Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase

Nucleic Acids Research

Volumn 38, Issue 3, 2009, Pages 958-969

  Laprise, Jennifer ^a,b   Yoneji, Sumiko ^a   Gardner, Jeffrey F ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN INTDOT; RECOMBINASE; UNCLASSIFIED DRUG; BACTERIOPHAGE RECEPTOR; DNA; INTEGRASE;

ARTICLE; BASE PAIRING; BINDING SITE; CONTROLLED STUDY; DNA CLEAVAGE; DNA SEQUENCE; DNA STRAND; ENZYME ACTIVITY; ISOMERIZATION; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROTEIN INTERACTION; SEQUENCE HOMOLOGY; BACTEROIDES; CHEMISTRY; ENZYMOLOGY; METABOLISM;

BACTEROIDES;

ATTACHMENT SITES, MICROBIOLOGICAL; BACTEROIDES; DNA; DNA CLEAVAGE; INTEGRASES; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 77950351936     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp927     Document Type: Article

References (48)

1. Macy, J.M. and Probst, I. (1979) The biology of gastrointestinal bacteroides. Ann. Rev. Microbiol., 33, 561-594.
2. Shoemaker, N.B., Vlamakis, H., Hayes, K. and Salyers, A.A. (2001) Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol., 67, 561-568.
3. Whittle, G., Shoemaker, N.B. and Salyers, A.A. (2002) The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes. Cell Mol. Life Sci., 59, 2044-2054.
4. Song, B., Shoemaker, N.B., Gardner, J.F. and Salyers, A.A. (2007) Integration site selection by the Bacteroides conjugative transposon CTnBST. J. Bacteriol., 189, 6594-6601.
5. Vincent Burrus, G.P., Bernard, D. and Guèdon, G. (2002) Conjugative transposons: the tip of the iceberg. Mol. Microbio., 46, 601-610.
6. Shoemaker, N.B., Barber, R.D. and Salyers, A.A. (1989) Cloning and characterization of a Bacteroides conjugal tetracycline-erythromycin resistance element by using a shuttle cosmid vector. J. Bacteriol., 171, 1294-1302.
7. Bedzyk, L.A., Shoemaker, N.B., Young, K.E. and Salyers, A.A. (1992) Insertion and excision of Bacteroides conjugative chromosomal elements. J. Bacteriol., 174, 166-172.
8. Shoemaker, N.B. and Salyers, A.A. (1990) A cryptic 65-kilobase-pair transposonlike element isolated from Bacteroides uniformis has homology with Bacteroides conjugal tetracycline resistance elements. J. Bacteriol., 172, 1694-1702.
9. Esposito, D. and Scocca, J.J. (1997) The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res., 25, 3605-3614.
10. Malanowska, K., Salyers, A.A. and Gardner, J.F. (2006) Characterization of a conjugative transposon integrase, IntDOT. Mol. Microbiol., 60, 1228-1240.
11. Nunes-Duby, S.E., Kwon, H.J., Tirumalai, R.S., Ellenberger, T. and Landy, A. (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res., 26, 391-406.
12. Rajeev, L., Malanowska, K. and Gardner, J.F. (2009) Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbio. Mol. Bio. Rev., 73, 300-309.
13. Cheng, C., Kussie, P., Pavletich, N. and Shuman, S. (1998) Conservation of Structure and Mechanism between Eukaryotic Topoisomerase I and Site-Specific Recombinases. Cell, 92, 841-850.
14. Azaro, M. and Landy, A. (2002) In Craig, N.L., Craigie, R., Gellert, M. and Lambowitz, A.M. (eds), Mobile DNA II. ASM Press, Washington, DC, pp. 119-148.
15. Craig, N.L. and Nash, H.A. (1983) The mechanism of phage lambda site-specific recombination: site-specific breakage of DNA by Int topoisomerase. Cell, 35, 795-803.
16. Nunes-Düby, S.E., Azaro, M.A. and Landy, A. (1995) Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr. Biol., 5, 139-148.
17. McCulloch, R., Coggins, L.W., Colloms, S.D. and Sherratt, D.J. (1994) Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo. EMBO J., 13, 1844-1855.
18. Blakely, G., Colloms, S., May, G., Burke, M. and Sherratt, D. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol., 3, 789-798.
19. Colloms, S.D., McCulloch, R., Grant, K., Neilson, L. and Sherratt, D.J. (1996) Xer-mediated site-specific recombination in vitro. EMBO J., 15, 1172-1181.
20. Nunes-Düby, S.E., Yu, D. and Landy, A. (1997) Sensing homology at the strand-swapping step in lambda excisive recombination. J. Mol. Biol., 272, 493-508.
21. Van Duyne, G.D. (2002) A Structural View of Tyrosine Recombinase Site-specific Recombination. ASM Press, Washington, DC.
