Mutations at residues 282, 286, and 293 of phage λ integrase exert pathway-specific effects on synapsis and catalysis in recombination

Journal of Bacteriology

Volumn 185, Issue 8, 2003, Pages 2653-2666

  Bankhead, Troy M ^a,c   Etzel, Bernard J ^a   Wolven, Felise ^a   Bordenave, Sylvain ^a   Boldt, Jeffrey L ^a   Larsen, Teresa A ^b   Segall, Anca M ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b Foundation for Scientific Literacy   (United States)

^c UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE LAMBDA; CATALYSIS; CHROMOSOME PAIRING; ENZYME ACTIVITY; ENZYME KINETICS; HOLLIDAY JUNCTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ATTACHMENT SITES, MICROBIOLOGICAL; BACTERIOPHAGE LAMBDA; CATALYSIS; CHROMOSOME PAIRING; ENDODEOXYRIBONUCLEASES; HOLLIDAY JUNCTION RESOLVASES; INTEGRASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; VIRAL PROTEINS; VIRUS INTEGRATION;

BACTERIOPHAGE LAMBDA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0037389327     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.8.2653-2666.2003     Document Type: Article

References (46)

1. Azaro, M. A., and A. Landy. 2002. λ integrase and the λ Int family, p. 118-148. In N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz (ed.), Mobile DNA II. American Society for Microbiology, Washington, D.C.
2. Bankhead, T., and A. M. Segall. 2000. Characterization of a mutation of bacteriophage lambda integrase. Putative role in core binding and strand exchange for a conserved residue. J. Biol. Chem. 275:36949-36956.
3. Burgin, A. B., Jr., and H. A. Nash. 1995. Suicide substrates reveal properties of the homology-dependent steps during integrative recombination of bacteriophage lambda. Curr. Biol. 5:1312-1321.
4. Burgin, A. B., Jr., and H. A. Nash. 1992. Symmetry in the mechanism of bacteriophage lambda integrative recombination. Proc. Natl. Acad. Sci. USA 89:9642-9646.
5. Cassell, G. D., and A. M. Segall. 2003. Mechanism of inhibition of site-specific recombination by the Holliday juriction-trapping peptide WKHYNY: insights into phage λ integrase-mediated strand exchange. J. Mol. Biol. 327:413-429.
6. Cassell, G., M. Klemm, C. Pinilla, and A. Segall. 2000. Dissection of bacteriophage lambda site-specific recombination using synthetic peptide combinatorial libraries. J. Mol. Biol. 299:1193-1202.
7. Cheng, C., P. Kussie, N. Pavletich, and S. Shuman. 1998. Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92:841-850.
8. Cheng, Q., B. M. Swalla, M. Beck, R. Alcaraz, Jr., R. I. Gumport, and J. F. Gardner. 2000. Specificity determinants for bacteriophage Hong Kong 022 integrase: analysis of mutants with relaxed core-binding specificities. Mol. Microbiol. 36:424-436.
9. Craig, N. L., and H. A. Nash. 1983. The mechanism of phage lambda site-specific recombination: site-specific breakage of DNA by Int topoisomerase. Cell 35:795-803.
10. Dorgai, L., S. Sloan, and R. A. Weisberg. 1998. Recognition of core binding sites by bacteriophage integrases. J. Mol. Biol. 277:1059-1070.
11. Dorgai, L., E. Yagil, and R. A. Weisberg. 1995. Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J. Mol. Biol. 252:178-188.
12. Enquist, L. W., and R. A. Weisberg. 1977. A genetic analysis of the att-int-xis region of coliphage lambda. J. Mol. Biol. 111:97-120.
13. Gardner, J. F., and H. A. Nash. 1986. Role of Escherichia coli IHF protein in lambda site-specific recombination. A mutational analysis of binding sites. J. Mol. Biol. 191:181-189.
14. Goodman, S. D., S. C. Nicholson, and H. A. Nash. 1992. Deformation of DNA during site-specific recombination of bacteriophage lambda: replacement of IHF protein by HU protein of sequence-directed bends. Proc. Natl. Acad. Sci. USA 89:11910-11914.
15. Gopaul, D. N., F. Guo, and G. D. Van Duyne. 1998. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:4175-4187.
16. Grishin, N. V. 2000. Two tricks in one bundle: helix-turn-helix gains enzymatic activity. Nucleic Acids Res. 28:2229-2233.
17. Guo, F., D. N. Gopaul, and G. D. Van Duyne. 1999. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA 96:7143-7148.
18. Guo, F., D. N. Gopaul, and G. D. van Duyne. 1997. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389:40-46.
19. Han, Y. W., R. I. Gumport, and J. F. Gardner. 1994. Mapping the functional domains of bacteriophage lambda integrase protein. J. Mol. Biol. 235:908-925.
20. Jessop, L. 2000. Architecture of the synaptic intermediates of the site-specific recombination pathways mediated by the bacteriophage lambda integrase. Ph.D. thesis. San Diego State University and University of California, San Diego, San Diego, Calif.
