Screen LibraryGenome engineering /
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| Group Author: | ; |
|---|---|
| Published: |
Academic Press,
|
| Publisher Address: | London, United Kingdom : |
| Publication Dates: | 2023. |
| Literature type: | Book |
| Language: | English |
| Edition: | First edition. |
| Series: |
Methods in microbiology,
volume 52 |
| Subjects: | |
| Carrier Form: | xvi, 234 pages : illustrations (chiefly color) ; 25 cm. |
| Bibliography: | Includes bibliographical references. |
| ISBN: |
9780128235409 0128235403 |
| Index Number: | QH442 |
| CLC: | Q78 |
| Call Number: | Q78/G335-6 |
| Contents: |
Intro -- Genome Engineering -- Copyright -- Contents -- Contributors -- Preface -- References -- Section I: Genome transformation -- Chapter 1: Genome transplantation in Mollicutes -- 1. The historical scientific context associated with genome transplantation -- 2. Mollicutes-The perfect model organisms for the establishment of GT -- 2.1. General characteristics of the Mollicutes -- 2.2. Transformation methods for Mollicutes -- 2.3. Transformable replicative plasmids -- 3. Baker's yeast-An engineering platform for microbial genomes -- 4. The GT protocol -- 4.1. Isolation of intact Mmc donor genomic DNA -- 4.2. Preparation of recipient Mcap cells -- 4.3. Transformation of Mcap with chromosomal DNA -- 4.4. Transplanted Mollicutes chromosomes -- 4.5. General comments about the GT protocol -- 4.6. Limiting factors involved in the GT process -- 4.6.1. Restriction-modification (R-M) systems -- 4.6.2. Phylogenetic distance of donor and recipient species -- 4.6.3. Selection of the recipient cell -- 4.6.4. DNA recombination -- 4.6.5. Nucleases -- 4.6.6. Toxin/antitoxin systems -- 4.6.7. Additional factors -- 5. Future perspectives -- 5.1. GT and Mollicutes -- 5.2. Adaptation of GT to bacterial species other than Mollicutes -- 6. Ethical considerations -- Acknowledgements -- Appendix -- A.1. Entrapping of intact donor chromosomes in agarose plugs -- A.1.1. Isolation of intact Mmc chromosomes from cultures -- A.1.2. Preparation of agarose plugs from yeast cultures containing modified donor chromosomes -- A.2. Genome transplantation using Mcap RE(-) as a recipient cell -- A.2.1. Release of intact chromosomes from agarose plugs -- A.2.2. Preparation of Mcap RE(-) recipient cells -- A.2.3. Transplantation of donor chromosomes into Mcap RE(-) recipient cells -- A.2.4. Screening of the transplants -- References -- Section II: Recombineering and engineering. 5. Learn and general considerations -- 5.1. Maximizing information from multi-factorial experiments: Sequential vs non-sequential optimisation -- 5.2. Case studies -- 6. Conclusions -- References -- Chapter 4: Recombineering -- 1. Introduction -- 2. History and development of recombineering -- 3. Molecular tools for recombineering -- 3.1. The RecBCD system -- 3.2. The RecF pathway -- 3.3. Lambda phage Red functions -- 3.4. Rac prophage encoded RecE and RecT -- 4. Steps involved in a typical recombineering experiment -- 4.1. Substrate DNA and its meticulous design -- 4.2. Provision for the Lambda Red recombination genes -- 4.2.1. For bacterial chromosomal DNA -- 4.2.2. For high and low copy number plasmids -- 4.3. Inducing the Red genes -- 4.4. Electroporation of the construct in the desired host -- 4.5. Growing and maintaining the electroporated cells -- 4.6. Selection and recombination of the clones -- 5. Uses of recombineering -- 5.1. Recombineering methods for inserting a selectable marker into the bacterial chromosome -- 5.2. Recombineering can be used for inserting non-selectable DNA fragments (Sharan et al., 2009) -- 5.2.1. Seamless method -- 5.2.2. Scarred method -- 6. Regulation and expression of recombineering gene -- 6.1. Lac promoter -- 6.2. Arabinose promoter -- 6.3. Lambda phage's own promoter-repressor system -- 7. Recombineering in various systems -- 7.1. In BAC (bacterial artificial chromosome) -- 7.1.1. Three step strategy -- 7.1.2. Four step strategy -- 7.1.3. ALFIRE (assisted large fragment insertion with red/ET recombination) -- 7.2. Recombineering in E. coli phages -- 7.3. Construction of Mycobacteriophage mutants by recombineering -- 7.3.1. Bacteriophage Recombineering of Electroporated DNA (BRED) -- 7.3.2. DADA-PCR: Deletion amplification assay PCR -- 7.3.3. BRED for point mutation -- 7.4. Recombineering in other strains. 