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Advances in APPLIED MICROBIOLOGY VOLUME 69 Advances in APPLIED MICROBIOLOGY VOLUME 69 Edited by ALLEN I. LASKIN Somerset, New Jersey, USA SIMA SARIASLANI Wilmington, Delaware, USA GEOFFREY M. GADD Dundee, Scotland, UK AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 525 B Street, Suite 1900, San Diego, CA 92101-4495, USA 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 32, Jamestown Road, London NW1 7BY, UK First edition 2009 Copyright # 2009 Elsevier Inc. 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 written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: [email protected]. Alternatively you can submit your request online by visiting the Elsevier web site at http://elsevier.com/locate/permissions, and selecting Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negli- gence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made ISBN: 978-0-12-374824-9 ISSN: 0065-2164 For information on all Academic Press publications visit our website at www.elsevierdirect.com Printed and bound in the USA 091010987654321 CONTENTS Contributors ix 1. Variation in Form and Function: The Helix-Turn-Helix Regulators of the GntR Superfamily Paul A. Hoskisson and Se´bastien Rigali I. Introduction 2 II. Helix-Turn-Helix DNA-Binding Proteins 2 III. GntR Regulators 3 IV. Distribution of GntR Regulators 4 V. Structure and Classification of GntR Regulators 6 VI. DNA Binding, Operator Sequences and Regulation 11 VII. Evolution of GntR Regulators 13 VIII. GntR Regulators in Primary Metabolism 15 IX. GntR Regulators in Virulence 15 X. GntR Regulators in Streptomyces Development and Antibiotic Production 16 XI. Biotechnology Implications 17 XII. Concluding Remarks 18 Acknowledgments 18 References 18 2. Biogenesis of the Cell Wall and Other Glycoconjugates of Mycobacterium tuberculosis Devinder Kaur, Marcelo E. Guerin, Henrieta Sˇkovierova´, Patrick J. Brennan, and Mary Jackson I. Introduction 24 II. The Mycobacterial Cell Envelope 26 III. The Capsular Polysaccharides 28 IV. The Non-Covalently Bound Glycoconjugates of the Outer Membrane 34 A. Phosphatidylinositol mannosides, lipomannan and lipoarabinomannan 34 B. Acyltrehaloses 44 C. p-Hydroxybenzoic acid derivatives and phenolic glycolipids 47 v vi Contents D. Mannosyl-b-1-phosphomycoketides 48 E. Glycoproteins 49 V. The Glycoconjugate Polymers of the Cell Wall Core 50 A. Arabinogalactan 50 B. Peptidoglycan 54 VI. Cytosolic Glycoconjugates 58 A. Polymethylated polysaccharides 58 B. Glycogen 60 C. Mycothiol 61 VII. Conclusions and Future Prospects 63 Acknowledgements 64 References 64 3. Antimicrobial Properties of Hydroxyxanthenes Joy G. Waite and Ahmed E. Yousef I. Definitions and Chemical Structures 80 II. Synthesis 81 III. Applications 83 A. Dyestuffs 83 B. Pesticides 83 C. Medical applications 84 D. Antimicrobials 84 IV. Antimicrobial Mechanism 85 A. Photooxidation and antimicrobial properties 85 B. Localization of hydroxyxanthenes in microbial cell 88 C. Relative resistance of microorganisms to hydroxyxanthenes 91 V. Conclusions 94 References 94 4. In Vitro Biofilm Models: An Overview Andrew J. McBain I. Introduction 100 II. Choosing the Experimental System 102 A. Pure culture, defined consortium or microcosm? 102 B. Continuous, semi-continuous or batch culture? 103 III. Closed System Biofilm Models 103 A. The agar plate: A simple biofilm model? 103 B. Biofilm models based on multi-well plates: Potential for high-throughput analyses 105 IV. Open System Biofilm Models 106 A. Suspended substratum reactors 106 B. Rotating reactors for control of shear stress 110 Contents vii C. The Robbins device and flow cells 110 D. Drip-fed biofilms 112 E. Perfused biofilm fermenters 116 V. Overview and Conclusions 126 References 126 5. Zones of Inhibition? The Transfer of Information Relating to Penicillin in Europe during World War II Gilbert Shama I. Introduction 134 II. Early Penicillin Research in Great Britain 134 III. Germany 137 IV. Holland 144 V. France 148 VI. Conclusions 155 Acknowledgements 156 References 156 6. The Genomes of Lager Yeasts Ursula Bond