Strain Engineering: Methods and Protocols

ISBN-13: 9781617791963 / Angielski / Twarda / 2011 / 496 str.

James A. Williams

Opis

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 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.

Spis treści

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-Sánchez, 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, Nikë 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