Metabolic Engineering, 1 by Sang Yup Lee

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Metabolic Engineering

Concepts and Applications



Edited by


Sang Yup Lee
Jens Nielsen
Gregory Stephanopoulos




Volume 13a




Logo: Wiley

Metabolic Engineering

Concepts and Applications



Edited by


Sang Yup Lee
Jens Nielsen
Gregory Stephanopoulos




Volume 13b




Logo: Wiley

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Cover Design Adam‐Design, Weinheim, Germany

To the memory of Maria Flytzani Stephanopoulos, a brilliant engineer‐scientist, who believed in metabolic engineering as catalysis of the future, and Hye Jean Hwang and Dina Petranovic Nielsen for their inspiration and unwavering support.


We are facing unprecedented challenges of climate change, increasing and aging population that is placing increasing pressure on limited resources, environmental problems including waste plastics, and more recently the COVID‐19 pandemic. Metabolic engineering will play increasingly important roles in addressing many of these challenges. The central theme is sustainability and the ability of metabolic engineering to create sustainable solutions by efficiently utilizing renewable resources. This goal has motivated the many contributors to this volume. Even under the extremely difficult conditions of COVID‐19 pandemic, experts worldwide happily agreed to contribute to a book on metabolic engineering and completed their chapters on time. We are most grateful to the authors for their commitment, dedication, and quality of their work.

This book comprises two parts, concepts and applications. The concept part starts with Chapter 1 on the history and perspectives of metabolic engineering, which also provides directions of future metabolic engineering studies. This introductory chapter is followed by an insightful Chapter 2 on genome‐scale modeling and simulation, which over the last couple of decades have become an essential tool to understand metabolism and design metabolic engineering strategies. Metabolic flux analysis provides quantitative information on how metabolic fluxes are distributed in a metabolic network, and thus is essential in metabolic engineering. Chapter 3 describes how metabolic fluxes are determined from data collected following labeling with stable isotopes. Genome‐scale metabolic simulation can be much better performed and more realistically with proper constraints. Chapter 4 describes how constraints from proteome data can be implemented to achieve this goal. Chapter 5 covers kinetic models that allow analysis of pathway fluxes based on enzyme and substrate concentrations and general enzyme properties. This chapter is followed by Chapter 6 on metabolic control analysis, which is a theoretical framework for understanding how changes in the activity of one or multiple enzymes affect the fluxes of metabolic networks and metabolite concentrations. Chapter 7 describes thermodynamics of metabolic pathways, focusing on thermodynamic feasibility of metabolic pathway reactions, which is essential in pathway design. Chapter 8 then naturally follows to describe how to design metabolic pathways through a four‐step strategy involving defining biochemical search space, pathway search, enzyme assignment for each reaction step, and evaluation of pathway performance. Metabolic engineering cannot exist without fully understanding metabolites. Chapter 9 describes how to perform metabolome analysis and data processing together with emerging trends of metabolomics. As the technologies for genome engineering of eukaryotes is far behind those of prokaryotes, we decided to have a specific Chapter 10 on genome editing of eukaryotes as the last chapter of Part 1. The chapter also describes general tools that can be employed in any cell type.

Part 2 is devoted to applications of metabolic engineering in different organisms. Besides traditional workhorse strains such as Escherichia coli (Chapter 11), Corynebacteria (Chapter 12), Bacillus (Chapter 13), and yeasts (Chapter 18), emerging host strains including Pseudomonas (Chapter 14), lactic acid bacteria (Chapter 15), Clostridia (Chapter 16), actinomycetes (Chapter 17), Yarrowia lipolytica (Chapter 19), filamentous fungi (Chapter 20), and photosynthetic organisms (Chapter 21) are covered. These chapters showcase how metabolic engineering is performed for the production of a vast array of example products including chemicals, fuels, materials, drugs, and natural functional compounds in respective organisms. The metabolic engineering strategies employed in these organisms are often universal, yet some are uniquely developed and applied to the specific host cell described in these chapters. We believe that these actual metabolic engineering examples will be helpful to those working on these and similar topics. The final Chapter 22 covers the topic of bioremediation considering the importance of developing strategies to deal with increasing stresses on the environment. This chapter emphasizes that metabolic engineering is not only important for “producing something useful for humans,” but also essential for “improving our environment.”

We anticipate that this book will serve as a textbook for senior undergraduate and junior graduate metabolic engineering classes. Also, the book will be a useful resource for researchers working in the field of metabolic engineering. We want to thank again all the authors who contributed their expertise to this volume. Last but not least, we want to thank the Wiley team, who worked tirelessly in communicating with authors, copy editing, and finalizing the book in such a nice manner. We hope that you will enjoy reading this book as much as we did during the editing process.

November 2020

Sang Yup Lee, Jens Nielsen,

and Gregory Stephanopoulos

Part 1