Strain Engineering: Methods and Protocols - Methods in Molecular Biology 2011 edition

Marc Notes: Includes bibliographical references and index.; This text presents powerful new genetic engineering-based strain engineering methods for rational modification of a variety of model organisms. It contains key notes and implementation advice from the experts. 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 KatsuhikoKitamoto 28. Selectable and Inheritable Gene Silencing through RNA Interference in the Unicellular Alga Chlamydomonas reinhardtii Karin Van Dijk and Nandita Sarkar"Jacket Description/Back: 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."