Table Of Content

Bacterial Membranes Structural and Molecular Biology Edited by Han Remaut Structural Biology Brussels Vrije Universiteit Brussel and VIB Brussels Belgium and Rémi Fronzes Groupe à 5 ans ‘Biologie Structurale de la Sécretion Bactérienne’ Institut Pasteur Paris France Caister Academic Press Copyright © 2014 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-908230-27-0 Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from Figures 8.1 and 8.3. Printed and bound in Great Britain Contents Contributors v Preface xi Part I Membrane Composition and Synthesis 1 1 Bacterial Cell Wall Growth, Shape and Division 3 Adeline Derouaux, Mohammed Terrak, Tanneke den Blaauwen and Waldemar Vollmer 2 The Outer Membrane of Gram-negative Bacteria: Lipopolysaccharide Biogenesis and Transport 55 Paola Sperandeo, Riccardo Villa, Gianni Dehò and Alessandra Polissi 3 Outer Membrane Protein Biosynthesis: Transport and Incorporation of Outer Membrane Proteins (in)to the Outer Membrane Bilayer 91 Kelly H. Kim, Suraaj Aulakh and Mark Paetzel 4 Bacterial Lipoproteins: Biogenesis, Virulence/ Pathogenicity and Trafficking 133 Hajime Tokuda, Peter Sander, Bok Luel Lee, Suguru Okuda, Thomas Grau, Andreas Tschumi, Juliane K. Brülle, Kenji Kurokawa and Hiroshi Nakayama 5 The Fascinating Coat Surrounding Mycobacteria 179 Mamadou Daffé and Benoît Zuber Part II Protein–Lipid Interactions 193 6 The Role of Lipid Composition on Bacterial Membrane Protein Conformation and Function 195 Vinciane Grimard, Marc Lensink, Fabien Debailleul, Jean-Marie Ruysschaert and Cédric Govaerts iv | Contents Part III Transport Across Bacterial Membranes 225 7 Bacterial ABC Transporters: Structure and Function 227 Anthony M. George and Peter M. Jones 8 Energy-coupled Transport Across the Outer Membrane of Gram-negative Bacteria 249 Volkmar Braun 9 The Permeability Barrier: Passive and Active Drug Passage Across Membranes 283 Kozhinjampara R. Mahendran, Robert Schulz, Helge Weingart, Ulrich Kleinekathöfer and Mathias Winterhalter 10 Targeting and Integration of Bacterial Membrane Proteins 303 Patrick Kuhn, Renuka Kudva, Thomas Welte, Lukas Sturm and Hans-Georg Koch 11 Envelope-spanning Secretion Systems in Gram-negative Bacteria 343 Matthias J. Brunner, Rémi Fronzes and Thomas C. Marlovits Part IV Signal Transduction Across Bacterial Membranes 385 12 Signalling Mechanisms in Prokaryotes 387 Mariano Martinez, Pedro M. Alzari and Gwénaëlle André-Leroux Part V Bacterial Membranes in Pathogenesis 413 13 Outer Membrane-embedded and -associated Proteins and their Role in Adhesion and Pathogenesis 415 Vincent van Dam, Virginie Roussel-Jazédé, Jesús Arenas, Martine P. Bos and Jan Tommassen 14 Bacterial Membranes as Drug Targets 449 Alvin Lo, Gaetano Castaldo and Han Remaut Index 491 Contributors Pedro M. Alzari Tanneke den Blaauwen Unite de Microbiologie Structurale and CNRS Bacterial Cell Biology UMR 3528 Swammerdam Institute for Life Sciences Institut Pasteur University of Amsterdam Paris Amsterdam France The Netherlands [email protected] [email protected] Gwénaëlle André-Leroux Martine P. Bos Unite de Microbiologie Structurale and CNRS Department of Molecular Microbiology and UMR 3528 Institute of Biomembranes Institut Pasteur Utrecht University Paris Utrecht France The Netherlands [email protected] [email protected] Jesús Arenas Volkmar Braun Department of Molecular Microbiology and Max Planck Institute for Developmental Institute of Biomembranes Biology Utrecht University Tübingen Utrecht Germany The Netherlands [email protected] [email protected] Juliane K. Brülle Suraaj Aulakh Institut für Medizinische Mikrobiologie Department of Molecular Biology and Universität Zürich Biochemistry Zurich Simon Fraser University Switzerland Burnaby [email protected] Canada [email protected] vi | Contributors Matthias J. Brunner Gianni Dehò Research Institute of Molecular Biotechnology Dipartimento di Scienze Biomolecolari e (IMBA) Biotecnologie Austrian Academy of Sciences; Università di Milano Research Institute of Molecular Pathology Milan (IMP) Italy Vienna [email protected] Austria [email protected] Adeline Derouaux Centre d´ingénierie des protéines Gaetano Castaldo Institut de Chimie Structural and Molecular Microbiology; Université de Liège Structural Biology Brussels Sart-Tilman VIB Department of Structural Biology Belgium Vrije Universiteit Brussel [email protected] Brussels Belgium Rémi Fronzes [email protected] Groupe à 5 ans ‘Biologie Structurale de la Sécretion Bactérienne’ Mamadou Daffé Institut Pasteur Department of Molecular Mechanisms of Paris Mycobacterial Infections France Institut de Pharmacologie et Biologie [email protected] Structurale du Centre National de la Recherche Scientifique (CNRS) Anthony M. George Université Paul Sabatier School of Medical and Molecular Biosciences Toulouse and iThree Institute France University of Technology Sydney [email protected] Broadway Australia Vincent van Dam [email protected] Department of Molecular Microbiology and Institute of Biomembranes Cédric Govaerts Utrecht