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Systems Microbiology Current Topics and Applications

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Systems Microbiology Current Topics and Applications Systems Microbiology Current Topics and Applications Edited by Brian D. Robertson Centre for Integrated Systems Biology and Bioinformatics Imperial College London and Brendan W. Wren London School of Hygiene and Tropical Medicine London UK Caister Academic Press Copyright © 2012 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: 978-1-908230-02-7 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 3.2 and 6.3. Printed and bound in Great Britain Contents Contributors v Preface ix 1 Mathematical Models for Systems Biology and How to Construct Them 1 Chris P. Barnes, Maxime Huvet, Nathan Harmston and Michael P.H. Stumpf 2 Dynamics and Robustness of Metabolic Networks: A Systems Biology Review of Escherichia coli Metabolism 17 Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla 3 Bacterial Chemotaxis: Rising Complexity 47 Diana Clausznitzer, Judith P. Armitage and Robert G. Endres 4 Systems Biology of Infection: The Pathogen Perspective 69 Dirk Bumann 5 Manipulating the Fight Between Human Host Cells and Intracellular Pathogens 77 Rico Barsacchi, Varadharajan Sundaramurthy, Kees Korbee, Jacques Neefjes, Tom H.M. Ottenhoff, Tiziana Scanu and Marino Zerial 6 How One Cell Eats Another: Principles of Phagocytosis 95 Sylvain Tollis, Navin Gopaldass, Thierry Soldati and Robert G. Endres 7 System-level Strategies for Studying the Metabolism of Mycobacterium tuberculosis 127 Dany J.V. Beste and Johnjoe McFadden iv | Contents 8 Sulfolobus Systems Biology: Cool Hot Design for Metabolic Pathways 151 Theresa Kouril, Alexey Kolodkin, Melanie Zaparty, Ralf Steuer, Peter Ruoff, Hans V. Westerhoff, Jacky Snoep, Bettina Siebers and the SulfoSYS consortium Index 169 Contributors Eivind Almaas Dany J.V. Beste Department of Biotechnology Faculty of Health and Medical Sciences Norwegian University of Science and University of Surrey Technology Guildford Trondheim UK Norway [email protected] [email protected] Per Bruheim Judith P. Armitage Department of Biotechnology Department of Biochemistry and Oxford Norwegian University of Science and Centre for Integrative Systems Biology Technology University of Oxford Trondheim Oxford Norway UK [email protected] [email protected] Dirk Bumann Chris P. Barnes Biozentrum Centre for Bioinformatics University of Basel Division of Molecular Biosciences Basel Imperial College London Switzerland London [email protected] UK [email protected] Diana Clausznitzer Division of Molecular Biosciences and Centre Rico Barsacchi for Integrative Systems Biology Max Planck Institute for Molecular Cell Imperial College Biology and Genetics London Dresden UK Germany [email protected] [email protected] vi | Contributors Robert G. Endres Kees Korbee Division of Molecular Biosciences & Centre for Department of Infectious Diseases Integrative Systems Biology Leiden University Medical Center Imperial College Leiden London The Netherlands UK [email protected] [email protected] Theresa Kouril Navin Gopaldass Faculty of Chemistry Departement de Biochimie Biofilm Centre Faculte des Sciences Molecular Enzymetechnology and Universite de Geneve Biochemistry Geneva University of Duisburg-Essen Switzerland Essen Germany navin.gopaldass.unige.ch [email protected] Nathan Harmston Centre for Bioinformatics Rahmi Lale Division of Molecular Biosciences Department of Biotechnology Imperial College London Norwegian University of Science and London Technology UK Trondheim Norway [email protected] [email protected] Maxime Huvet Centre for Bioinformatics Johnjoe McFadden Division of Molecular Biosciences Faculty of Health and Medical Sciences Imperial College London Guildford London UK UK [email protected] [email protected] Jacques Neefjes Alexey Kolodkin The Netherlands Cancer Institute Netherlands Institute for Systems Biology Amsterdam VU University Amsterdam The Netherlands Amsterdam [email protected] The Netherlands; Luxembourg Centre for Systems Biomedicine University of Luxembourg Tom H.M. Ottenhoff Esch-sur-Alzette Department of Infectious Diseases Luxembourg Leiden University Medical Center Leiden [email protected] The Netherlands [email protected] Contributors | vii Brian D. Robertson Thierry Soldati Centre for Integrated Systems Biology and Departement de Biochimie Bioinformatics