Pratyoosh Shukla Brett I. Pletschke Editors Advances in Enzyme Biotechnology Advances in Enzyme Biotechnology Pratyoosh Shukla • Brett I. Pletschke Editors Advances in Enzyme Biotechnology Editors Pratyoosh Shukla Brett I. Pletschke Department of Microbiology Department of Biochemistry, Maharshi Dayanand University Microbiology and Biotechnology Rohtak, Haryana , India 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. 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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 51st 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 num- ber of invited speakers from abroad. The meeting covered various fi elds of microbiology, including agricultural and soil microbiology, algal biotech- nology, biodiversity, biofuel and bioenergy, bioinformatics and metagenom- ics, 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 dedi- cated 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 computa- tional enzyme design and enzyme mutations. The fact that most of the chap- ters 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 environ- ment 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 fi lled 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 RNDr. Peter Biely, DrSc Institute of Chemistry, Center for Glycomics Bratislava , Slovakia September 11, 2012 Preface There has been a rapid expansion of the knowledge base in the fi eld 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 applica- tions, ranging from bio remediation, biomonitoring, biosensor development, bioconversion to biofuels and other biotechnologically important value- added 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 under- standing 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 signifi cant 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 indus- trial enzymes. The various other topics ranging from the synthesis of prebi- otic 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 method- ologies available for motif fi nding in biological sequences (Chap. 8 ), charac- teristic 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 indus- tries (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 fi nd 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 com- ments from all those who use this book. Haryana, India Pratyoosh Shukla Grahamstown, South Africa 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 Modifi cation of Polyphenolic Antioxidants ....................................................... 9 Kazi Zubaida Gulshan Ara , Samiullah Khan , Tejas S. Kulkarni , Tania Pozzo , and Eva Nordberg Karlsson 3 On the Enzyme Specifi city 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 Identifi cation 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