University Department of Structure and Function of Utrecht Biological Membranes The Netherlands Structural Biology and Bioinformatics Center [email protected] Université Libre de Bruxelles Brussels Fabien Debailleul Belgium Department of Structure and Function of [email protected] Biological Membranes Structural Biology and Bioinformatics Center Thomas Grau Université Libre de Bruxelles Roche Diagnostics Ltd Brussels Rotkreuz Belgium Switzerland [email protected] [email protected] Contributors | vii Vinciane Grimard Patrick Kuhn Department of Structure and Function of Institut für Biochemie und Molekularbiologie Biological Membranes ZBMZ Structural Biology and Bioinformatics Center Albert-Ludwigs-Universität Freiburg Université Libre de Bruxelles Freiburg Brussels Germany Belgium [email protected] [email protected] Kenji Kurokawa Peter M. Jones Division of Phamaceutical Cell Biology School of Medical and Molecular Biosciences Faculty of Pharmaceutical Sciences and iThree Institute Nagasaki International University University of Technology Sydney Nagasaki Broadway Japan Australia [email protected] [email protected] Bok Luel Lee Kelly H. Kim National Research Laboratory of Defense Department of Molecular Biology and Proteins Biochemistry College of Pharmacy Simon Fraser University Pusan National University Burnaby Busan Canada Korea [email protected] [email protected] Ulrich Kleinekathöfer Marc Lensink School of Engineering and Science Interdisciplinary Research Institute (IRI) – Jacobs University Bremen Computational Biology Bremen USR3078 CNRS Germany Villeneuve d’Ascq France [email protected] [email protected] Hans-Georg Koch Institut für Biochemie und Molekularbiologie Alvin Lo ZBMZ Structural and Molecular Microbiology, Albert-Ludwigs-Universität Freiburg Structural Biology Brussels Freiburg VIB Department of Structural Biology Germany Vrije Universiteit Brussel Brussels [email protected] Belgium Renuka Kudva [email protected] Institut für Biochemie und Molekularbiologie ZBMZ Albert-Ludwigs-Universität Freiburg Freiburg Germany [email protected] viii | Contributors Kozhinjampara R. Mahendran Mark Paetzel Jacobs University Bremen Department of Molecular Biology and School of Engineering and Science Biochemistry Bremen Simon Fraser University Germany Burnaby British Columbia mahendran.kozhinjampararadhakrishnan@ Canada chem.ox.ac.uk [email protected] Thomas C. Marlovits Research Institute of Molecular Biotechnology Alessandra Polissi (IMBA) Dipartimento di Biotecnologie e Bioscienze Austrian Academy of Sciences Università di Milano-Bicocca Research Institute of Molecular Pathology Milan (IMP) Italy Vienna [email protected] Austria [email protected] Han Remaut Structural Biology Brussels Mariano Martinez Vrije Universiteit Brussel and VIB Unite de Microbiologie Structurale and CNRS Brussels UMR 3528 Belgium Institut Pasteur [email protected] Paris France Virginie Roussel-Jazédé [email protected] Department of Molecular Microbiology and Institute of Biomembranes Hiroshi Nakayama Utrecht University Biomolecular Characterization Team Utrecht RIKEN The Netherlands Wako [email protected] Japan [email protected] Jean-Marie Ruysschaert Department of Structure and Function of Suguru Okuda Biological Membranes Department of Chemistry and Chemical Structural Biology and Bioinformatics Center Biology Université Libre de Bruxelles Harvard University Brussels Cambridge, MA Belgium USA [email protected] [email protected] Peter Sander Institut für Medizinische Mikrobiologie Universität Zürich Zurich Switzerland [email protected] Contributors | ix Robert Schulz Andreas Tschumi Jacobs University Bremen Institut für Medizinische Mikrobiologie School of Engineering and Science Universität Zürich Bremen Zurich Germany Switzerland [email protected] [email protected] Paola Sperandeo Riccardo Villa Dipartimento di Biotecnologie e Bioscienze Dipartimento di Biotecnologie e Bioscienze Università di Milano-Bicocca Università di Milano-Bicocca Milan Milan Italy Italy [email protected] [email protected] Lukas Sturm Waldemar Vollmer Institut für Biochemie und Molekularbiologie Centre for Bacterial Cell Biology ZBMZ Institute for Cell and Molecular Biosciences Albert-Ludwigs-Universität Freiburg Newcastle University Freiburg Newcastle upon Tyne Germany UK [email protected] [email protected] Mohammed Terrak Helge Weingart Centre d’ingénierie des protéines School of Engineering and Science Institut de Chimie Jacobs University Bremen Université de Liège Bremen Sart-Tilman Germany Belgium [email protected] [email protected] Thomas Welte Hajime Tokuda Institut für Biochemie und Molekularbiologie Faculty of Nutritional Sciences ZBMZ University of Morioka Albert-Ludwigs-Universität Freiburg Takizawa Freiburg Iwate Germany Japan [email protected] [email protected] Mathias Winterhalter Jan Tommassen School of Engineering and Science Department of Molecular Microbiology and Jacobs University Bremen Institute of Biomembranes Bremen Utrecht University Germany Utrecht [email protected] The Netherlands [email protected]