHPut ClonIng, ExPrEssIon sCrEEnIng,
and oPtImIzatIon
1 Recombinant Protein Expression in E. coli: A Historical Perspective ........ 3
Opher Gileadi
2 N- and C-Terminal Truncations to Enhance Protein Solubility
and Crystallization: Predicting Protein Domain Boundaries
with Bioinformatics Tools........................................ 11
Christopher D.O. Cooper and Brian D. Marsden
3 Harnessing the Profinity eXact™ System for Expression and Purification
of Heterologous Proteins in E. coli ................................. 33
Yoav Peleg, Vadivel Prabahar, Dominika Bednarczyk, and Tamar Unger
4 ESPRIT: A Method for Defining Soluble Expression Constructs
in Poorly Understood Gene Sequences .............................. 45
Philippe J. Mas and Darren J. Hart
5 Optimizing Expression and Solubility of Proteins in E. coli
Using Modified Media and Induction Parameters ...................... 65
Troy Taylor, John-Paul Denson, and Dominic Esposito
6 Optimization of Membrane Protein Production Using Titratable
Strains of E. coli ............................................... 83
Rosa Morra, Kate Young, David Casas-Mao, Neil Dixon,
and Louise E. Bird
7 Optimizing E. coli-Based Membrane Protein Production
Using Lemo21(DE3) or pReX and GFP-Fusions....................... 109
Grietje Kuipers, Markus Peschke, Nurzian Bernsel Ismail,
Anna Hjelm, Susan Schlegel, David Vikström, Joen Luirink,
and Jan-Willem de Gier
8 High Yield of Recombinant Protein in Shaken E. coli Cultures
with Enzymatic Glucose Release Medium EnPresso B................... 127
Kaisa Ukkonen, Antje Neubauer, Vinit J. Pereira, and Antti Vasala
Part II ProtEIn PurIfICatIon and solubIlIty EnHanCEmEnt
9 A Generic Protocol for Purifying Disulfide-Bonded Domains
and Random Protein Fragments Using Fusion Proteins
with SUMO3 and Cleavage by SenP2 Protease........................ 141
Hüseyin Besir
vii
viii Contents
10 A Strategy for Production of Correctly Folded Disulfide-Rich Peptides
in the Periplasm of E. coli ........................................ 155
Natalie J. Saez, Ben Cristofori-Armstrong, Raveendra Anangi,
and Glenn F. King
11 Split GFP Complementation as Reporter of Membrane Protein
Expression and Stability in E. coli : A Tool to Engineer Stability
in a LAT Transporter ........................................... 181
Ekaitz Errasti-Murugarren, Arturo Rodríguez-Banqueri,
and José Luis Vázquez-Ibar
12 Acting on Folding Effectors to Improve Recombinant Protein Yields
and Functional Quality .......................................... 197
Ario de Marco
13 Protein Folding Using a Vortex Fluidic Device ........................ 211
Joshua Britton, Joshua N. Smith, Colin L. Raston, and Gregory A. Weiss
14 Removal of Affinity Tags with TEV Protease.......................... 221
Sreejith Raran-Kurussi, Scott Cherry, Di Zhang, and David S. Waugh
Part III CasE studIEs to ProduCE CHallEngIng ProtEIns
and sPECIfIC ProtEIn famIlIEs
15 Generation of Recombinant N-Linked Glycoproteins in E. coli ............ 233
Benjamin Strutton, Stephen R.P. Jaffé, Jagroop Pandhal,
and Phillip C. Wright
16 Production of Protein Kinases in E. coli.............................. 251
Charlotte A. Dodson
17 Expression of Prokaryotic Integral Membrane Proteins in E. coli........... 265
James D. Love
18 Multiprotein Complex Production in E. coli:
The SecYEG- SecDFYajC- YidC Holotranslocon........................ 279
Imre Berger, Quiyang Jiang, Ryan J. Schulze, Ian Collinson,
and Christiane Schaffitzel
19 Membrane Protein Production in E. coli Lysates in Presence
