Engineering Complex Phenotypes in Industrial Strains

This book highlights current trends and developments in the area of engineering strains. The book details the current and future tools used in the production of bulk chemicals and biofuels from renewable biomass using green technologies. Complex phenotypes are traits in a microbe that requires multiple genetic changes to be modulated simultaneously in the microorganism’s DNA. Knowing what those genetic changes are for a given trait and how to make those changes in the most efficient way forms the motivation behind writing this book. This book explains the newer tools to develop and enable engineered strains at time scales much faster that the natural evolution process so that we can increase a cells' production of a certain substance, increase process productivity, and extend metabolic capability. This book provides a one stop platform of reference for practicing researchers in the field of industrial biotechnology. This book also explains that the commercial success of a process that uses microbial catalysts over platforms that use chemical catalysts and fossil fuels depends on the time it takes to engineer these microbes to perform the desired reaction under harsh manufacturing conditions and at rates that meets the criteria for economic feasibility.

Foreword vii
John Pierce

Preface ix

Contributors xi

1 Classical Strain Improvement 1
Nathan Crook and Hal S. Alper

2 Tracer-Based Analysis of Metabolic Flux Networks 35
Michael Dauner

3 Integration of “Omics” Data with Genome-Scale Metabolic Models 77
Stephen Van Dien, Priti Pharkya, and Robin Osterhout

4 Strain Improvement via Evolutionary Engineering 111
Byoungjin Kim, Jing Du, and Huimin Zhao

5 Rapid Fermentation Process Development and Optimization 133
Jun Sun and Lawrence Chew

6 The Clavulanic Acid Strain Improvement Program at DSM Anti-Infectives 169
Bert Koekman and Marcus Hans

7 Metabolic Engineering of Recombinant E. coli for the Production of 3-Hydroxypropionate 185
Tanya Warnecke Lipscomb, Matthew L. Lipscomb, Ryan T. Gill, and Michael D. Lynch

8 Complex System Engineering: A Case Study for an Unsequenced Microalga 201
Michael T. Guarnieri, Lieve M.L. Laurens, Eric P. Knoshaug, Yat-Chen Chou, Bryon S. Donohoe, and Philip T. Pienkos

9 Meiotic Recombination-Based Genome Shuffling of Saccharomyces Cerevisiae and Schefferomyces Stiptis for Increased Inhibitor Tolerance to Lignocellulosic Substrate Toxicity 233
Dominic Pinel and Vincent J.J. Martin

Index 251

“This book should be valuable to engineers, biochemists, and students who seek to understand the science and practice of engineering biocatalysts for industrial applications.” (Chemical Engineering Progress, 1 January 2013)

RANJAN PATNAIK, PhD, is a chemical engineer by profession with 17 years of practical experience in the field of industrial biotechnology that includes small biotech start-ups and large enterprises. His research interests are in the field of metabolic engineering, fermentation optimization, process integration and R&D technology management. He currently heads the biofuels research group at DuPont Knowledge Center (DKC), Hyderabad, India. Prior to his current role, he had a variety of responsibilities within the biochemical sciences & engineering division of CR&D, E. I. du Pont de Nemours and Company, Wilmington, DE, USA.

Sets forth current strategies for engineering biocatalysts for the production of bulk chemicals and biofuels

With coverage of biocatalysts ranging from E. coli and Streptomyces to yeast and microalgae, this book explains current trends and developments in engineering industrial strains for the production of bulk chemicals and biofuels from renewable biomass. The authors guide readers through tested and proven tools and methodologies, providing plenty of examples that enable readers to engineer the complex traits and phenotypes needed for particular biocatalysts and bioprocesses.

Engineering Complex Phenotypes in Industrial Strains features contributions from pioneers and leading international experts in the field. These authors offer insights into their thought processes as they initiate and develop a commercial biocatalyst engineering project. The first five chapters describe the current tools and technologies available for engineering and characterizing a complex phenotype in an industrial strain. The next four chapters feature detailed case studies:

• Clavulanic acid strain improvement program
• Metabolic engineering of recombinant E. coli for the production of 3-hydroxypropionate
• Complex system engineering: case study for an unsequenced microalga
• Meiotic recombination-based genome shuffling of Saccharomyces cerevisiae and Scheffersomyces stipitis for increased inhibitor tolerance to lignocellulosic substrate toxicity

These case studies underscore the many disciplines that underlie the engineering of biocatalysts as well as illustrate in detail the application of the tools and methodologies discussed in the first half of the book.

Engineering Complex Phenotypes in Industrial Strains is ideal for students and professionals in chemical engineering who need to understand the science and practice of engineering biocatalysts for a broad range of industrial applications.