Sequence in attB that affect the ability of ΦC31 integrase to synapse and to activate DNA cleavage

Nucleic Acids Research

Volumn 35, Issue 10, 2007, Pages 3407-3419

  Gupta, Milind ^a   Till, Rob ^b   Smith, Margaret C M ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; INTEGRASE; MUTANT PROTEIN; BACTERIAL DNA; BACTERIOPHAGE RECEPTOR;

ARTICLE; BINDING AFFINITY; CHROMOSOME PAIRING; CONTROLLED STUDY; DNA BINDING; DNA CLEAVAGE; DNA CONFORMATION; DNA INTEGRATION; DNA RECOMBINATION; DNA SEQUENCE; GENE MUTATION; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; SYNAPSE; BACTERIOPHAGE; BINDING SITE; CHEMISTRY; ENZYME ACTIVATION; ENZYMOLOGY; GENETIC RECOMBINATION; METABOLISM; MUTAGENESIS;

SYNAPSIS;

ATTACHMENT SITES, MICROBIOLOGICAL; BACTERIOPHAGES; BINDING SITES; DNA, BACTERIAL; ENZYME ACTIVATION; INTEGRASES; MUTAGENESIS; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 34250807697     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm206     Document Type: Article

References (46)

1. Bateman,J.R., Lee,A.M. and Wu,C.T. (2006) Site-specific transformation of Drosophila via φC31 integrase-mediated cassette exchange. Genetics, 173, 769-777.
2. Andreas,S., Schwenk,F., Kuter-Luks,B., Faust,N. and Kuhn,R. (2002) Enhanced efficiency through nuclear localization signal fusion on phage φC31-integrase: Activity comparison with Cre and FLPe recombinase in mammalian cells. Nucleic Acids Res., 30, 2299-2306.
3. Belteki,G., Gertsenstein,M., Ow,D.W. and Nagy,A. (2003) Site-specific cassette exchange and germline transmission with mouse ES cells expressing φC31 integrase. Nat Biotechnol., 21, 321-324.
4. Dafhnis-Calas,F., Xu,Z., Haines,S., Malla,S.K., Smith,M.C.M. and Brown,W.R. (2005) Iterative in vivo assembly of large and complex transgenes by combining the activities of φC31 integrase and Cre recombinase. Nucleic Acids Res., 33, e189.
5. Khan,M.S., Khalid,A.M. and KMalik,K.A. (2005) Phage φC31 integrase: A new tool in plastid genome engineering. Trends in Plant Science, 10, 1-3.
6. Malla,S., Dafhnis-Calas,F., Brookfield,J.F., Smith,M.C.M. and Brown,W.R. (2005) Rearranging the centromere of the human Y chromosome with φC31 integrase. Nucleic Acids Res., 33, 6101-6113.
7. Thomason,L.C., Calendar,R. and Ow,D.W. (2001) Gene insertion and replacement in Schizosaccharomyces pombe mediated by the Streptomyces bacteriophage φC31 site-specific recombination system. Mol. Gen. Genom., 265, 1031-1038.
8. Nkrumah,L.J., Muhle,R.A., Moura,P.A., Ghosh,P., Hatfull,G.F., Jacobs,W.R.Jr and Fidock,D.A. (2006) Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase. Nat. Methods, 3, 615-621.
9. Thyagarajan,B., Olivares,E.C., Hollis,R.P., Ginsburg,D.S. and Calos,M.P. (2001) Site-specific genomic integration in mammalian cells mediated by phage φC31 integrase. Mol Cell Biol., 21, 3926-3934.
10. Groth,A.C., Olivares,E.C., Thyagarajan,B. and Calos,M.P. (2000) A phage integrase directs efficient site-specific integration in human cells. Proc. Natl Acad. Sci. USA, 97, 5995-6000.
11. Olivares,E.C., Hollis,R.P., Chalberg,T.W., Meuse,L., Kay,M.A. and Calos,M.P. (2002) Site-specific genomic integration produces therapeutic Factor IX levels in mice. Nat. Biotechnol., 20, 1124-1128.
