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Strain Engineering By James A. Williams

Strain Engineering by James A. Williams

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Summary

Classical methods for microbial strain engineering, used to improve the production of bioproducts, have serious drawbacks and have been found to be unsuitable for complex strain development applications.

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Strain Engineering Summary

Strain Engineering: Methods and Protocols by James A. Williams

Classical methods for microbial strain engineering, used to improve the production of bioproducts, have serious drawbacks and have been found to be unsuitable for complex strain development applications. In Strain Engineering: Methods and Protocols, powerful new genetic engineering-based strain engineering methods are presented for rational modification of a variety of model organisms. These methods are particularly powerful when utilized to manipulate microbes for which sequenced and annotated genomes are available. Collectively, these methods systematically introduce genome alterations in a precise manner, allowing the creation of novel strains carrying only desired genome alterations. In the first section, E. coli-based bacterial strain engineering strategies are reviewed, while the second section presents analogous microbial engineering strategies for eukaryotic cells using the yeast Saccharomyces cerevisiae as a model. The third section covers examples of the proliferative adaptations of these base technologies to strain engineer industrially important prokaryotic or eukaryotic microbial systems. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, Strain Engineering: Methods and Protocols serves as an ideal guide to scientists in academia, pharmaceutical science, and biotechnology who perform microbial strain engineering.

Table of Contents

Part 1. E. coli

1. Bacterial Genome Reengineering

Jindan Zhou and Kenneth E. Rudd

2. Targeted Chromosomal Gene Knockout using PCR Fragments

Kenan C. Murphy

3. Scarless Chromosomal Gene Knockout Methods

Bong Hyun Sung, Jun Hyoung Lee, and Sun Chang Kim

4. Random Chromosomal Gene Disruption In vivo using Transposomes

Les M. Hoffman

5. Genome Engineering using Targeted Oligonucleotide Libraries and Functional Selection

Elie J. Diner, Fernando Garza-Sanchez, and Christopher S. Hayes

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

Alison K. Hottes and Saeed Tavazoie

7. Optimization of Synthetic Operons using Libraries of Post-Transciptional Regulatory Elements

Daniel E. Agnew and Brian F. Pfleger

8. Marker Free Chromosomal Expression of Foreign and Native Genes in E. coli

Chung-Jen Chiang, Po Ting Chen, Shan-Yu Chen, and Yun-Peng Chao

9. Array-based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli

Mohan Babu, Alla Gagarinova, and Andrew Emili

10. Assembling New E. coli Strains by Transduction using Phage P1

Sean D. Moore

Part II. Saccharomyces cerevisiae

11. Yeast Bioinformatics and Strain Engineering Resources

Audrey L. Atkin

12. Delete and Repeat: A Comprehensive Toolkit for Sequential Gene Knock-out in the Budding Yeast Saccharomyces cerevisiae

Johannes H. Hegemann and Sven Boris Heick

13. Genome-wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans

Tao Xu, Nike Bharucha, and Anuj Kumar

14. Signature-tagged Mutagenesis to Characterize Genes Through Competitive Selection of Barcoded Genome Libraries

Julia Oh and Corey Nislow

15. Global Strain Engineering by Mutant Transcription Factors

Amanda M. Lanza and Hal S. Alper

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

Andreas Kaufmann and Michael Knop

Part III. Strain Engineering Other Industrially Important Microbes

17. Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

Medha Bhagwat and Arvind A. Bhagwat

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

Tohru Suzuki and Kazumasa Yasui

19. Broad-host-range Plasmid Vectors for Gene Expression in Bacteria

Rahmi Lale, Trygve Brautaset, and Svein Valla

20. Simple Method for Introducing Marker-free Deletions in the Bacillus subtilis Genome

Takuya Morimoto, Katsutoshi Ara, Katsuya Ozaki, and Naotake Ogasawara

21. Transposon-mediated Random Mutagenesis of Bacillus subtilis

Adam C. Wilson and Hendrik Szurmant

22. Integrative Food Grade Expression System for Lactic Acid Bacteria

Grace L. Douglas, Yong Jun Goh and Todd R. Klaenhammer

23. ClosTron-mediated Engineering of Clostridium

Sarah A. Kuehne, John T. Heap, Clare M. Cooksley, Stephen T. Cartman, and Nigel P. Minton

24. High Throughput Transposon Mutagenesis of Corynebacterium glutamicum

Nobuaki Suzuki , Masayuki Inui, and Hideaki Yukawa

25. Mini-Mu Transposon Mutagenesis of Ethanologenic Zymomonas mobilis

Katherine M. Pappas

26. Engineering Thermoacidophilic Archaea using Linear DNA Recombination

Yukari Maezato, Karl Dana, and Paul Blum

27. Targeted Gene Disruption in Koji Mold Aspergillus oryzae

Jun-ichi Maruyama and Katsuhiko Kitamoto

28. Selectable and Inheritable Gene Silencing through RNA Interference in the Unicellular Alga Chlamydomonas reinhardtii

Karin Van Dijk and Nandita Sarkar

Additional information

NLS9781493958467
9781493958467
1493958461
Strain Engineering: Methods and Protocols by James A. Williams
New
Paperback
Humana Press Inc.
20160823
480
null null null null null null null null null null
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