I. Introduction 160 II. Classification 160 III. The Lager Yeasts: Saccharomyces pastorianus 162 IV. Lager Yeast Chromosomes: Types 162 V. Genome Sequence Analysis of the Lager Yeast Strain 167 VI. Chromosome Copy Number 168 VII. Consequences of Genome Rearrangements 169 VIII. The Dynamic Genome of Lager Yeasts 170 IX. Gene Expression Patterns of Lager Yeasts 175 X. Expression Compared to Haploid S. cerevisiae 178 XI. Conclusions 178 References 179 Index 183 Contents of Previous Volumes 189 Color Plate Section CONTRIBUTORS Ursula Bond School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland Patrick J. Brennan Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523- 1682, USA Marcelo E. Guerin Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523- 1682, USA Paul A. Hoskisson Strathclyde Institute of Pharmacy and Biological Science, University of Strathclyde, Royal College Building, George Street, Glasgow, United Kingdom. Mary Jackson Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523- 1682, USA Devinder Kaur Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523- 1682, USA Andrew J. McBain School of Pharmacy and Pharmaceutical Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom Se´bastien Rigali Centre d’Inge´nierie des Prote´ines, Universite´ de Lie`ge, Institut de Chimie B6, Sart-Tilman, B-4000 Lie`ge, Belgium ix x Contributors Gilbert Shama Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom Henrieta Sˇ kovierova´ Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523- 1682, USA Joy G. Waite Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA Ahmed E. Yousef Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA CHAPTER 1 Variation in Form and Function: The Helix-Turn-Helix Regulators of the GntR Superfamily † Paul A. Hoskisson* and Se´bastien Rigali Contents I. Introduction 2 II. Helix-Turn-Helix DNA-Binding Proteins 2 III. GntR Regulators 3 IV. Distribution of GntR Regulators 4 V. Structure and Classification of GntR Regulators 6 VI. DNA Binding, Operator Sequences and Regulation 11 VII. Evolution of GntR Regulators 13 VIII. GntR Regulators in Primary Metabolism 15 IX. GntR Regulators in Virulence 15 X. GntR Regulators in Streptomyces Development and Antibiotic Production 16 XI. Biotechnology Implications 17 XII. Concluding Remarks 18 Acknowledgments 18 References 18 Abstract One of the most abundant and widely distributed groups of Helix- turn-helix (HTH) transcription factors is the metabolite-responsive GntR family of regulators (>8500 members in the Pfam database; Jan 2009). These proteins contain a DNA-binding HTH domain at the N terminus of the protein and an effector-binding and/or * Strathclyde Institute of Pharmacy and Biological Science, University of Strathclyde, Royal College Building, George Street, Glasgow, United Kingdom { Centre d’Inge´nierie des Prote´ines, Universite´de Lie`ge, Institut de Chimie B6, Sart-Tilman, B-4000 Lie`ge, Belgium Advances in Applied Microbiology, Volume 69 # 2009 Elsevier Inc. ISSN 0065-2164, DOI: 10.1016/S0065-2164(09)69001-8 All rights reserved. 1 2 Paul A. Hoskisson and Se´bastien Rigali oligomerisation domain at the C terminus, where upon on binding an effector molecule, a conformational change occurs in the protein which influences the DNA-binding properties of the regu- lator resulting in repression or activation of transcription. This review summarises what we know about the distribution, structure, function and classification of these regulators and suggests that they may have a future role in biotechnology. ...endless forms most beautiful and most wonderful have been and are being, evolved. Charles Darwin, 1859 I. INTRODUCTION As bacteria sense different micro-environments, they modify their gene expression appropriately to enable them to respond to the prevailing conditions. Often the signal sensed within the cell is a metabolic interme- diate, and these are sensed by many classes of helix-turn-helix (HTH) transcription factor, through which they modulate gene expression. The effector molecules bound by these proteins are often related catabolic substrates, substrates and/or intermediates