7.5. Gram negative bacteria -- 7.5.1. Recombineering in Shewanella -- 7.5.2. Recombineering in Vibrio natriegens -- 7.5.3. Recombineering in Vibrio cholerae -- 7.5.4. Recombineering in Photorhabdus luminescens -- 7.5.5. Recombineering in Pseudomonas -- 7.5.6. Recombineering in Salmonella enterica -- 7.5.7. Recombineering in Klebsiella pneumoniae -- 7.5.8. Recombineering in Yersinia pestis -- 7.5.9. Recombineering in Zymomonas mobilis -- 7.6. Gram positive strains -- 7.6.1. Recombineering in mycobacteria -- 8. Future prospects of recombineering -- References -- Further reading -- Section III: CRISPR -- Chapter 5: Applications of CRISPR/Cas9 in the field of microbiology -- 1. Overview of CRISPR/Cas9 biology -- 2. Applications of CRISPR/Cas9 -- 3. Recent uses of CRISPR/Cas9-based technologies in microbiology -- 3.1. Bacterial gene expression and CRISPR/Cas9 -- 3.2. Bacterial resistance and CRISPR/Cas9 -- 3.3. Delivery strategies via CRISPR/Cas9 -- 3.4. Bacterial infections and CRISPR/Cas9 -- 4. Techniques utilizing CRISPR/Cas9 -- 4.1. Mouse model techniques -- 4.2. Techniques based on organoid models -- 4.3. Techniques based on cell lines -- 4.4. Techniques based on targeting miRNA -- 4.5. CRISPR/Cas9 in clinical trails -- 5. Challenges in the field of CRISPR/Cas9 system -- 6. Conclusion -- References -- Chapter 6: Genome engineering in Aspergillus niger -- 1. Introduction -- 2. Materials -- 2.1. Nucleotide preparation or construction -- 2.2. Manipulation of strains -- 2.3. Measurement of enzyme activity -- 2.4. Detection of secondary metabolism -- 3. Methods -- 3.1. Choice of appropriate Cas9 protein expression plasmids -- 3.2. Construction of sgRNAs -- 3.2.1. sgRNAs expression in vivo through plasmids -- 3.2.2. sgRNAs synthesis in vitro -- 3.3. Preparation of donor DNAs -- 3.3.1. Construction of donor DNAs with short homologous arms (39bp). 3.3.2. Construction of donor DNAs with long homologous arms (500-2000bp) -- 3.4. Transformation of host strains and verification of positive transformants -- 3.5. Detecting the yield of target products and evaluation of the genome edit effect or efficiency -- 3.5.1. Detecting the activity of glucose oxidase -- 3.5.2. Secondary metabolism detection -- 4. Notes -- References -- Section IV: Transformation -- Chapter 7: Natural transformation as a tool in Acinetobacter baylyi: Evolution by amplification of gene copy number -- 1. Introduction -- 2. General considerations -- 2.1. Design of the amplicon and synthetic bridging fragment -- 2.2. Chromosomal integration by natural transformation -- 2.3. Selection of amplification mutants -- 2.4. Interpreting gene copy number estimations and obtaining single-copy mutants -- 3. Material and equipment -- 3.1. Strains and culture media -- 3.2. Reagents for DNA manipulation -- 3.3. Equipment -- 4. Experimental procedures -- 4.1. Construction of the amplicon and chromosomal integration -- 4.2. Construction of the SBF and amplification of gene copy number -- 4.3. Adaptive laboratory evolution and monitoring of gene copy number over time -- 4.3.1. Adaptive laboratory evolution by serial transfer -- 4.3.2. Gene copy number analysis by quantitative PCR -- 4.4. Obtaining single-copy mutants from EASy -- 4.4.1. Isolation and screening by colony PCR -- 4.4.2. Allelic replacement in evolved populations -- 5. Summary and concluding remarks -- Acknowledgements -- References -- Chapter 8: Natural transformation as a tool in Acinetobacter baylyi: Streamlined engineering and mutational analysis -- 1. Introduction -- 2. General considerations -- 2.1. Convenience and optimization -- 2.2. Preparation of recipient cells and donor DNA -- 2.3. Introduction of DNA into cells, and growth conditions following transformation. |