Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway

Journal of Molecular Biology

Volumn 346, Issue 2, 2005, Pages 493-504

  Vazquez, Mariel ^a   Colloms, Sean D ^b   Sumners, De Witt ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c FLORIDA STATE UNIVERSITY   (United States)

Author keywords

DNA knots; site specific recombination; tangle equations; topological mechanism; Xer recombination

Indexed keywords

RECOMBINASE; UNCLASSIFIED DRUG; XER PROTEIN;

ANALYTIC METHOD; ARTICLE; EXPERIMENT; MATHEMATICAL ANALYSIS; MOLECULAR BIOLOGY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; TANGLE ANALYSIS;

EID: 12544251405     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.11.055     Document Type: Article

References (41)

1. P.D. Sadowski Site-specific genetic recombination: hops, flips, and flops FASEB J. 7 1993 760 767
2. B. Hallet, and D.J. Sherratt Transposition and site-specific recombination adapting DNA cut-and-paste mechanism to a variety of genetic rearrangements FEMS Microbiol. Rev. 1997 21
3. N.R. Cozzarelli, M.A. Kraznow, S.P. Gerrard, and J.H. White A topological treatment of recombination and topoisomerases Cold Spring Harbor Symp. Quant. Biol. 49 1984 383 400
4. W.M. Stark, and M.R. Boocock Topological selectivity in site-specific recombination D.J. Sherratt Mobile Genetic Elements 1995 IRL Press at Oxford University Oxford 101 129
5. D.W. Sumners, C. Ernst, N.R. Cozzarelli, and S.J. Spengler Mathematical analysis of the mechanisms of DNA recombination using tangles Quart. Rev. Biophys. 28 1995 253 313
6. A. Landy Coming or going its another pretty picture for the lambda-Int family album Proc. Natl Acad. Sci. USA 96 1999 7122 7124
7. S.E. Nunes-Düby, H.J. Kwon, R.S. Tirumalai, T. Ellenberger, and A. Landy Similarities and differences among 105 members of the Int family of site-specific recombinases Nucl. Acids Res. 26 1998 391 406
8. W.M. Stark, M.R. Boocock, and D.J. Sherratt Catalysis by site-specific recombinases Trends Genet. 8 1992 432 439
9. M. Vazquez, and D.W. Sumners Tangle analysis of Gin site-specific recombination Math. Proc. Cambridge Phil. Soc. 136 2004 565 582
10. C. Ernst, and D.W. Sumners A calculus for rational tangles: applications to DNA recombination Math. Proc. Cambridge Phil. Soc. 108 1990 489 515
11. M.J. McIlwraith, M.R. Boocock, and W.M. Stark Tn3 resolvase catalyses multiple recombination events without intermediate rejoining of DNA ends J. Mol. Biol. 266 1997 108 121
12. S.A. Wasserman, J.M. Dungan, and N.R. Cozzarelli Discovery of a predicted DNA knot substantiates a model for site-specific recombination Science 229 1985 171 174
13. N.J. Crisona, R.L. Weinberg, B.J. Peter, D.W. Sumners, and N.R. Cozzarelli The topological mechanism of phage lambda integrase J. Mol. Biol. 289 1999 747 775
14. I. Grainge, D. Buck, and M. Jayaram Geometry of site alignment during Int family recombination: antiparallel synapsis by the FLP recombinase J. Mol. Biol. 298 2000 749 764
15. S.D. Colloms, J. Bath, and D.J. Sherratt Topological selectivity in Xer site-specific recombination Cell 88 1997 855 864
16. I. Darcy Biological distances on DNA knots and links: applications to Xer recombination J. Knot Theory Ramif. 10 2001 269 294
17. D.K. Summers, and D.J. Sherratt Multimerization of high copy number plasmids causes instability: ColE1 encodes a determinant essential for plasmid monomerization and stability Cell 36 1984 1097 1103
18. C. Alén, D.J. Sherratt, and S.D. Colloms Direct interaction of aminopeptidase A with recombination site DNA in Xer site-specific recombination EMBO J. 16 1997 5188 5197
19. J. Bath, D.J. Sherratt, and S.D. Colloms Topology of Xer recombination on catenanes produced by lambda integrase J. Mol. Biol. 289 1999 873 883
20. S.D. Colloms, R. McCulloch, K. Grant, L. Neilson, and D.J. Sherratt Xer-mediated site-specific recombination in vitro EMBO J. 15 1996 1172 1181
21. R. McCulloch, W. Coggins, S.D. Colloms, and D.J. Sherratt Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo EMBO J. 13 1994 1844 1855
22. M. Bregu, D.J. Sherratt, and S.D. Colloms Accessory factors determine the order of strand exchange in Xer recombination at psi EMBO J. 21 2002 3888 3897
23. K. Murasugi Knot Theory, Its Applications (Translated by B. Kurpita) 1996 Birkhauser Boston, MA
24. D. Rolfsen Knots Mathematics Lecture Series 7 1976 Publish or Perish Berkeley, CA
25. G. Burde, and H. Zieschang Knots P. Gabriel de Gruytier Studies in Mathematics vol. 5 1985 Walter de Gruyter Berlin
26. J.H. Conway An enumeration of knots and links, and some of their algebraic properties Computational Problems in Abstract Algebra 1967 Pergamon Oxford, UK pp. 329-358
27. J.R. Goldman, and L.H. Kauffman Rational tangles Advan. Appl. Math. 18 1997 300 332
28. C. Ernst, and D.W. Sumners Solving tangle equations arising in a DNA recombination model Math. Proc. Cambridge Phil. Soc. 126 1999 23 36
29. Y. Saka, and M. Vazquez TangleSolve: topological analysis of site-specific recombination Bioinformatics 18 2002 1011 1012
30. Vazquez, M. (2000). Tangle analysis of site-specific recombination: Gin and Xer systems. PhD dissertation in mathematics, Florida State University, Tallahassee, FL.
31. G.D. Van Duyne A structural view of Cre-loxP site-specific recombination Annu. Rev. Biophys. Biomol. Struct. 30 2001 87 104
32. L.K. Arciszewska, and D.J. Sherratt Xer site-specific recombination in vitro EMBO J. 14 1995 2112 2120
33. W.M. Stark, D.J. Sherratt, and M.R. Boocock Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions Cell 58 1989 779 790
34. S.C. Gourlay, and S.D. Colloms Control of Cre recombination by regulatory elements from Xer recombination systems Mol. Microbiol. 52 2004 53 65
35. D.N. Gopaul, F. Guo, and G.D. Van Duyne Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination EMBO J. 17 1998 4175 4187
36. N. Sträter, D.J. Sherratt, and S.D. Colloms X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination EMBO J. 18 1999 4513 4522
37. W.B.R. Lickorish Prime knots and tangles Trans. Am. Math. Soc. 267 1981 321 332
38. S.A. Bleiler Knots prime on many strings Trans. Am. Math. Soc. 282 1984 385 401
39. M. Hirasawa, and K. Shimokawa Dehn surgeries on strongly invertible knots which yield lens spaces Proc. Am. Math. Soc. 128 2000 3445 3451
40. C. Ernst Tangle equations J. Knot Theory Ramif. 5 1996 145 159
41. C. Ernst Tangle equations II J. Knot Theory Ramif. 6 1997 1 11