Control of directionality in the DNA strand-exchange reaction catalysed by the tyrosine recombinase TnpI

Nucleic Acids Research

Volumn 38, Issue 6, 2009, Pages 2044-2056

  Vanhooff, Virginie ^a,c   Normand, Christophe ^a,d   Galloy, Christine ^a,e   Segall, Anca M ^b   Hallet, Bernard ^a  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c NV Roche SA   (Belgium)

^d Université Paul Sabatier   (France)

^e Eppendorf Array Technologies   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN TNPI; RECOMBINASE; TYROSINE; UNCLASSIFIED DRUG; DNA POLYMERASE; TNPI RECOMBINASE;

ARTICLE; BINDING AFFINITY; CHROMOSOME PAIRING; CONTROLLED STUDY; DNA RECOMBINATION; DNA REPAIR; DNA SEQUENCE; DNA STRAND; DNA STRAND EXCHANGE; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; SYNAPSE; TRANSPOSON; AMINO ACID SEQUENCE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; DNA CLEAVAGE; GENETIC RECOMBINATION; METABOLISM; PROTEIN MOTIF;

SYNAPSIS;

AMINO ACID MOTIFS; BIOCATALYSIS; DNA CLEAVAGE; DNA NUCLEOTIDYLTRANSFERASES; MODELS, MOLECULAR; RECOMBINASES; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, AMINO ACID;

EID: 77951243564     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1187     Document Type: Article

References (49)

