Abstract
The λ phage Red proteins greatly enhance homologous recombination in Escherichia coli. Red-mediated recombination or “recombineering” can be used to construct targeted gene deletions as well as to introduce point mutations into the genome. Here, we describe our method for scanning mutagenesis using recombineered oligonucleotide libraries. This approach entails randomization of specific codons within a target gene, followed by functional selection to isolate mutants. Oligonucleotide library mutagenesis has generated hundreds of novel antibiotic resistance mutations in genes encoding ribosomal proteins, and should be applicable to other systems for which functional selections exist.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Court D. L., Sawitzke J. A., and Thomason L. C. (2002) Genetic engineering using homologous recombination. Annu Rev Genet 36, 361–388.
Thomason L., Court D. L., Bubunenko M., Costantino N., Wilson H., Datta S., et al. (2007) Recombineering: genetic engineering in bacteria using homologous recombination. Curr Protoc Mol Biol Chapter 1, Unit 1 16.
Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 2006 0008.
Swingle B., Markel E., Costantino N., Bubunenko M. G., Cartinhour S., and Court D. L. (2010) Oligonucleotide recombination in Gram-negative bacteria. Mol Microbiol 75, 138–148.
van Kessel J. C., Marinelli L. J., and Hatfull G. F. (2008) Recombineering mycobacteria and their phages. Nat Rev Microbiol 6, 851–857.
Ellis H. M., Yu D., DiTizio T., and Court D. L. (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 98, 6742–6746.
Costantino N., and Court D. L. (2003) Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc Natl Acad Sci U S A 100, 15748–15753.
Diner E. J., and Hayes C. S. (2009) Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics. J Mol Biol 386, 300–315.
Holberger L. E., and Hayes C. S. (2009) Ribosomal protein S12 and aminoglycoside antibiotics modulate A-site mRNA cleavage and transfer-messenger RNA activity in Escherichia coli. J Biol Chem 284, 32188–32200.
DeWilde M., and Wittmann-Liebold B. (1973) Localization of the amino-acid exchange in protein S5 from an Escherichia coli mutant resistant to spectinomycin. Mol Gen Genet 127, 273–276.
Funatsu G., Nierhaus K., and Wittmann-Liebold B. (1972) Ribosomal proteins. XXII. Studies on the altered protein S5 from a spectinomycin-resistant mutant of Escherichia coli. J Mol Biol 64, 201–209.
Funatsu G., Schiltz E., and Wittmann H. G. (1972) Ribosomal proteins. XXVII. Localization of the amino acid exchanges in protein S5 from two Escherichia coli mutants resistant to spectinomycin. Mol Gen Genet 114, 106–111.
Itoh T. (1976) Amino acid replacement in the protein S5 from a spectinomycin resistant mutant of Bacillus subtilis. Mol Gen Genet 144, 39–42.
Kehrenberg C., and Schwarz S. (2007) Mutations in 16S rRNA and ribosomal protein S5 associated with high-level spectinomycin resistance in Pasteurella multocida. Antimicrob Agents Chemother 51, 2244–2246.
He X., Miao V., and Baltz R. H. (2005) Spectinomycin resistance in rpsE mutants is recessive in Streptomyces roseosporus. J Antibiot (Tokyo) 58, 284–288.
Kirthi N., Roy-Chaudhuri B., Kelley T., and Culver G. M. (2006) A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity. RNA 12, 2080–2091.
Datsenko K. A., and Wanner B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97, 6640–6645.
Datta S., Costantino N., and Court D. L. (2006) A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109–115.
Cha R. S., Zarbl H., Keohavong P., and Thilly W. G. (1992) Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. PCR Methods Appl 2, 14–20.
Acknowledgment
This work was supported by grant R01 GM078634 from the National Institutes of Health.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Diner, E.J., Garza-Sánchez, F., Hayes, C.S. (2011). Genome Engineering Using Targeted Oligonucleotide Libraries and Functional Selection. In: Williams, J. (eds) Strain Engineering. Methods in Molecular Biology, vol 765. Humana Press. https://doi.org/10.1007/978-1-61779-197-0_5
Download citation
DOI: https://doi.org/10.1007/978-1-61779-197-0_5
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-196-3
Online ISBN: 978-1-61779-197-0
eBook Packages: Springer Protocols