12. Held,P.K., Olivares,E.C., Aguilar,C.P., Finegold,M., Calos,M.P. and Grompe,M. (2005) In vivo correction of murine hereditary tyrosinemia type I by φC31 integrase-mediated gene delivery. Mol. Ther., 11, 399-408.
13. Portlock,J.L., Keravala,A., Bertoni,C., Lee,S., Rando,T.A. and Calos,M.P. (2006) Long-term increase in mVEGF164 in mouse hindlimb muscle mediated by phage φC31 integrase after nonviral DNA delivery. Hum. Gene Ther., 17, 871-876.
14. Keravala,A., Portlock,J.L., Nash,J.A., Vitrant,D.G., Robbins,P.D. and Calos,M.P. (2006) φC31 integrase mediates integration in cultured synovial cells and enhances gene expression in rabbit joints. J. Gene Med., 8, 1008-1017.
15. Bertoni,C., Jarrahian,S., Wheeler,T.M., Li,Y., Olivares,E.C., Calos,M.P. and Rando,T.A. (2006) Enhancement of plasmid-mediated gene therapy for muscular dystrophy by directed plasmid integration. Proc. Natl. Acad. Sci. USA, 103, 419-424.
16. Thorpe,H.M. and Smith,M.C.M. (1998) In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proc. Natl Acad. Sci. USA, 95, 5505-5510.
17. Ghosh,P., Kim,A.I. and Hatfull,G.F. (2003) The orientation of mycobacteriophage Bxb1 integration is solely dependent on the central dinucleotide of attP and attB. Mol. Cell, 12, 1101-1111.
18. Azaro,M.A. and Landy,A. (2002). In: Craig,N. L., Craigie,R., Gellert,M. and Lambowitz,A. M. (eds), Mobile DNA II, ASM Press, Washington D.C., pp. 118-148.
19. Ghosh,P., Wasil,L.R. and Hatfull,G.F. (2006) Control of phage Bxb1 excision by a novel recombination directionality factor. PLoS Biol. 4, e186.
20. Smith,M.C.M. and Thorpe,H.M. (2002) Diversity in the serine recombinases. Mol. Microbiol., 44, 299-307.
21. Craig,N.L. (2002) In: Craig,N. L., Craigie,R., Gellert,M. and Lambowitz,A. M. (eds), Mobile DNA II, American Society for Microbiology, Washington DC, pp. 3-11.
22. Biswas,T., Aihara,H., Radman-Livaja,M., Filman,D., Landy,A. and Ellenberger,T. (2005) A structural basis for allosteric control of DNA recombination by lambda integrase. Nature, 435, 1059-1066.
23. Radman-Livaja,M., Biswas,T., Ellenberger,T., Landy,A. and Aihara,H. (2006) DNA arms do the legwork to ensure the directionality of lambda site-specific recombination. Curr. Opin. Struct. Biol., 16, 42-50.
24. Grindley,N.D.F. (2002) In: Craig,N. L., Craigie,R., Gellert,M. and Lambowitz,A. M. (eds), Mobile DNA II, ASM Press, Washington, pp. 272-302.
25. Yang,W. and Steitz,T.A. (1995) Crystal-structure of the site-specific recombinase gamma-delta resolvase complexed with a 34bp cleavage site. Cell, 82, 193-207.
26. Ghosh,P., Pannunzio,N.R. and Hatfull,G.F. (2005) Synapsis in phage Bxb1 integration: Selection mechanism for the correct pair of recombination sites. J. Mol. Biol., 349, 331-348.
27. Smith,M.C.A., Till,R., Brady,K., Soultanas,P., Thorpe,H. and Smith,M.C.M. (2004) Synapsis and DNA cleavage in φC31 integrase-mediated site-specific recombination. Nucleic Acids Res. 32, 2607-2617.
28. Smith,M.C.A., Till,R. and Smith,M.C.M. (2004) Switching the polarity of a bacteriophage integration system. Mol. Microbiol., 51, 1719-1728.