21. Jessop, L., T. Bankhead, D. Wong, and A. M. Segall. 2000. The amino terminus of bacteriophage lambda integrase is involved in protein-protein interactions during recombination. J. Bacteriol. 182:1024-1034.
22. Kim, S., and A. Landy. 1992. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science 256:198-203.
23. Kim, S., L. Moitoso de Vargas, S. E. Nunes-Duby, and A. Landy. 1990. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in lambda attL. Cell 63:773-781.
24. Klemm, M., C. Cheng, G. Cassell, S. Shuman, and A. M. Segall. 2000. Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases. J. Mol. Biol. 299:1203-1216.
25. Krogh, B. O., and S. Shuman. 2000. Catalytic mechanism of DNA topoisomerase IB. Mol. Cell 5:1035-1041.
26. Kwon, H. J., R. Tirumalai, A. Landy, and T. Ellenberger. 1997. Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science 276:126-131.
27. Landy, A. 1989. Dynamic, structural, and regulatory aspects of lambda sitespecific recombination. Annu. Rev. Biochem. 58:913-949.
28. Moitoso de Vargas, L., C. A. Pargellis, N. M. Hasan, E. W. Bushman, and A. Landy. 1988. Autonomous DNA binding domains of lambda integrase recognize two different sequence families. Cell 54:923-929.
29. Nagaraja, R., and R. A. Weisberg. 1990. Specificity determinants in the attachment sites of bacteriophages HK022 and lambda. J. Bacteriol. 172:6540-6550.
30. Nash, H. A. 1996. Site-specific recombination: integration, excision, resolution, and inversion of defined DNA segments, p. 2363-2376. In F. H. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
31. Nash, H. A., and C. A. Robertson. 1989. Heteroduplex substrates for bacteriophage lambda site-specific recombination: cleavage and strand transfer products. EMBO J. 8:3523-3533.
32. Numrych, T. E., R. I. Gumport, and J. F. Gardner. 1990. A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage lambda. Nucleic Acids Res. 18:3953-3959.
33. Nunes-Duby, S. E., H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy. 1998. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26:391-406.
34. Nunes-Duby, S. E., D. Yu, and A. Landy. 1997. Sensing homology at the strand-swapping step in lambda excisive recombination. J. Mol. Biol. 272:493-508.
35. Pargellis, C. A., S. E. Nunes-Duby, L. M. de Vargas, and A. Landy. 1988. Suicide recombination substrates yield covalent lambda integrase-DNA complexes and lead to identification of the active site tyrosine. J. Biol. Chem. 263:7678-7685.
36. Richet, E., P. Abcarian, and H. A. Nash. 1988. Synapsis of attachment sites during lambda integrative recombination involves capture of naked DNA by a protein-DNA complex. Cell 52:9-17.
37. Ross, W., and A. Landy. 1982. Bacteriophage lambda Int protein recognizes two classes of sequence in the phage att site: characterization of arm-type sites. Proc. Natl. Acad. Sci. USA 79:7724-7728.
38. Sarkar, D., M. Radman-Livaja, and A. Landy. 2001. The small DNA binding domain of lambda integrase is a context-sensitive modulator of recombinase functions. EMBO J. 20:1203-1212.
39. Segall, A. M. 1998. Analysis of higher order intermediates and synapsis in the bent-L pathway of bacteriophage lambda site-specific recombination. J. Biol. Chem. 273:24258-24265.
40. Segall, A. M., S. D. Goodman, and H. A. Nash. 1994. Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13:4536-4548.
41. Segall, A. M., and H. A. Nash. 1996. Architectural flexibility in lambda site-specific recombination: three alternate conformations channel the attL site into three distinct pathways. Genes Cells 1:453-463.
42. Segall, A. M., and H. A. Nash. 1993. Synaptic intermediates in bacteriophage lambda site-specific recombination: integrase can align pairs of attachment sites. EMBO J. 12:4567-4576.
43. Tirumalai, R. S., E. Healey, and A. Landy. 1997. The catalytic domain of lambda site-specific recombinase. Proc. Natl. Acad. Sci. USA 94:6104-6109.
44. Tirumalai, R. S., H. J. Kwon, E. H. Cardente, T. Ellenberger, and A. Landy. 1998. Recognition of core-type DNA sites by lambda integrase. J. Mol. Biol. 279:513-527.
45. Wojciak, J. M., D. Sarkar, A. Landy, and R. T. Clubb. 2002. Arm-site binding by lambda integrase: solution structure and functional characterization of its amino-terminal domain. Proc. Natl. Acad. Sci. USA 99:3434-3439.
46. Yagil, E., L. Dorgai, and R. A. Weisberg. 1995. Identifying determinants of recombination specificity: construction and characterization of chimeric bacteriophage integrases. J. Mol. Biol. 252:163-177.