Pseudomonas: Molecular and Applied Biology

Transcription

1 Pseudomonas: Molecular and Applied Biology

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3 Editor Pseudomonas: Molecular and Applied Biology

4 Editor Department of Microbiology Punjab Agricultural University Ludhiana, Punjab India ISBN ISBN (ebook) DOI / Library of Congress Control Number: # Springer International Publishing Switzerland 2016 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. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland

5 Fondly dedicated to Iqbal Kahlon

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7 Preface In the early 1970s, when I joined the bandwagon of Pseudomonas as a postdoc at the Technical University of Denmark, Copenhagen, Pseudomonas was considered as a vaguely defined genus comprising soil-borne saprophytes, at times associated with wound infection. However, with the developments in molecular biology, genetic engineering, PCR, DNA, and genome sequencing supported by technological developments and computer-based databases, Pseudomonas has attained the position of a model organism for in silico modeling and systems biology where large chunks of unwanted DNA segment can be replaced by desired ones. Presently, it is an important organism for biotechnological production of novel chemicals and pharmaceuticals as well as for scientific pursuits for exploring new areas of its vast activities. This volume was planned with a view to provide concise and comprehensive information to young graduates, teachers, and research workers to visualize the potential of this important and diverse group. The first chapter on Phylogeny and Molecular Taxonomy has been contributed by distinguished scientists, Elena Garcia-Valdes and Jorge Lalucat, who discuss how the taxonomy of Pseudomonas has undergone a change and the members that were not true Pseudomonas were assigned to other subclasses of Proteobacteria. Pseudomonas aeruginosa an opportunistic pathogen is notorious for hospitalacquired infection, multiple drug resistance, and a cause of CF of lungs.quorum sensing and the mechanism of pathogenesis and virulence have been discussed. Two chapters on cell envelope and metabolic network highlight the structure and function of cell envelope, particularly the outer membrane and the vast metabolic potential of Pseudomonas. Mono- and di-oxygenases are the key enzymes for degradation of recalcitrant molecules, and a chapter on these has been included. One chapter is dedicated to genome and comparative genomics of important species. Also a chapter on in silico modeling and use of bioinformatics and databases has been included. Two chapters on applied biology elaborate on commercial exploitation for production of novel molecules and biopolymers. The other highlights their role in degradation of organic chemical pollutants and bioremediation. The last two deal with Pseudomonas plant interactions: one exclusively deals with plant pathogenesis by Pseudomonas syringae and the other elaborates their role on biocontrol of plant diseases and direct and indirect plant growth promotion. vii

8 viii Preface I would like to place on record my appreciation and thanks to Alena and Jorge who were the first to accept my request to contribute a chapter on phylogeny and taxonomy. This acted as a catalyst and was a source of encouragement. I am equally grateful to Drs Levin, Parveen Sharma, Nagina, Swaranjit, Prince Sharma, and Saini and their colleagues for their outstanding contributions and making this volume possible. I owe a great deal to my family, particularly my wife, Sukhdeep, for her all-round support and help. I do hope to compensate my lovely grandchildren Abhay and Amie by giving them more time now. Financial support by way of grant from the Department of Science and Technology, Government of India, New Delhi, is acknowledged with thanks. I am grateful to Principal, SCD Govt College, Ludhiana, and Prof Dr B M Sarwar, Head, Dept of Botany, for implementation and smooth functioning of the project at their esteemed institute. Lastly, I am grateful to my mentors, students, friends, and relatives who have been part of this beautiful journey. Timely help of Mr. Gurdeep Singh for computer typing is acknowledged with thanks. Ludhiana, Punjab, India December 14, 2015

9 Contents 1 Pseudomonas: Molecular Phylogeny and Current Taxonomy... 1 Elena García-Valdés and Jorge Lalucat 2 Cell Envelope: Molecular Architecture and Function Pseudomonas: The Versatile and Adaptive Metabolic Network Partap Bir Singh, Harvinder Singh Saini, and 4 Pseudomonas: Genome and Comparative Genomics Pseudomonas Oxygenases: Nature and Function Abha Shukla, Brijdeep Singh, Swaranjit Singh Cameotra, and 6 Quorum Sensing in Pseudomonas aeruginosa: Mechanism and Regulation of Virulence Sajal Sarabhai, Amanjot Kaur, Neena Capalash, and Prince Sharma 7 In Silico Comparative Analysis of Type VI Secretion Systems in Pseudomonas putida LS Parveen Kumar Sharma, Jilagamazhi Fu, Richard Sparling, and David Bernard Levin 8 Pseudomonas for Industrial Biotechnology Biodegradation and Bioremediation of Organic Chemical Pollutants by Pseudomonas ix

10 x Contents 10 Pseudomonas-Plant Interactions I: Plant Growth Promotion and Defense-Mediated Mechanisms Hammad Khan, Nagina Parmar, and 11 Pseudomonas-Plant Interactions II: Biology and Pathogenesis of Pseudomonas syringae

11 List of Contributors Swaranjit Singh Cameotra Institute of Microbial Technology, Chandigarh, India Neena Capalash Department of Biotechnology, Punjab University, Chandigarh, India Jilagamazhi Fu Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada Elena García-Valdés Microbiologia, Department de Biologia and IMEDEA (CSIC-UIB), Universitat de les Illes Balear, Palma de Mallorca, Spain Department of Microbiology, Punjab Agricultural University, Ludhiana, India Amanjot Kaur Department of Microbiology, Punjab University, Chandigarh, India Hammad Khan Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada Jorge Lalucat Microbiologia, Department de Biologia and IMEDEA (CSIC- UIB), Universitat de les Illes Balear, Palma de Mallorca, Spain David Bernard Levin Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada Nagina Parmar Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada Harvinder Singh Saini Department of Microbiology, Guru Nanak Dev University, Amritsar, India Sajal Sarabhai Department of Microbiology, Punjab University, Chandigarh, India Prince Sharma Department of Microbiology, Punjab University, Chandigarh, India xi

12 xii List of Contributors Parveen Kumar Sharma Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada Abha Shukla Institute of Microbial Technology, Chandigarh, India Brijdeep Singh Global Cancer Care, Chandigarh, India Partap Bir Singh Department of Microbiology, Guru Nanak Dev University, Amritsar, India Richard Sparling Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada

13 About the Editor holds a Ph.D. in Microbiology from CCS Haryana Agricultural University, Hisar, India, and Postdoctorate experience at Institute of Microbiology, Technical University of Denmark, Copenhagen, where he started working on Pseudomonas. After his return to India in 1976, he joined the Punjab Agricultural University, Ludhiana, and held the position of Professor cum Head, Department of Microbiology, and was Director (Biotechnology) Punjab State Council for Science and Technology, Government of Punjab, Chandigarh. His area of specialization has been Pseudomonas Genetics and Bioremediation and has successfully completed a number of research projects sanctioned by different departments of Government of India. He has over hundred publications in this area and has successfully guided 20 Master s and 15 Doctorate students. His work is well accepted and recognized and he has to his credit the first ever report on NIC, the nicotine-nicotinic acid degradative plasmid in Pseudomonas convexa. xiii