Metabolic Pathway Engineering

Metabolic engineering is a rapidly evolving field that is being applied for the optimization of many different industrial processes. In this issue of Advances in Biochemical Engineering/Biotechnology, developments in different areas of metabolic engineering are reviewed. The contributions discuss the application of metabolic engineering in the improvement of yield and productivity - illustrated by amino acid production and the production of novel compounds - in the production of polyketides and extension of the substrate range - and in the engineering of S. cerevisiae for xylose metabolism, and the improvement of a complex biotransformation process.

This book illustrates experimental and computational methodologies used to achieve cost effective biological processes for the production of fuels and biochemicals through multiple approaches to increasing yield, titers, and productivity in a robust host. The volume includes the most recent and cutting-edge aspects of pathway engineering, flux analysis, and metabolic enzyme engineering. Each chapter highlights the complexity and challenges of the problem as well as the methods used to solve this problem or changes needed in current methods. As a part of the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that gives researchers a much needed boost. Authoritative and practical, Metabolic Pathway Engineering benefits not only scientists working on more fundamental aspects of this endeavor but also those in the biochemical industry working on strain engineering for robust industrial processes.

This second volume of the Metabolic Pathway Engineering Handbook delves into evolutionary tools and gene expression tools for metabolic pathway engineering. It covers applications of emerging technologies including recent research genome-wide technologies, DNA and phenotypic microarrays, and proteomics tools for experimentally determining flux thro

This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.

Learn more about foundational and advanced topics in metabolic engineering in this comprehensive resource edited by leaders in the field Metabolic Engineering: Concepts and Applications delivers a one-stop resource for readers seeking a complete description of the concepts, models, and applications of metabolic engineering. This guide offers practical insights into the metabolic engineering of major cell lines, including E. Coli, Bacillus and Yarrowia Lipolytica, and organisms, including human, animal, and plant). The distinguished editors also offer readers resources on microbiome engineering and the use of metabolic engineering in bioremediation. Written in two parts, Metabolic Engineering begins with the essential models and strategies of the field, like Flux Balance Analysis, Quantitative Flux Analysis, and Proteome Constrained Models. It also provides an overview of topics like Pathway Design, Metabolomics, and Genome Editing of Bacteria and Eukarya. The second part contains insightful descriptions of the practical applications of metabolic engineering, including specific examples that shed light on the topics within. In addition to subjects like the metabolic engineering of animals, humans, and plants, you’ll learn more about: Metabolic engineering concepts and a historical perspective on their development The different modes of analysis, including flux balance analysis and quantitative flux analysis An illuminating and complete discussion of the thermodynamics of metabolic pathways The Genome architecture of E. coli, as well as genome editing of both bacteria and eukarya An in-depth treatment of the application of metabolic engineering techniques to organisms including corynebacterial, bacillus, and pseudomonas, and more Perfect for students of biotechnology, bioengineers, and biotechnologists, Metabolic Engineering: Concepts and Applications also has a place on the bookshelves of research institutes, biotechnological institutes and industry labs, and university libraries. It's comprehensive treatment of all relevant metabolic engineering concepts, models, and applications will be of use to practicing biotechnologists and bioengineers who wish to solidify their understanding of the field.

Metabolic systems engineering combines the tools and approaches of systems biology, synthetic biology, and evolutionary engineering. This book reviews studies on metabolism, from the earliest work of Lavoisier and Buchner to current cutting-edge research in metabolic systems engineering. This technology has been used in bioengineering applications to create high-performing microbes and plants that produce important chemicals, pharmaceuticals, crops, and other natural products. Current applications include optimizing metabolic pathways to enhance degradation of biomass for biofuel production and accelerated processing of environmental waste products and contaminants. The book includes examples to illustrate the applications of this technology in the optimization of metabolic pathways to create robust industrial strains as well as in the engineering of biological processes involving health and diseases of humans, animals, and plants. Written by a seasoned computational biologist with many years of experience in genomics, bioinformatics, and systems biology, this book will appeal to anyone interested in metabolic systems analysis and metabolic pathway engineering.

This first volume of the Metabolic Pathway Engineering Handbook provides an overview of metabolic pathway engineering with a look towards the future. It discusses cellular metabolism, including transport processes inside the cell and energy generating reactions, as well as rare metabolic conversions. This volume also explores balances and reaction

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Systems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production. Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story – from genomes and networks via discovery and design to industrial implementation practises. This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.

This volume outlines key steps associated with the design, building, and testing of synthetic metabolic pathways for optimal cell factory performance and robustness, and illustrates how data-driven learning from these steps can be used for rational cost-effective engineering of cell factories with improved performance. Chapters are divided into four sections focusing on the four steps of the iterative design-build-test-learn cycle related to modern cell factory engineering. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study of this vital field.