Advanced Biotechnology 1. Aufl.
The latest volume in the Advanced Biotechnology series provides an overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside describing tools for genetic and metabolic engineering for strain improvement, the authors also impart topical information on computational tools, safety aspects and industrial-scale production. Following an introduction to general concepts, historical developments and future technologies, the text goes on to cover multi-purpose bacterial cell factories, including those organisms that exploit anaerobic biosynthetic power. Further chapters deal with microbes used for the production of high-value natural compounds and those obtained from alternative raw material sources, concluding with eukaryotic workhorses. Of interest to biotechnologists and microbiologists, as well as those working in the biotechnological, chemical, food and pharmaceutical industries.The latest volume in the Advanced Biotechnology series provides an overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside describing tools for genetic and metabolic engineering for strain improvement, the authors also impart topical information on computational tools, safety aspects and industrial-scale production. Following an introduction to general concepts, historical developments and future technologies, the text goes on to cover multi-purpose bacterial cell factories, including those organisms that exploit anaerobic biosynthetic power. Further chapters deal with microbes used for the production of high-value natural compounds and those obtained from alternative raw material sources, concluding with eukaryotic workhorses. Of interest to biotechnologists and microbiologists, as well as those working in the biotechnological, chemical, food and pharmaceutical industries.
List of Contributors XVII About the Series Editors XXIX Preface XXXI Part I Industrial Biotechnology: From Pioneers to Visionary 1 1 History of Industrial Biotechnology 3Arnold L. Demain, Erick J. Vandamme, John Collins, and Klaus Buchholz 1.1 The Beginning of Industrial Microbiology 3 1.2 Primary Metabolites and Enzymes 7 1.3 The Antibiotic Era 16 1.4 The Biotechnology Era Between 1970 and 2015 27 1.5 How Pioneering Developments Led to Genetic Engineering 48 References 73 2 Synthetic Biology: An Emerging Approach for Strain Engineering 85Jie Sun and Hal Alper 2.1 Introduction 85 2.2 Basic Elements 86 2.3 Functional and Robust Modules 96 2.4 Microbial Communities 102 2.5 Conclusions and Future Prospects 104 Acknowledgments 104 References 104 3 Toward Genome-Scale Metabolic Pathway Analysis 111Jürgen Zanghellini, Matthias P. Gerstl, Michael Hanscho, Govind Nair, Georg Regensburger, Stefan Müller, and Christian Jungreuthmayer 3.1 Introduction 111 3.2 DD Method 114 3.3 Calculating Short EFMs in Genome-Scale Metabolic Networks 116 3.4 Conclusions 120 Acknowledgments 121 References 121 4 Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping 125Ashty S. Karim, Quentin M. Dudley, and Michael C. Jewett 4.1 Introduction 125 4.2 Background 127 4.3 The Benefits of Cell-Free Systems 129 4.4 Challenges and Opportunities in Cell-Free Systems 135 4.5 Recent Advances 140 4.6 Summary 141 Acknowledgments 141 References 142 Part II Multipurpose Bacterial Cell Factories 149 5 Industrial Biotechnology: Escherichia coli as a Host 151Matthew Theisen and James C. Liao 5.1 Introduction 151 5.2 E. coli Products 152 5.3 Rewiring Central Metabolism 165 5.4 Alternative Carbon Sources 167 5.5 E. coli Techniques and Concerns 169 5.6 Conclusions 170 References 171 6 Industrial Microorganisms: Corynebacterium glutamicum 183Judith Becker and Christoph Wittmann 6.1 Introduction 183 6.2 Physiology and Metabolism 185 6.3 Genetic Manipulation of Corynebacterium glutamicum 192 6.4 Systems Biology of Corynebacterium glutamicum 196 6.5 Application in Biotechnology 200 6.6 Conclusions and Perspectives 202 References 203 7 Host Organisms: Bacillus