Full Description
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.
Contents
Parts characterization for tunable protein expression.- Enzyme nicotinamide cofactor specificity reversal guided by automated structural analysis and library design.- Bacterial genome editing strategy for control of transcription and protein stability.- An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.- Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design.- Extended Metabolic Space Modeling.- Computational Methods to Assess the Production.- Designing and Implementing Algorithmic DNA Assembly Pipelines for Multi-gene Systems.- An adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism.- CRISPR-Cas9 toolkit for Actinomycete Genome Editing.- Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast using CasEMBLR.- A modified Gibson assembly method for cloning large DNA fragments with high GC contents.- Coupling Yeast Golden Gate and VEGAS for efficient assembly of the violacein pathway in Saccharomyces cerevisiae.- Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites For Phenotyping Of Microorganisms.- Selection of Highly Expressed Gene Variants in Escherichia coli using Translationally-coupled Antibiotic Selection Markers.- Design, Engineering, and Characterization Of Prokaryotic Ligand-binding Transcriptional Activators as Biosensors in Yeast.- A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers against Small Molecules.- High-throughput Microfluidics for the Screening Of Yeast Libraries.- Growth-Coupled Carotenoids Production Using Adaptive Laboratory Evolution.- Two scale 13C Metabolic Flux Analysis for Metabolic Engineering.
