Advances in Enzyme Biotechnology

Advances in Enzyme Biotechnology

Pratyoosh Shukla Brett I. Pletschke Editors Advances in Enzyme Biotechnology

Editors Pratyoosh Shukla Department of Microbiology Maharshi Dayanand University Rohtak, Haryana, India Brett I. Pletschke Department of Biochemistry, Microbiology and Biotechnology Rhodes University Grahamstown, South Africa ISBN 978-81-322-1093-1 ISBN 978-81-322-1094-8 (ebook) DOI 10.1007/978-81-322-1094-8 Springer New Delhi Heidelberg New York Dordrecht London Library of Congress Control Number: 2013945175 Springer India 2013 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. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. 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. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Foreword This book is a collection of few recent discoveries in enzyme biotechnology by leading researchers in Enzyme Technology and further some selected contributions presented at the 51 st Annual Conference of the Association of Microbiologists of India (AMI- 2010) which was organized at the beautiful campus of Birla Institute of Technology in Mesra, Ranchi, India, during December 14 17, 2010. The book is edited by Dr. Pratyoosh Shukla, one of the executive members of the Organizing Committee and Prof. Brett I. Pletschke from Rhodes University in Grahamstown, South Africa, who was one of the leading invited speakers of the meeting. The meeting was attended mainly by participants from India but was also made international by a number of invited speakers from abroad. The meeting covered various fields of microbiology, including agricultural and soil microbiology, algal biotechnology, biodiversity, biofuel and bioenergy, bioinformatics and metagenomics, environmental microbiology, enzyme technology, and food and medical microbiology. An important feature of the meeting was participation of industrial researchers which contributed to fruitful interactions between industrial and academic research indispensable for the development of new progressive biotechnologies. The majority of chapters in the book are dedicated to industrially important enzymes modifying plant polysaccharides and lignin. On one hand, the chapters review the current state of the art in the areas of production and application of glycoside hydrolyses, esterases, and lignin-degrading enzymes, while on the other hand, they describe modern trends in the development of enzyme technologies, including the computational enzyme design and enzyme mutations. The fact that most of the chapters originate in India demonstrates rapid emergence of research activity and enormous interest leading to the development of new enzyme technologies in the country. As we know India is a country which is heavily populated, and the sustainability of this country is very strongly dependent on environment friendly biotechnologies. Finally, I would also like to emphasize the general tone of the meeting which was optimistic and enthusiastic about emerging novel applications of enzymes and processes producing usable energy for the future. This book also represents a powerful exposure of important research of the present time to young researchers who filled the v

vi Foreword meeting/lecture rooms. The hard work of the organizers of the meeting and the editors of this volume is greatly appreciated. Slovak Academy of Sciences Institute of Chemistry, Center for Glycomics Bratislava, Slovakia September 11, 2012 RNDr. Peter Biely, DrSc

Preface There has been a rapid expansion of the knowledge base in the field of enzyme biotechnology over the past few years. Much of this expansion has been driven by the bio-discovery of many new enzymes from a wide range of environments, some extreme in nature, followed by subsequent protein (enzyme) engineering. These enzymes have found a wide range of applications, ranging from bio remediation, biomonitoring, biosensor development, bioconversion to biofuels and other biotechnologically important valueadded products, etc. The major goal of this book is to provide the reader with an updated view of the latest developments in the area of enzyme biotechnology. This book presents an exceptional combination of fascinating topics and the reader will be pleased to see that the latest technologies available for an improved understanding of enzymes are included in the book. For example, a thermostable enzyme with sugar metabolic activity is improved by targeted mutagenesis (Chap. 1 ). The reader will note that there is a significant focus on the role of hydrolases (Chap. 2 ) and other depolymerising enzymes in this book, as these enzymes form a major component of the annual revenue generated by industrial enzymes. The various other topics ranging from the synthesis of prebiotic galacto-oligosaccharides (Chap. 3 ), biomass-degrading enzymes, in general, mannanases (Chap. 4 ), glycoside hydrolases and their synergistic interactions (Chap. 5 ), manganese peroxidases (Chap. 6 ) to the modern trends in experimental techniques in enzyme technology (Chap. 7 ) are also covered in the present book. Further, the most up-to-date studies related to an overview of the methodologies available for motif finding in biological sequences (Chap. 8 ), characteristic molecular features and functional aspects of chitin deacetylases (Chap. 9 ), the role of enzymes in plant microbe interactions (Chap. 10 ) and the bioprospecting of industrial enzymes in various grain-processing industries (Chap. 11 ) have also been included. Moreover, the readers of the book will be delighted to see that the most up to date technologies available for a better understanding of enzymes are included in this book to enhance the learning skills in key facets of research in enzyme biotechnology. vii

viii Preface We hope that the reader will find the information presented here valuable and stimulating. We acknowledge and are indebted to all those who have generously contributed to the completion of this book, and welcome comments from all those who use this book. Haryana, India Grahamstown, South Africa Pratyoosh Shukla Brett I. Pletschke

Contents 1 Improvement of Thermostable Enzyme with Sugar Metabolic Activity by Targeted Mutagenesis... 1 Yutaka Kawarabayasi 2 Glycoside Hydrolases for Extraction and Modification of Polyphenolic Antioxidants... 9 Kazi Zubaida Gulshan Ara, Samiullah Khan, Tejas S. Kulkarni, Tania Pozzo, and Eva Nordberg Karlsson 3 On the Enzyme Specificity for the Synthesis of Prebiotic Galactooligosaccharides... 23 Barbara Rodriguez-Colinas, Lucia Fernandez-Arrojo, Miguel de Abreu, Paulina Urrutia, Maria Fernandez-Lobato, Antonio O. Ballesteros, and Francisco J. Plou 4 Microbial Mannanases: Properties and Applications... 41 Hemant Soni and Naveen Kango 5 Enzyme Synergy for Enhanced Degradation of Lignocellulosic Waste... 57 J. Susan van Dyk and Brett I. Pletschke 6 Manganese Peroxidases: Molecular Diversity, Heterologous Expression, and Applications... 67 Samta Saroj, Pragati Agarwal, Swati Dubey, and R.P. Singh 7 Advance Techniques in Enzyme Research... 89 Debamitra Chakravorty and Sanjukta Patra 8 Regulatory Motif Identification in Biological Sequences: An Overview of Computational Methodologies... 111 Shripal Vijayvargiya and Pratyoosh Shukla 9 Chitin Deacetylase: Characteristic Molecular Features and Functional Aspects... 125 Nidhi Pareek, V. Vivekanand, and R.P. Singh 10 Role of Enzymes and Proteins in Plant-Microbe Interaction: A Study of M. oryzae Versus Rice... 137 Jahangir Imam, Mukund Variar, and Pratyoosh Shukla ix

x Contents 11 Industrial Enzyme Applications in Biorefineries for Starchy Materials... 147 Vipul Gohel, Gang Duan, and Vimal Maisuria About the Editors...... 175