subtilis 221Hans-Peter Hohmann, Jan M. van Dijl, Laxmi Krishnappa, and Zoltán Prágai 7.1 Introduction and Scope 221 7.2 Identification of Genetic Traits Pertinent to Enhanced Biosynthesis of a Value Product 222 7.3 Traits to Be Engineered for Enhanced Synthesis and Secretion of Proteinaceous Products 225 7.4 Engineering of Genetic Traits in Bacillus subtilis 231 7.5 Genome Reduction 245 7.6 Significance of Classical Strain Improvement in Times of Synthetic Biology 247 7.7 Resource-Efficient B. subtilis Fermentation Processes 252 7.8 Safety of Bacillus subtilis 254 7.9 Bacillus Production Strains on the Factory Floor: Some Examples 258 Acknowledgments 280 References 280 8 HostOrganism: Pseudomonas putida 299Ignacio Poblete-Castro, José M. Borrero-de Acuña, Pablo I. Nikel, Michael Kohlstedt, and Christoph Wittmann 8.1 Introduction 299 8.2 Physiology and Metabolism 300 8.3 Genetic Manipulation 304 8.4 Systems Biology 307 8.5 Application in Biotechnology 311 8.6 Future Outlook 315 References 315 Part III Exploiting Anaerobic Biosynthetic Power 327 9 Host Organisms: Clostridium acetobutylicum/Clostridium beijerinckii and Related Organisms 329Frank R. Bengelsdorf, Anja Poehlein, Stefanie K. Flitsch, Sonja Linder, Bettina Schiel-Bengelsdorf, Benjamin A. Stegmann, Preben Krabben, Edward Green, Ying Zhang, Nigel Minton, and Peter Dürre 9.1 Introduction 329 9.2 Microorganisms 330 9.3 Bacteriophages 332 9.4 ABE Fermentation of Solvent-Producing Clostridium Strains 336 9.5 Genome-Based Comparison of Solvent-Producing Clostridium Strains 342 9.6 Regulation of Solvent Formation in C. acetobutylicum 345 9.7 Genetic Tools for Clostridial Species 346 9.8 Industrial Application of ABE Fermentation 353 Acknowledgments 355 References 355 10 Advances in Consolidated Bioprocessing Using Clostridium thermocellum and Thermoanaerobacter saccharolyticum 365Lee R. Lynd, Adam M. Guss, Michael E. Himmel, Dhananjay Beri, Chris Herring, Evert K. Holwerda, Sean J. Murphy, Daniel G. Olson, Julie Paye, Thomas Rydzak, Xiongjun Shao, Liang Tian, and Robert Worthen 10.1 Introduction 365 10.2 CBP Organism Development Strategies 366 10.3 Plant Cell Wall Solubilization by C. thermocellum 367 10.4 Bioenergetics of C. thermocellum Cellulose Fermentation 372 10.5 Metabolic Engineering 378 10.6 Summary and Future Directions 386 Acknowledgments 388 References 388 11 Lactic Acid Bacteria 395Luciana Ruiz-Rodríguez, Juliana Bleckwedel, Maria Eugenia Ortiz, Micaela Pescuma, and Fernanda Mozzi 11.1 Introduction 395 11.2 Fermented Foods 398 11.3 Industrially Relevant Compounds 406 11.4 Conclusions 434 Conflict of Interest 435 References 435 Contents to Volume 2 List of Contributors XV About the Series Editors XXVII Preface XXIX Part IV Microbial Treasure Chests for High-Value Natural Compounds 453 12 Host Organisms: Myxobacterium 455Silke C. Wenzel and Rolf Müller 13 Host Organism: Streptomyces 487Oksana Bilyk and Andriy Luzhetskyy Part V Extending the Raw Material Basis for Bioproduction 505 14 Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective 507Andrew J. Loder, Benjamin M. Zeldes, Jonathan M. Conway, James A. Counts, Christopher T. Straub, Piyum A. Khatibi, Laura L. Lee, Nicholas P. Vitko, Matthew W. Keller, Amanda M. Rhaesa, Gabe M. Rubinstein, Israel M. Scott, Gina L. Lipscomb, Michael W.W. Adams, and Robert M. Kelly 15 Cyanobacteria as a Host Organism 581Fabienne Duchoud, Derrick S.W. Chuang, and James C. Liao 16 Host Organisms: Algae 605Elizabeth A. Specht, Prema S. Karunanithi, Javier A. Gimpel, William S. Ansari, and Stephen P. Mayfield Part VI Eukaryotic Workhorses: Complex Cells Enable Complex Products 643 17 Host Organisms: Mammalian Cells 645Jennifer Pfizenmaier and Ralf Takors18 Industrial Microorganisms: Saccharomyces cerevisiae and other Yeasts 673Diethard Mattanovich, Brigitte Gasser, Michael Egermeier, Hans Marx, and Michael Sauer 19 Industrial Microorganisms: Pichia pastoris 687Diethard Mattanovich, Michael Sauer, and Brigitte Gasser Index 715