of Preassembled Nanodiscs ....................................... 291
Ralf-Bernhardt Rues, Alexander Gräwe, Erik Henrich,
and Frank Bernhard
20 Not Limited to E. coli: Versatile Expression Vectors for Mammalian
Protein Expression ............................................. 313
Katharina Karste, Maren Bleckmann, and Joop van den Heuvel
21 A Generic Protocol for Intracellular Expression
of Recombinant Proteins in Bacillus subtilis........................... 325
Trang Phan, Phuong Huynh, Tuom Truong, and Hoang Nguyen
Part IV aPPlICatIons of E. coli ExPrEssIon
22 In Vivo Biotinylation of Antigens in E. coli ........................... 337
Susanne Gräslund, Pavel Savitsky, and Susanne Müller-Knapp
Contents ix
23 Cold-Shock Expression System in E. coli for Protein NMR Studies ......... 345
Toshihiko Sugiki, Toshimichi Fujiwara, and Chojiro Kojima
24 High-Throughput Production of Proteins in E. coli for Structural Studies . . . . 359
Charikleia Black, John J. Barker, Richard B. Hitchman,
Hok Sau Kwong, Sam Festenstein, and Thomas B. Acton
25 Mass Spectrometric Analysis of Proteins ............................. 373
Rod Chalk
26 How to Determine Interdependencies of Glucose and Lactose Uptake
Rates for Heterologous Protein Production with E. coli.................. 397
David J. Wurm, Christoph Herwig, and Oliver Spadiut
27 Interfacing Biocompatible Reactions with Engineered Escherichia coli ....... 409
Stephen Wallace and Emily P. Balskus
Index ............................................................... 423
Contributors
tHomas b. aCton • Evotec (US), Princeton, NJ, USA
raVEEndra anangI • Institute for Molecular Bioscience, The University of Queensland,
Brisbane, QLD, Australia
EmIly P. balskus • Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA, USA
JoHn J. barkEr • Evotec Ltd, Abingdon, Oxfordshire, UK
domInIka bEdnarCzyk • Department of Bimolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
ImrE bErgEr • The School of Biochemistry, University Walk, University of Bristol, Clifton,
UK; The European Molecular Biology Laboratory (EMBL), BP 181, Unit of Virus Host
Cell Interactions (UVHCI), Horowitz, Grenoble Cedex, France
frank bErnHard • Centre for Biomolecular Magnetic Resonance, Institute for Biophysical
Chemistry, Goethe-University of Frankfurt/Main, Frankfurt/Main, Germany
HüsEyIn bEsIr • Protein Expression and Purification Core Facility, EMBL Heidelberg,
Heidelberg, Germany
louIsE E. bIrd • Oxford Protein Production Facility-UK, Research Complex at Harwell,
Rutherford Appleton Laboratory, Oxfordshire, UK; Division of Structural Biology, Henry
Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
CHarIklEIa blaCk • Evotec Ltd, Abingdon, Oxfordshire, UK
marEn blECkmann • Helmholtz Zentrum für Infektionsforschung GmbH, Braunschweig,
Germany
JosHua brItton • Department of Chemistry, University of California, Irvine, CA, USA;
Centre for NanoScale Science and Technology, School of Chemical and Physical Sciences,
Flinders University, Adelaide, SA, Australia
daVId Casas-mao • Research Complex at Harwell, Rutherford Appleton Laboratory,
Oxfordshire, UK; School of Biosciences, University of Nottingham, Loughborough,
Leicestershire, UK
rod CHalk • Structural Genomics Consortium (SGC), Nuffield Department of Medicine,
University of Oxford, Oxford, UK
sCott CHErry • Macromolecular Crystallography Laboratory, Center for Cancer Research,
National Cancer Institute at Frederick, Frederick, MD, USA
Ian CollInson • The School of Biochemistry, University Walk, University of Bristol,
Clifton, UK
