Synthetic Metabolic Pathways: Methods and Protocols

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