Structure-guided reprogramming of serine recombinase DNA sequence specificity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 2, 2011, Pages 510-515

  Gaj, Thomas ^a   Mercer, Andrew C ^a   Gersbach, Charles A ^a,b   Gordley, Russell M ^a   Barbas III, Carlos F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b Duke University   (United States)

Author keywords

Gene targeting; Protein engineering; Site specific recombination; Zinc finger recombinase

Indexed keywords

ALANINE; AMINO ACID; ANTIBIOTIC AGENT; BETA FRUCTOFURANOSIDASE; DNA; ENZYME; GIN PROTEIN; HYGROMYCIN; PUROMYCIN; RECOMBINASE; RESOLVASE; SERINE RECOMBINASE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; ZINC FINGER RECOMBINASE FUSION PROTEIN;

ANIMAL CELL; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE MU; BACTERIOPHAGE TN3; CATALYSIS; CONTROLLED STUDY; DNA INTEGRATION; DNA RECOMBINATION; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENE MUTATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; NONHUMAN; NUCLEAR REPROGRAMMING; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; TRANSGENE;

ENTEROBACTERIA PHAGE MU; ESCHERICHIA COLI;

EID: 79551676837     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1016462108     Document Type: Article

References (35)

1. Grindley ND, Whiteson KL, Rice PA (2006) Mechanisms of site-specific recombination. Annu Rev Biochem 75:567-605.
2. Sorrell DA, Kolb AF (2005) Targeted modification of mammalian genomes. Biotechnol Adv 23:431-469.
3. Akopian A, Marshall Stark W (2005) Site-specific DNA recombinases as instruments for genomic surgery. Adv Genet 55:1-23.
4. Bischof J, Basler K (2008) Recombinases and their use in gene activation, gene inactivation, and transgenesis. Methods in Molecular Biology 420:175-195.
5. Ginsburg DS, Calos MP (2005) Site-specific integration with PhiC31 integrase for prolonged expression of therapeutic genes. Adv Genet 54:179-187.
6. Wilson TJ, Kola I (2001) The LoxP/CRE system and genome modification. Methods in Molecular Biology 158:83-94.
7. Buchholz F, Angrand PO, Stewart AF (1998) Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat Biotechnol 16:657-662.
8. Buchholz F, Stewart AF (2001) Alteration of Cre recombinase site specificity by substrate-linked protein evolution. Nat Biotechnol 19:1047-1052. (Pubitemid 33041889)
9. Sarkar I, Hauber I, Hauber J, Buchholz F (2007) HIV-1 proviral DNA excision using an evolved recombinase. Science 316:1912-1915.
10. Voziyanov Y, Stewart AF, Jayaram M (2002) A dual reporter screening system identifies the amino acid at position 82 in Flp site-specific recombinase as a determinant for target specificity. Nucleic Acids Res 30:1656-1663.
11. Bolusani S, et al. (2006) Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites. Nucleic Acids Res 34:5259-5269.
12. Dorgai L, Yagil E, Weisberg RA (1995) Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J Mol Biol 252:178-188.
13. Gersbach CA, Gaj T, Gordley RM, Barbas CF, 3rd (2010) Directed evolution of recombinase specificity by split gene reassembly. Nucleic Acids Res 38:4198-4206.
14. Konieczka JH, Paek A, Jayaram M, Voziyanov Y (2004) Recombination of hybrid target sites by binary combinations of Flp variants: mutations that foster interprotomer collaboration and enlarge substrate tolerance. J Mol Biol 339:365-378.
15. Hacein-Bey-Abina S, et al. (2003) LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302:415-419.
16. Schmidt EE, et al. (2000) Illegitimate Cre-dependent chromosome rearrangements in transgenic mouse spermatids. Proc Natl Acad Sci USA 97:13702-13707.
17. Loonstra A, et al. (2001) Growth inhibition and DNA damage induced by Cre recombinase in mammalian cells. Proc Natl Acad Sci USA 98:9209-9214. (Pubitemid 32743895)
18. Akopian A, He J, Boocock MR, Stark WM (2003) Chimeric recombinases with designed DNA sequence recognition. Proc Natl Acad Sci USA 100:8688-8691.
19. Gordley RM, Smith JD, Graslund T, Barbas CF, 3rd (2007) Evolution of programmable zinc finger-recombinases with activity in human cells. J Mol Biol 367:802-813.
20. Gordley RM, Gersbach CA, Barbas CF, 3rd (2009) Synthesis of programmable integrases. Proc Natl Acad Sci USA 106:5053-5058.
21. Smith MC, Thorpe HM (2002) Diversity in the serine recombinases. Mol Microbiol 44:299-307.
22. Carroll D (2008) Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther 15:1463-1468.
23. Segal DJ, Dreier B, Beerli RR, Barbas CF, 3rd (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc Natl Acad Sci USA 96:2758-2763.
24. Dreier B, et al. (2005) Development of zinc finger domains for recognition of the 5′-CNN-3′ family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 280:35588-35597.
25. Dreier B, et al. (2001) Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 276:29466-29478. (Pubitemid 37452042)
26. Gonzalez B, et al. (2010) Modular system for the construction of zinc-finger libraries and proteins. Nat Protoc 5:791-810.
27. Segal DJ, et al. (2003) Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins. Biochemistry 42:2137-2148.
28. Maeder ML, et al. (2008) Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294-301.
29. Yang W, Steitz TA (1995) Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site. Cell 82:193-207.
30. Li W, et al. (2005) Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs. Science 309:1210-1215.
31. Hughes RE, et al. (1990) Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell 63:1331-1338.
32. Sluka JP, et al. (1990) Importance of minor-groove contacts for recognition of DNA by the binding domain of Hin recombinase. Biochemistry 29:6551-6561.
33. Klippel A, Cloppenborg K, Kahmann R (1988) Isolation and characterization of unusual gin mutants. Embo J 7:3983-3989.
34. Arnold PH, et al. (1999) Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. Embo J 18:1407-1414.
35. Cunningham BC, Wells JA (1989) High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244:1081-1085.