Industrial Biotechnology

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 the Academy of Technical Sciences (Denmark), the National Academy of Engineering (USA), the Royal Danish Academy of Science and Letters, the American Institute for Medical and Biological Engineering and the Royal Swedish Academy of Engineering Sciences.Professor Gregory Stephanopoulos is the W. H. Dow Professor of Chemical Engineering at the Massachusetts Institute of Technology (MIT, USA) and Director of the MIT Metabolic Engineering Laboratory. He is also Instructor of Bioengineering at Harvard Medical School (since 1997). He received his BS degree from the National Technical University of Athens and his PhD from the University of Minnesota (USA). He has co-authored approximately 400 research papers and 50 patents, along with the first textbook on Metabolic Engineering. He has been recognized by numerous awards from the American Institute of Chemical Engineers (AIChE) (Wilhelm, Walker and Founders awards), American Chemical Society (ACS), Society of industrial Microbiology (SIM), BIO (Washington Carver Award), the John Fritz Medal of the American Association of Engineering Societies, and others. In 2003 he was elected member of the National Academy of Engineering (USA) and in 2014 President of AIChE.

• List of Contributors XVIIAbout the Series Editors XXIXPreface XXXIPart I Industrial Biotechnology: From Pioneers to Visionary 11 History of Industrial Biotechnology 3Arnold L. Demain, Erick J. Vandamme, John Collins, and Klaus Buchholz1.1 The Beginning of Industrial Microbiology 31.2 Primary Metabolites and Enzymes 71.3 The Antibiotic Era 161.4 The Biotechnology Era Between 1970 and 2015 271.5 How Pioneering Developments Led to Genetic Engineering 48References 732 Synthetic Biology: An Emerging Approach for Strain Engineering 85Jie Sun and Hal Alper2.1 Introduction 852.2 Basic Elements 862.3 Functional and Robust Modules 962.4 Microbial Communities 1022.5 Conclusions and Future Prospects 104Acknowledgments 104References 1043 Toward Genome-Scale Metabolic Pathway Analysis 111Jürgen Zanghellini, Matthias P. Gerstl, Michael Hanscho, Govind Nair, Georg Regensburger, Stefan Müller, and Christian Jungreuthmayer3.1 Introduction 1113.2 DD Method 1143.3 Calculating Short EFMs in Genome-Scale Metabolic Networks 1163.4 Conclusions 120Acknowledgments 121References 1214 Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping 125Ashty S. Karim, Quentin M. Dudley, and Michael C. Jewett4.1 Introduction 1254.2 Background 1274.3 The Benefits of Cell-Free Systems 1294.4 Challenges and Opportunities in Cell-Free Systems 1354.5 Recent Advances 1404.6 Summary 141Acknowledgments 141References 142Part II Multipurpose Bacterial Cell Factories 1495 Industrial Biotechnology: Escherichia coli as a Host 151Matthew Theisen and James C. Liao5.1 Introduction 1515.2 E. coli Products 1525.3 Rewiring Central Metabolism 1655.4 Alternative Carbon Sources 1675.5 E. coli Techniques and Concerns 1695.6 Conclusions 170References 1716 Industrial Microorganisms: Corynebacterium glutamicum 183Judith Becker and Christoph Wittmann6.1 Introduction 1836.2 Physiology and Metabolism 1856.3 Genetic Manipulation of Corynebacterium glutamicum  1926.4 Systems Biology of Corynebacterium glutamicum  1966.5 Application in Biotechnology 2006.6 Conclusions and Perspectives 202References 2037 Host Organisms: Bacillus subtilis 221Hans-Peter Hohmann, Jan M. van Dijl, Laxmi Krishnappa, and Zoltán Prágai7.1 Introduction and Scope 2217.2 Identification of Genetic Traits Pertinent to Enhanced Biosynthesis of a Value Product 2227.3 Traits to Be Engineered for Enhanced Synthesis and Secretion of Proteinaceous Products 2257.4 Engineering of Genetic Traits in Bacillus subtilis  2317.5 Genome Reduction 2457.6 Significance of Classical Strain Improvement in Times of Synthetic Biology 2477.7 Resource-Efficient B. subtilis Fermentation Processes 2527.8 Safety of Bacillus subtilis  2547.9 Bacillus Production Strains on the Factory Floor: Some Examples 258Acknowledgments 280References 2808 HostOrganism: Pseudomonas putida 299Ignacio Poblete-Castro, José M. Borrero-de Acuña, Pablo I. Nikel, Michael Kohlstedt, and Christoph Wittmann8.1 Introduction 2998.2 Physiology and Metabolism 3008.3 Genetic Manipulation 3048.4 Systems Biology 3078.5 Application in Biotechnology 3118.6 Future Outlook 315References 315Part III Exploiting Anaerobic Biosynthetic Power 3279 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 Dürre9.1 Introduction 3299.2 Microorganisms 3309.3 Bacteriophages 3329.4 ABE Fermentation of Solvent-Producing Clostridium Strains 3369.5 Genome-Based Comparison of Solvent-Producing Clostridium Strains 3429.6 Regulation of Solvent Formation in C. acetobutylicum  3459.7 Genetic Tools for Clostridial Species 3469.8 Industrial Application of ABE Fermentation 353Acknowledgments 355References 35510 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 Worthen10.1 Introduction  36510.2 CBP Organism Development Strategies 36610.3 Plant Cell Wall Solubilization by C. thermocellum  36710.4 Bioenergetics of C. thermocellum Cellulose Fermentation 37210.5 Metabolic Engineering 37810.6 Summary and Future Directions 386Acknowledgments 388References 38811 Lactic Acid Bacteria 395Luciana Ruiz-Rodríguez, Juliana Bleckwedel, Maria Eugenia Ortiz, Micaela Pescuma, and Fernanda Mozzi11.1 Introduction 39511.2 Fermented Foods 39811.3 Industrially Relevant Compounds 40611.4 Conclusions 434Conflict of Interest 435References 435Contents to Volume 2List of Contributors XVAbout the Series Editors XXVIIPreface XXIXPart IV Microbial Treasure Chests for High-Value Natural Compounds 45312 Host Organisms: Myxobacterium 455Silke C. Wenzel and Rolf Müller13 Host Organism: Streptomyces 487Oksana Bilyk and Andriy LuzhetskyyPart V Extending the Raw Material Basis for Bioproduction 50514 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. Kelly15 Cyanobacteria as a Host Organism 581Fabienne Duchoud, Derrick S.W. Chuang, and James C. Liao16 Host Organisms: Algae 605Elizabeth A. Specht, Prema S. Karunanithi, Javier A. Gimpel, William S. Ansari, and Stephen P. MayfieldPart VI Eukaryotic Workhorses: Complex Cells Enable Complex Products 64317 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 Sauer19 Industrial Microorganisms: Pichia pastoris 687Diethard Mattanovich, Michael Sauer, and Brigitte GasserIndex 715