Faculte des Sciences Imperial College Universite de Geneve London Geneva UK Switzerland [email protected] [email protected] Peter Ruoff Ralf Steuer Centre of Organelle Research Manchester Centre for Integrative Systems University of Stavanger Biology Stavanger University of Manchester Norway Manchester UK [email protected] [email protected] Tiziana Scanu The Netherlands Cancer Institute Michael P.H. Stumpf Amsterdam Centre for Bioinformatics The Netherlands Division of Molecular Biosciences Imperial College London t.scanu.nki.nl London UK Bettina Siebers Faculty of Chemistry [email protected] Biofilm Centre Molecular Enzymetechnology and Varadharajan Sundaramurthy Biochemistry Max Planck Institute for Molecular Cell University of Duisburg-Essen Biology and Genetics Essen Dresden Germany Germany [email protected] [email protected] Jacky Snoep Sylvain Tollis Netherlands Institute for Systems Biology Division of Molecular Biosciences & Centre for Free University Amsterdam Integrative Systems Biology Amsterdam Imperial College The Netherlands; London Manchester Centre for Integrative Systems UK Biology [email protected] University of Manchester Manchester UK; Svein Valla Department of Biochemistry Department of Biotechnology Stellenbosch University Norwegian University of Science and Matieland Technology South Africa Trondheim Norway [email protected] [email protected] viii | Contributors Hans V. Westerhoff Melanie Zaparty Netherlands Institute for Systems Biology Institute for Molecular and Cellular Anatomy Free University Amsterdam University of Regensburg Amsterdam Regensburg The Netherlands; Germany Manchester Centre for Integrative Systems [email protected] Biology University of Manchester Manchester Marino Zerial UK Max Planck Institute for Molecular Cell Biology and Genetics [email protected] Dresden Germany Brendan Wren [email protected] London School of Hygiene and Tropical Medicine and Centre for Integrated Systems Biology and Bioinformatics Imperial College London UK [email protected] Dedicated to our deceased colleagues, Jaroslav Stark and Emmanuelle Caron, pioneers in systems biology. Preface Systems biology aims to study the dynamic interactions of more than one component in a biological system in order to understand and predict the behaviour of the system as a whole. Typical approaches involve an iterative cycle of ‘dry lab’ modelling and ‘wet lab’ verification. Bringing order to biological data that inherently have noise due to a multitude of variables has previously been considered too challenging. However, systems biology is now a rapidly expanding discipline fuelled by the ‘omics’ era that is coupled to several new technologi- cal advances that have increased the precision of data obtainable. This has provided the bit parts of complex living cells. New challenges arise to put these levels of information together including finding a common language of the difference omics data sets (e.g. genomics, tran- scriptomics, proteomics, metabolomics). The sheer complexity of biological systems means that systems biology is a fledgling sci- ence. However, a focus on simple single cell organisms such as bacteria aids tractability and means that systems microbiology is a rapidly maturing science. This book will include case studies on single microbial species (e.g. bacteria and archaea), systems analysis of microbial phenomena (e.g. chemotaxis and phagocytosis) and this is complemented with theoretical approaches and mathematical modelling. Figure 0.1 Systems biology illustrating the iterative cycle of ‘dry lab’ modelling and ‘wet lab’ verification. Concept and design by Jaroslav Stark. Index A Expression levels 17, 26, 31, 57, 60, 141 Actin 80, 81, 85, 95–120 Extremophiles 152–153 Amoeba 95, 96, 102, 113–118 F Archaea 48, 151–163 ATP 19, 25, 48, 56, 58, 109, 133, 134, 136, Flux–balance analysis see FBA 138, 153–156, 158, 159 FBA 17, 18–20, 22–24, 133–136, 139, 140, 142, 144, 145 B G Bayesian statistics 4, 8, 9–10 Boolean networks 4, 7 Gene essentiality 135, 138, 139, 141, 143 C expression profiling 71–72 13C-isotope knock-out 21, 26–30, 143 labelling 32, 37, 38–39 Genome annotation 132, 133, 138–139 metabolic flux analysis 31, 37, 39, 144 Genomics 31, 71, 90, 127, 140, 153 Carbohydrate metabolism 153 Glycolysis 128, 132, 137, 142, 151, 156–159, Cell cycle 2, 48, 86 163 Chemical genetics 88–90 Graphical models 3–5 Chemotaxis
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