Synthetic Metabolic Pathways: Methods and Protocols

Description

This volume outlines key steps associated with the design, building, and testing of synthetic metabolic pathwaysfor 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. Front Matter ....Pages i-xii Front Matter ....Pages 1-1 Parts Characterization for Tunable Protein Expression (Michael S. Klausen, Morten O. A. Sommer)....Pages 3-14 Enzyme Nicotinamide Cofactor Specificity Reversal Guided by Automated Structural Analysis and Library Design (Jackson K. B. Cahn, Sabine Brinkmann-Chen, Frances H. Arnold)....Pages 15-26 Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability (Ida Lauritsen, Virginia Martínez, Carlotta Ronda, Alex Toftgaard Nielsen, Morten H. H. Nørholm)....Pages 27-37 An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization (Sean M. Halper, Daniel P. Cetnar, Howard M. Salis)....Pages 39-61 Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design (Mohammad Mazharul Islam, Rajib Saha)....Pages 63-82 Extended Metabolic Space Modeling (Pablo Carbonell, Baudoin Delépine, Jean-Loup Faulon)....Pages 83-96 Computational Methods to Assess the Production Potential of Bio-Based Chemicals (Miguel A. Campodonico, Sumesh Sukumara, Adam M. Feist, Markus J. Herrgård)....Pages 97-116 Front Matter ....Pages 117-117 Multiplex Genome Editing in Escherichia coli (Sheila Ingemann Jensen, Alex Toftgaard Nielsen)....Pages 119-129 Designing and Implementing Algorithmic DNA Assembly Pipelines for Multi-Gene Systems (Szu-Yi Hsu, Michael J. Smanski)....Pages 131-147 An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism (Tian Zhang, Pier-Luc Tremblay)....Pages 149-161 CRISPR-Cas9 Toolkit for Actinomycete Genome Editing (Yaojun Tong, Helene Lunde Robertsen, Kai Blin, Tilmann Weber, Sang Yup Lee)....Pages 163-184 Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR (Tadas Jakočiūnas, Emil D. Jensen, Michael K. Jensen, Jay D. Keasling)....Pages 185-201 A Modified Gibson Assembly Method for Cloning Large DNA Fragments with High GC Contents (Lei Li, Weihong Jiang, Yinhua Lu)....Pages 203-209 Coupling Yeast Golden Gate and VEGAS for Efficient Assembly of the Violacein Pathway in Saccharomyces cerevisiae (James Chuang, Jef D. Boeke, Leslie A. Mitchell)....Pages 211-225 Front Matter ....Pages 227-227 Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites for Phenotyping of Microorganisms (Christoph Halbfeld, Jörg Ingo Baumbach, Lars M. Blank, Birgitta E. Ebert)....Pages 229-258 Selection of Highly Expressed Gene Variants in Escherichia coli Using Translationally Coupled Antibiotic Selection Markers (Maja Rennig, Daniel O. Daley, Morten H. H. Nørholm)....Pages 259-268 Design, Engineering, and Characterization of Prokaryotic Ligand-Binding Transcriptional Activators as Biosensors in Yeast (Francesca Ambri, Tim Snoek, Mette L. Skjoedt, Michael K. Jensen, Jay D. Keasling)....Pages 269-290 A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers Against Small Molecules (Lasse H. Lauridsen, Holger B. Doessing, Katherine S. Long, Alex T. Nielsen)....Pages 291-306 High-Throughput Microfluidics for the Screening of Yeast Libraries (Mingtao Huang, Haakan N. Joensson, Jens Nielsen)....Pages 307-317 Growth-Coupled Carotenoids Production Using Adaptive Laboratory Evolution (Luis H. Reyes, Katy C. Kao)....Pages 319-330 Front Matter ....Pages 331-331 Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering (David Ando, Hector Garcia Martin)....Pages 333-352 Back Matter ....Pages 353-354