CHrIstoPHEr d.o. CooPEr • Department of Biological Sciences, School of Applied Sciences,
University of Huddersfield, Huddersfield, West Yorkshire, UK
bEn CrIstoforI-armstrong • Institute for Molecular Bioscience, The University of
Queensland, QLD, Australia
JoHn-Paul dEnson • Protein Expression Laboratory, Cancer Research Technology
Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
nEIl dIxon • Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
CHarlottE a. dodson • Molecular Medicine, National Heart & Lung Institute,
Imperial College London, London, UK
xi
xii Contributors
EkaItz ErrastI-murugarrEn • Institute for Research in Biomedicine (IRB Barcelona),
Barcelona Institute of Science and Technology, Barcelona, Spain
domInIC EsPosIto • Protein Expression Laboratory, Cancer Research Technology Program,
Frederick National Laboratory for Cancer Research, Frederick, MD, USA
sam fEstEnstEIn • Evotec Ltd, Abingdon, Oxfordshire, UK
tosHImICHI fuJIwara • Institute for Protein Research, Osaka University, Osaka, Japan
Jan-wIllEm dE gIEr • Department of Biochemistry and Biophysics, Center for
Biomembrane Research, Stockholm University, Stockholm, Sweden; Xbrane Biopharma
AB, Solna, Sweden
oPHEr gIlEadI • Structural Genomics Consortium, University of Oxford, Headington,
Oxford, UK
susannE gräslund • Structural Genomics Consortium, Department of Biochemistry
and Biophysics, Karolinska Institutet, Solna, Sweden
alExandEr gräwE • Centre for Biomolecular Magnetic Resonance, Institute for Biophysical
Chemistry, Goethe-University of Frankfurt/Main, Frankfurt/Main, Germany
darrEn J. Hart • Institut de Biologie Structurale (IBS), CNRS, CEA, Université
Grenoble Alpes, Grenoble, France
ErIk HEnrICH • Centre for Biomolecular Magnetic Resonance, Institute for Biophysical
Chemistry, Goethe-University of Frankfurt/Main, Frankfurt/Main, Germany
CHrIstoPH HErwIg • Research Division Biochemical Engineering, Institute of Chemical
Engineering, TU Wien, Vienna, Austria; Christian Doppler Laboratory for Mechanistic
and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering,
TU Wien, Vienna, Austria
JooP Van dEn HEuVEl • Helmholtz Zentrum für Infektionsforschung GmbH,
Braunschweig, Germany
rICHard b. HItCHman • Evotec Ltd, Abingdon, Oxfordshire, UK
anna HJElm • Department of Biochemistry and Biophysics, Center for Biomembrane
Research, Stockholm University, Stockholm, Sweden
nurzIan bErnsEl IsmaIl • Xbrane Biopharma AB, Solna, Sweden
stEPHEn r.P. Jaffé • Department of Chemical and Biological Engineering,
ChELSI Institute, University of Sheffield, Sheffield, UK
QuIyang JIang • The European Molecular Biology Laboratory (EMBL), BP 181, and Unit
of Virus Host Cell Interactions (UVHCI), Horowitz, Grenoble Cedex, France
katHarIna karstE • Helmholtz Zentrum für Infektionsforschung GmbH, Braunschweig,
Germany
glEnn f. kIng • Institute for Molecular Bioscience, The University of Queensland, QLD,
Australia
CHoJIro koJIma • Institute for Protein Research, Osaka University, Osaka, Japan
grIEtJE kuIPErs • Department of Biochemistry and Biophysics, Center for Biomembrane
Research, Stockholm University, Stockholm, Sweden; Xbrane Biopharma AB, Solna, Sweden
Hok sau kwong • Evotec Ltd, Abingdon, Oxfordshire, UK
JamEs d. loVE • Department of Biochemistry, Albert Einstein College of Medicine at
Yeshiva University, Bronx, NY, USA; ATUM, Newark, CA, USA
JoEn luIrInk • The Amsterdam Institute of Molecules, Medicines and Systems, VU University
Amsterdam, Amsterdam, The Netherlands
arIo dE marCo • Department of Biomedical Sciences and Engineering, University of Nova
Gorica, Vipava, Slovenia