1. Craig,N., Craigie,R., Gellert,M. and Lambowitz,A. (2002) (eds), Mobile DNA II. ASM Press, Washington, DC.
2. Hallet,B. and Sherratt,D.J. (1997) Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev., 21, 157-178.
3. Curcio,M.J. and Derbyshire,K.M. (2003) The outs and ins of transposition: from mu to kangaroo. Nat. Rev. Mol. Cell Biol., 4, 865-877.
4. Van Duyne,G.D. (2001) A structural view of cre-loxp site-specific recombination. Annu. Rev. Biophys. Biomol. Struct., 30, 87-104.
5. Grindley,N.D., Whiteson,K.L. and Rice,P.A. (2006) Mechanisms of site-specific recombination. Annu. Rev. Biochem., 75, 567-605.
6. Chen,Y. and Rice,P.A. (2003) New insight into site-specific recombination from Flp recombinase-DNA structures. Annu. Rev. Biophys. Biomol. Struct., 32, 135-159.
7. Grainge,I. and Jayaram,M. (1999) The integrase family of recombinase: organization and function of the active site. Mol. Microbiol., 33, 449-456.
8. Sherratt,D.J. and Wigley,D.B. (1998) Conserved themes but novel activities in recombinases and topoisomerases. Cell, 93, 149-152.
9. Aihara,H., Huang,W.M. and Ellenberger,T. (2007) An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Mol. Cell, 27, 901-913.
10. Kobryn,K. and Chaconas,G. (2002) ResT, a telomere resolvase encoded by the Lyme disease spirochete. Mol. Cell, 9, 195-201.
11. Nunes-Duby,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.
12. 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.
13. Chen,Y., Narendra,U., Iype,L.E., Cox,M.M. and Rice,P.A. (2000) Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell, 6, 885-897.
14. 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.
15. Guo,F., Gopaul,D.N. and Van Duyne,G.D. (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature, 389, 40-46.
16. MacDonald,D., Demarre,G., Bouvier,M., Mazel,D. and Gopaul,D.N. (2006) Structural basis for broad DNA-specificity in integron recombination. Nature, 440, 1157-1162.
17. Lee,L. and Sadowski,P.D. (2005) Strand selection by the tyrosine recombinases. Prog. Nucleic Acid Res. Mol. Biol., 80, 1-42.
18. Hallet,B., Vanhooff,V. and Cornet,F. (2004) DNA site-specific resolution systems. In Funnell,B. and Phillips,G. (eds), Plasmid Biology. ASM Press, Washington, DC, pp. 145-179.
19. Vanhooff,V., Galloy,C., Agaisse,H., Lereclus,D., Revet,B. and Hallet,B. (2006) Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol. Microbiol., 60, 617-629.
20. Sambrook,J., Fritsch,E.F. and Maniatis,T. (2009) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
21. Cassell,G., Klemm,M., Pinilla,C. and Segall,A. (2000) Dissection of bacteriophage lambda site-specific recombination using synthetic peptide combinatorial libraries. J. Mol. Biol., 299, 1193-1202.
22. 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.
23. Turlan,C., Loot,C. and Chandler,M. (2004) IS911 partial transposition products and their processing by the Escherichia coli RecG helicase. Mol. Microbiol., 53, 1021-1033.
24. Val,M.E., Bouvier,M., Campos,J., Sherratt,D., Cornet,F., Mazel,D. and Barre,F.X. (2005) The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae. Mol. Cell, 19, 559-566.
25. Crisona,N.J., Weinberg,R.L., Peter,B.J., Sumners,D.W. and Cozzarelli,N.R. (1999) The topological mechanism of phage lambda integrase. J. Mol. Biol., 289, 747-775.
26. Grainge,I., Buck,D. and Jayaram,M. (2000) Geometry of site alignment during int family recombination: antiparallel synapsis by the Flp recombinase. J. Mol. Biol., 298, 749-764.
27. Klemm,M., Cheng,C., Cassell,G., Shuman,S. and Segall,A.M. (2000) Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases. J. Mol. Biol., 299, 1203-1216.
28. Parsons,R.L., Prasad,P.V., Harshey,R.M. and Jayaram,M. (1988) Step-arrest mutants of FLP recombinase: implications for the catalytic mechanism of DNA recombination. Mol. Cell Biol., 8, 3303-3310.
29. Zhu,X.D. and Sadowski,P.D. (1995) Cleavage-dependent ligation by the FLP recombinase. Characterization of a mutant FLP protein with an alteration in a catalytic amino acid. J. Biol. Chem., 270, 23044-23054.
30. Franz,B. and Landy,A. (1995) The Holliday junction intermediates of lambda integrative and excisive recombination respond differently to the bending proteins integration host factor and excisionase. EMBO J., 14, 397-406.
31. 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.
32. Nunes-Duby,S.E., Matsumoto,L. and Landy,A. (1987) Site-specific recombination intermediates trapped with suicide substrates. Cell, 50, 779-788.
33. 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.
34. Bregu,M., Sherratt,D.J. and Colloms,S.D. (2002) Accessory factors determine the order of strand exchange in Xer recombination at psi. EMBO J., 21, 3888-3897.
35. Azaro,M. and Landy,A. (2002) Lambda integrase and the lambda int family. In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A. (eds), Mobile DNA II. ASM Press, Washington, DC, pp. 118-148.
36. 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.
37. Yates,J., Zhekov,I., Baker,R., Eklund,B., Sherratt,D.J. and Arciszewska,L.K. (2006) Dissection of a functional interaction between the DNA translocase, FtsK, and the XerD recombinase. Mol.Microbiol., 59, 1754-1766.
38. Colloms,S.D., Bath,J. and Sherratt,D.J. (1997) Topological selectivity in Xer site-specific recombination. Cell, 88, 855-864.
39. Reijns,M., Lu,Y., Leach,S. and Colloms,S.D. (2005) Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex. Mol. Microbiol., 57, 927-941.
40. Ferreira,H., Sherratt,D. and Arciszewska,L. (2001) Switching catalytic activity in the XerCD site-specific recombination machine. J. Mol. Biol., 312, 45-57.
41. Whiteson,K.L., Chen,Y., Chopra,N., Raymond,A.C. and Rice,P.A. (2007) Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chem. Biol., 14, 121-129.
42. Gelato,K.A., Martin,S.S. and Baldwin,E.P. (2005) Reversed DNA strand cleavage specificity in initiation of Cre-LoxP recombination induced by the His289Ala active-site substitution. J. Mol. Biol., 354, 233-245.
43. Ghosh,K., Lau,C.K., Guo,F., Segall,A.M. and Van Duyne,G.D. (2005) Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination. J. Biol. Chem., 280, 8290-8299.
44. Radman-Livaja,M., Shaw,C., Azaro,M., Biswas,T., Ellenberger,T. and Landy,A. (2003) Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex. Mol. Cell, 11, 783-794.
45. Arciszewska,L.K., Baker,R.A., Hallet,B. and Sherratt,D.J. (2000) Coordinated control of XerC and XerD catalytic activities during Holliday junction resolution. J. Mol. Biol., 299, 391-403.
46. Azaro,M.A. and Landy,A. (1997) The isomeric preference of Holliday junctions influences resolution bias by lambda integrase. EMBO J., 16, 3744-3755.
47. Ghosh,K., Lau,C.K., Gupta,K. and Van Duyne,G.D. (2005) Preferential synapsis of loxP sites drives ordered strand exchange in Cre-loxP site-specific recombination. Nat. Chem. Biol., 1, 275-282.
48. Lee,L. and Sadowski,P.D. (2001) Directional resolution of synthetic holliday structures by the Cre recombinase. J. Biol. Chem., 276, 31092-31098.
49. 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.