Christoph Wittmann is Director of the Institute of Systems Biotechnology at Saarland University, Saarbrücken, Germany. Having obtained his academic degrees from Braunschweig Technical University, Germany, he was postdoc at Helsinki University, Finland, held chairs for Biotechnology at Münster University, Germany, and for Biochemical Engineering at Braunschweig Technical University and was invited guest professor at Université Rangueil de Toulouse, France, before taking up his present position. He has authored more than 150 scientific publications, more than 20 books and book chapters, holds more than 20 patents and has received several scientific awards, including the Young Scientist Award of the European Federation of Biotechnology, and is board member of various scientific journals. James Liao is currently President of Academia Sinica in Taiwan. Having obtained his PhD degree from University of Wisconsin, Madison, USA, he started his career at Eastman Kodak Company, before moving to Texas A&M, USA, and then to the University of California in Los Angeles (UCLA), USA, for his academic career. Professor Liao has received numerous scientific awards, including the US Presidential Green Chemistry Challenge Award and the Italian ENI award in renewable energy. He is also a member of the US National Academy of Sciences, National Academy of Engineering, and Academia Sinica in Taiwan. Sang Yup Lee is Distinguished Professor at the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST). He is currently the Director of the Center for Systems and Synthetic Biotechnology, Director of the BioProcess Engineering Research Center, and Director of the Bioinformatics Research Center. He has published more than 500 journal papers, 64 books and book chapters, and more than 580 patents (either registered or applied). He received numerous awards, including the National Order of Merit, the Merck Metabolic Engineering Award, the ACS Marvin Johnson Award, Charles Thom Award, Amgen Biochemical Engineering Award, Elmer Gaden Award, POSCO TJ Park Prize, and HoAm Prize. He currently is Fellow of American Association for the Advancement of Science, the American Academy of Microbiology, American Institute of Chemical Engineers, Society for Industrial Microbiology and Biotechnology, American Institute of Medical and Biological Engineering, the World Academy of Science, the Korean Academy of Science and Technology, and the National Academy of Engineering of Korea. He is also Foreign Member of National Academy of Engineering USA. He is currently honorary professor of the University of Queensland (Australia), honorary professor of the Chinese Academy of Sciences, honorary professor of Wuhan University (China), honorary professor of Hubei University of Technology (China), honorary professor of Beijing University of Chemical Technology (China), and advisory professor of the Shanghai Jiaotong University (China). Lee is the Editor-in-Chief of the Biotechnology Journal and Associate Editor and board member of numerous other journals. Lee is currently serving as a member of Presidential Advisory Committee on Science and Technology (Korea). Jens Nielsen is Professor and Director to Chalmers University of Technology (Sweden) since 2008. He obtained an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Technical University of Denmark (DTU) and after that established his independent research group and was appointed full Professor there in 1998. He was Fulbright visiting professor at MIT in 1995-1996. At DTU, he founded and directed the Center for Microbial Biotechnology. Jens Nielsen has published more than 350 research papers, co-authored more than 40 books and he is inventor of more than 50 patents. He has founded several companies that have raised more than 20 million in venture capital. He has received numerous Danish and international awards and is member of
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