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A Bacterial One-Hybrid System to Isolate Homing Endonuclease Variants with Altered DNA Target Specificities

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Gene Correction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1114))

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Abstract

Chromosomal cleavage near the site of mutations that cause disease can facilitate the targeted repair of the locus. Gene therapy protocols therefore require the engineering of DNA endonucleases that target specific genomic loci. Here, we describe a bacterial one-hybrid selection system that has been used to isolate derivatives of the I-SceI homing endonuclease from combinatorial libraries that display altered DNA recognition specificities. The construction of plasmid expression libraries, the development of reporter strains, and the utilization of these components in the bacterial one-hybrid system are detailed.

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References

  1. Gimble FS (2000) Invasion of a multitude of genetic niches by homing endonuclease genes. FEMS Microbiol Lett 185:99–107

    Article  CAS  PubMed  Google Scholar 

  2. Redondo P, Prieto J, Munoz IG et al (2008) Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature 456(7218):107–111

    Article  CAS  PubMed  Google Scholar 

  3. Chen Z, Zhao H (2005) A highly sensitive selection method for directed evolution of homing endonucleases. Nucleic Acids Res 33(18):e154

    Article  PubMed Central  PubMed  Google Scholar 

  4. Doyon JB, Pattanayak V, Meyer CB et al (2006) Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J Am Chem Soc 128(7):2477–2484

    Article  CAS  PubMed  Google Scholar 

  5. Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 372(5):1305–1319

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Jarjour J, West-Foyle H, Certo MT et al (2009) High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res 37(20):6871–6880

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Joshi R, Ho KK, Tenney K et al (2011) Evolution of I-SceI homing endonucleases with increased DNA recognition site specificity. J Mol Biol 405(1):185–200

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Ashworth J, Havranek JJ, Duarte CM et al (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441(7093):656–659

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Ashworth J, Taylor GK, Havranek JJ et al (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 38(16):5601–5608

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Chica RA, Doucet N, Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 16(4):378–384

    Article  CAS  PubMed  Google Scholar 

  11. Gimble FS, Moure CM, Posey KL (2003) Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system. J Mol Biol 334(5):993–1008

    Article  CAS  PubMed  Google Scholar 

  12. Eklund JL, Ulge UY, Eastberg J et al (2007) Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease. Nucleic Acids Res 35(17):5839–5850

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Chames P, Epinat JC, Guillier S et al (2005) In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination. Nucleic Acids Res 33(20):e178

    Article  PubMed Central  PubMed  Google Scholar 

  14. Chen Z, Wen F, Sun N et al (2009) Directed evolution of homing endonuclease I-SceI with altered sequence specificity. Protein Eng Des Sel 22:249–256

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Serebriiskii IG, Fang R, Latypova E et al (2005) A combined yeast/bacteria two-hybrid system: development and evaluation. Mol Cell Proteomics 4(6):819–826

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Serebriiskii IG, Joung JK (2002) Yeast and bacterial two-hybrid selection systems for studying protein-protein interactions. In: Golemis E (ed) Protein-protein interactions: a molecular cloning manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 93–142

    Google Scholar 

  17. Volles MJ, Lansbury PTJ (2005) A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries. Nucleic Acids Res 33:3667–3677

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Joung JK, Ramm EI, Pabo CO (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A 97(13):7382–7387

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Gimble FS, Stephens BW (1995) Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease. J Biol Chem 270:5849–5856

    Article  CAS  PubMed  Google Scholar 

  20. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714–2723

    Article  CAS  PubMed  Google Scholar 

  21. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera - visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    Article  CAS  PubMed  Google Scholar 

  22. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18(20):6097–6100

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

We thank Weijia Luo, Jennifer L. Meyers, and Kristen Tenney for the technical assistance. This work was supported by grants from the National Institutes of Health (GM 070553) and the National Science Foundation (MCB-0321550) to F.S.G. Figures 1 and 2 reprinted from [7] with permission from Elsevier.

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Joshi, R., Gimble, F.S. (2014). A Bacterial One-Hybrid System to Isolate Homing Endonuclease Variants with Altered DNA Target Specificities. In: Storici, F. (eds) Gene Correction. Methods in Molecular Biology, vol 1114. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-761-7_14

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  • DOI: https://doi.org/10.1007/978-1-62703-761-7_14

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-760-0

  • Online ISBN: 978-1-62703-761-7

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