22. Nash, H.A. (1983) Purification and properties of the bacteriophage lambda Int protein. Methods Enzymol., 100, 210-216.
23. Trask, D.K., DiDonato, J.A. and Muller, M.T. (1984) Rapid detection and isolation of covalent DNA/protein complexes: application to topoisomerase I and II. EMBO J., 3, 671-676.
24. Cheng, Q., Wesslund, N., Shoemaker, N.B., Salyers, A.A. and Gardner, J.F. (2002) Development of an in vitro integration assay for the Bacteroides conjugative transposon CTnDOT. J. Bacteriol., 184, 4829-4837.
25. Cheng, Q., Paszkiet, B.J., Shoemaker, N.B., Gardner, J.F. and Salyers, A.A. (2000) Integration and excision of a Bacteroides conjugative transposon, CTnDOT. J. Bacteriol., 182, 4035-4043.
26. Malanowska, K., Yoneji, S., Salyers, A.A. and Gardner, J.F. (2007) CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges. Nucleic Acids Res., 35, 5861-5873.
27. Kitts, P.A., Nash, H.A. and Laboratory of Molecular Biology, N.I.o.M.H.B.M.D. (1988) Bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges. J. Mol. Biol., 204, 95-107.
28. Richet, E., Abcarian, P. and Nash, H.A. (1988) Synapsis of attachment sites during lambda integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell, 52, 9-17.
29. Hsu, P.L., Ross, W. and Landy, A. (1980) The lambda phage att site: functional limits and interaction with Int protein. Nature, 285, 85-91.
30. Lee, L. and Sadowski, P.D. (2005) Progress in Nucleic Acid Research and Molecular Biology, Vol. 80. Academic Press, New York, pp. 1-42.
31. Amin, A.A., Beatty, L.G. and Sadowski, P.D. (1990) Synaptic intermediates promoted by the FLP recombinase. J. Mol. Biol., 214, 55-72.
32. Guo, F., Gopaul, D.N. and Van Duyne, G.D. (1999) Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl Acad. Sci. USA, 96, 7143-7148.
33. Martin, S.S., Pulido, E., Chu, V.C., Lechner, T.S. and Baldwin, E.P. (2002) The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex. J. Mol. Biol., 319, 107-127.
34. Lee, L. and Sadowski, P.D. (2003) Sequence of the loxP site determines the order of strand exchange by the Cre recombinase. J. Mol. Biol., 326, 397-412.
35. Hallet, B., Arciszewska, L.K. and Sherratt, D.J. (1999) Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination. Mol. Cell, 4, 949-959.
36. Arciszewska, L.K. and Sherratt, D.J. (1995) Xer site-specific recombination in vitro. EMBO J., 14, 2112-2120.
37. Aussel, L., Barre, F.-X., Aroyo, M., Stasiak, A., Stasiak, A.Z. and Sherratt, D. (2002) FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell, 108, 195-205.
38. Recchia, G.D., Aroyo, M., Wolf, D., Blakely, G. and Sherratt, D.J. (1999) FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J., 18, 5724-5734.
39. Patsey, R.L. and Bruist, M.F. (1995) Characterization of the interaction between the lambda intasome and attB. J. Mol. Biol., 252, 47-58.
40. Ross, W. and Landy, A. (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.
41. Kitts, P.A. and Nash, H.A. (1988) Bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges. J. Mol. Biol., 204, 95-107.
42. Warren, D., Laxmikanthan, G. and Landy, A. (2008) A chimeric Cre recombinase with regulated directionality. Proc. Natl Acad. Sci. USA, 105, 18278-18283.
43. Dichiara, J.M., Mattis, A.N. and Gardner, J.F. (2007) IntDOT interactions with core-and arm-type sites of the conjugative transposon CTnDOT. J. Bacteriol., 189, 2692-2701.
44. Lee, J. and Jayaram, M. (1995) Role of partner homology in DNA recombination. J. Biol. Chem., 270, 4042-4052.
45. Hoess, R.H., Wierzbicki, A. and Abremski, K. (1986) The role of the loxP spacer region in PI site-specific recombination. Nucleic Acids Res., 14, 2287-2300.
46. Weisberg, R.A., Enquist, L.W., Foeller, C. and Landy, A. (1983) Role for DNA homology in site-specific recombination. The isolation and characterization of a site affinity mutant of coliphage lambda. J. Mol. Biol., 170, 319-342.
47. Bauer, C.E., Gardner, J.F. and Gumport, R.I. (1985) Extent of sequence homology required for bacteriophage lambda site-specific recombination. J. Mol. Biol., 181, 187-197.
48. Ross, W. and Landy, A. (1983) Patterns of lambda Int recognition in the regions of strand exchange. Cell, 33, 261-272.