Mechanism of inhibition of site-specific recombination by the Holliday junction-trapping peptide WKHYNY: Insights into phage λ integrase-mediated strand exchange

Journal of Molecular Biology

Volumn 327, Issue 2, 2003, Pages 413-429

  Cassell, Geoffrey D ^a,b   Segall, Anca M ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

Bacteriophage integrase; Holliday junction; Peptide inhibitors; Site specific recombination; Strand exchange

Indexed keywords

INTEGRASE; PEPTIDE; RECOMBINASE; TRYPTOPHYLLYSYLHISTIDYLTYROSYLASPARAGINYLTYROSINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; BIOACCUMULATION; BIOAVAILABILITY; CELL SPECIFICITY; DNA CLEAVAGE; HOLLIDAY JUNCTION; MUTATION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REGULATORY MECHANISM;

BACTERIOPHAGE LAMBDA;

EID: 0037459219     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00058-5     Document Type: Article

References (30)

1. Landy A. Mechanistic and structural complexity in the site-specific recombination pathways of Int and FLP. Curr. Opin. Genet. Dev. 3:1993;699-707.
2. Nash H.A. Site-specific recombination: integration, excision, resolution, and inversion of defined DNA segments. Neidhardt F.H.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. 2nd edit. 1996;2363-2376 ASM Press, Washington DC.
3. Segall A.M., Nash H.A. Architectural flexibility in lambda site-specific recombination: three alternate conformations channel the attL site into three distinct pathways. Genes Cells. 1:1996;453-463.
4. Segall A.M. Analysis of higher order intermediates and synapsis in the bent-L pathway of bacteriophage lambda site-specific recombination. J. Biol. Chem. 273:1998;24258-24265.
5. Bankhead T., Segall A.M. Characterization of a mutation of bacteriophage lambda integrase: putative mechanistic role for a conserved residue. J. Biol. Chem. 275:2000;36949-36956.
6. Segall A.M., Nash H.A. Synaptic intermediates in bacteriophage lambda site-specific recombination: integrase can align pairs of attachment sites. EMBO J. 12:1993;4567-4576.
7. Kitts P.A., Nash H.A. Homology-dependent interactions in phage lambda site-specific recombination. Nature. 329:1987;346-348.
8. Kitts P.A., Nash H.A. Bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges. J. Mol. Biol. 204:1988;95-107.
9. Kitts P.A., Nash H.A. An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA. Nucl. Acids Res. 16:1988;6839-6856.
10. Burgin A.B. Jr, Nash H.A. Symmetry in the mechanism of bacteriophage lambda integrative recombination. Proc. Natl Acad. Sci. USA. 89:1992;9642-9646.
11. Burgin A.B. Jr, Nash H.A. Suicide substrates reveal properties of the homology-dependent steps during integrative recombination of bacteriophage lambda. Curr. Biol. 5:1995;1312-1321.
12. Nunes-Duby S.E., Matsumoto L., Landy A. Site-specific recombination intermediates trapped with suicide substrates. Cell. 50:1987;779-788.
13. Nunes-Duby S.E., Azaro M.A., Landy A. Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr. Biol. 5:1995;139-148.
14. Azaro M.A., Landy A. The isomeric preference of Holliday junctions influences resolution bias by lambda integrase. EMBO J. 16:1997;3744-3755.
15. Cassell G., Klemm M., Pinilla C., Segall A. Dissection of bacteriophage λ site-specific recombination using synthetic peptide combinatorial libraries. J. Mol. Biol. 299:2000;1193-1202.
16. Klemm M., Cheng C., Cassell G., Shuman S., Segall A.M. Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases. J. Mol. Biol. 299:2000;1203-1216.
17. Hsu P.L., Landy A. Resolution of synthetic att-site Holliday structures by the integrase protein of bacteriophage lambda. Nature. 311:1984;721-726.
18. de Massy B., Dorgai L., Weisberg R.A. Mutations of the phage lambda attachment site alter the directionality of resolution of Holliday structures. EMBO J. 8:1989;1591-1599.
19. Franz B., Landy A. Interactions between lambda Int molecules bound to sites in the region of strand exchange are required for efficient Holliday junction resolution. J. Mol. Biol. 215:1990;523-535.
20. Franz B., Landy A. The Holliday junction intermediates of lambda integrative and excisive recombination respond differently to the bending proteins integration host factor and excisionase. EMBO J. 14:1995;397-406.
21. Pena C.E., Kahlenberg J.M., Hatfull G.F. Assembly and activation of site-specific recombination complexes. Proc. Natl Acad. Sci. USA. 97:2000;7760-7765.
22. Burgin A.B. Jr, Huizenga B.N., Nash H.A. A novel suicide substrate for DNA topoisomerases and site-specific recombinases. Nucl. Acids Res. 23:1995;2973-2979.
23. Weisberg R.A., Enquist L.W., Foeller C., Landy A. Role for DNA homology in site-specific recombination. The isolation and characterization of a site affinity mutant of coliphage lambda. J. Mol. Biol. 170:1983;319-342.
24. Esposito D., Scocca J.J. The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucl. Acids Res. 25:1997;3605-3614.
25. Nunes-Duby S.E., Kwon H.J., Tirumalai R.S., Ellenberger T., Landy A. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucl. Acids Res. 26:1998;391-406.
26. Gopaul D.N., Van Duyne G.D. Structure and mechanism in site-specific recombination. Curr. Opin. Struct. Biol. 9:1999;14-20.
27. Chen Y., Narendra U., Iype L.E., Cox M.M., Rice P.A. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell. 6:2000;885-897.
28. Gopaul D.N., Guo F., Van Duyne G.D. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:1998;4175-4187.
29. Han Y.W., Gumport R.I., Gardner J.F. Mapping the functional domains of bacteriophage lambda integrase protein. J. Mol. Biol. 235:1994;908-925.
30. Bankhead T.M., Etzel B., Wolven F., Bordenave S., Boldt J.L., Larsen T., Segall A.M. Mutations at residues 282, 286 and 293 of phage λ integrase exert pathway-specific effects on synapsis and catalysis in recombination. J. Bacteriol. 2003;. In press.