29. Thorpe,H.M., Wilson,S.E. and Smith,M.C.M. (2000) Control of directionality in the site-specific recombination system of the Streptomyces phage φC31. Mol. Microbiol., 38, 232-241.
30. Adams,V., Lucet,I.S., Tynan,F.E., Chiarezza,M., Howarth,P.M., Kim,J., Rossjohn,J., Lyras,D. and Rood,J.I. (2006) Two distinct regions of the large serine recombinase TnpX are required for DNA binding and biological function. Mol. Microbiol., 60, 591-601.
31. Crellin,P.K. and Rood,J.I. (1997) The resolvase/invertase domain of the site-specific recombinase TnpX is functional and recognizes a target sequence that resembles the junction of the circular form of the Clostridium perfringens transposon Tn4451. J. Bacteriol., 179, 5148-5156.
32. Wang,H. and Mullany,P. (2000) The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. J. Bacteriol., 182, 6577-6583.
33. Johnson,R.C. (2002). In: Craig,N. L., Craigie,R., Gellert,M. and Lambowitz,A. M. (eds), Mobile DNA II, ASM Press, Washington DC, pp. 230-271.
34. Li,W., Kamtekar,S., Xiong,Y., Sarkis,G.J., Grindley,N.D.F. and Steitz,T.A. (2005) Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs. Science, 309, 1210-1215.
35. Nollmann,M., He,J., Byron,O. and Stark,W.M. (2004) Solution structure of the Tn3 resolvase-crossover site synaptic complex. Mol. Cell, 16, 127-137.
36. Stark,W.M., Boocock,M.R. and Sherratt,D.J. (1992) Catalysis by site-specific recombinases. Trends Genet., 8, 432-439.
37. Kamtekar,S., Ho,R.S., Cocco,M.J., Li,W., Wenwieser,S.V., Boocock,M.R., Grindley,N.D.F. and Steitz,T.A. (2006) Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination. Proc. Natl. Acad. Sci. USA, 103, 10642-10647.
38. Stark,W.M., Grindley,N.D.F., Hatfull,G.F. and Boocock,M.R. (1991) Resolvase-catalyzed reactions between sites differing in the central dinucleotide of subsite-I. EMBO J., 10, 3541-3548.
39. Kuhstoss,S. and Rao,R.N. (1991) Analysis of the integration function of the streptomycete bacteriophage φc31. J. Mol. Biol., 222, 897-908.
40. Breuner,A., Brondsted,L. and Hammer,K. (2001) Resolvase-like recombination performed by the TP901-1 integrase. Microbiology, 147, 2051-2063.
41. Combes,P., Till,R., Bee,S. and Smith,M.C.M. (2002) The streptomyces genome contains multiple pseudo-attB sites for the (φ C31-encoded site-specific recombination system. J. Bacteriol., 184, 5746-5752.
42. Chalberg,T.W., Portlock,J.L., Olivares,E.C., Thyagarajan,B., Kirby,P.J., Hillman,R.T., Hoelters,J. and Calos,M.P. (2006) Integration specificity of phage φC31 integrase in the human genome. J. Mol. Biol., 357 28-48.
43. Murry,J., Sassetti,C.M., Moreira,J., Lane,J. and Rubin,E.J. (2005) A new site-specific integration system for mycobacteria. Tuberculosis (Edinb), 85, 317-323.
44. Sambrook,J. and Russell,D.W. (2001) edn. Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
45. Bradford,M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 72, 248-254.
46. Lucet,I.S., Tynan,F.E., Adams,V., Rossjohn,J., Lyras,D. and Rood,J.I. (2005) Identification of the structural and functional domains of the large serine recombinase TnpX from Clostridium perfringens. J. Biol. Chem., 280, 2503-2511.