Strain Engineering

Methods and Protocols

Editors:

ISBN: 978-1-61779-196-3 (Print) 978-1-61779-197-0 (Online)

Table of contents (29 protocols)

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  1. Front Matter

    Pages i-xi

  2. E. coli

    1. Front Matter

      Pages 1-1

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      Pages 3-25

      Bacterial Genome Reengineering

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      Pages 27-42

      Targeted Chromosomal Gene Knockout Using PCR Fragments

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      Pages 43-54

      Scarless Chromosomal Gene Knockout Methods

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      Pages 55-70

      Random Chromosomal Gene Disruption In Vivo Using Transposomes

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      Pages 71-82

      Genome Engineering Using Targeted Oligonucleotide Libraries and Functional Selection

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      Pages 83-97

      Microarray-Based Genetic Footprinting Strategy to Identify Strain Improvement Genes after Competitive Selection of Transposon Libraries

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      Pages 99-111

      Optimization of Synthetic Operons Using Libraries of Post-Transcriptional Regulatory Elements

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      Pages 113-123

      Marker-Free Chromosomal Expression of Foreign and Native Genes in Escherichia coli

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      Pages 125-153

      Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli

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      Pages 155-169

      Assembling New Escherichia coli Strains by Transduction Using Phage P1

  3. Saccharomyces cerevisiae

    1. Front Matter

      Pages 171-171

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      Pages 173-187

      Yeast Bioinformatics and Strain Engineering Resources

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      Pages 189-206

      Delete and Repeat: A Comprehensive Toolkit for Sequential Gene Knockout in the Budding Yeast Saccharomyces cerevisiae

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      Pages 207-224

      Genome-Wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans

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      Pages 225-252

      Signature-tagged Mutagenesis to Characterize Genes Through Competitive Selection of Bar-coded Genome Libraries

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      Pages 253-274

      Global Strain Engineering by Mutant Transcription Factors

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      Pages 275-294

      Genomic Promoter Replacement Cassettes to Alter Gene Expression in the Yeast Saccharomyces cerevisiae

  4. Strain Engineering Other Industrially Important Microbes

    1. Front Matter

      Pages 295-295

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      Pages 297-307

      Microbial Genome Analysis and Comparisons: Web-Based Protocols and Resources

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      Pages 309-326

      Plasmid Artificial Modification: A Novel Method for Efficient DNA Transfer into Bacteria

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      Pages 327-343

      Broad-Host-Range Plasmid Vectors for Gene Expression in Bacteria

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      Pages 345-358

      A Simple Method for Introducing Marker-Free Deletions in the Bacillus subtilis Genome

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