Mechanical Constraints on Hin Subunit Rotation Imposed by the Fis/Enhancer System and DNA Supercoiling during Site-Specific Recombination

Molecular Cell

Volumn 34, Issue 6, 2009, Pages 746-759

  Dhar, Gautam ^a   Heiss, John K ^a   Johnson, Reid C ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA; PROTEINS

Indexed keywords

CYSTEINE; DNA; FACTOR FOR INVERSION STIMULATION; PROTEIN HIN; RECOMBINASE; TETRAMER; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CHIRALITY; CONTROLLED STUDY; CROSS LINKING; DNA CLEAVAGE; DNA HELIX; DNA RECOMBINATION; DNA STRAND; DNA SUPERCOILING; ENHANCER REGION; ENZYME ACTIVE SITE; ENZYME SUBUNIT; MOLECULAR STABILITY; NUCLEOTIDE SEQUENCE; PROTEIN PROTEIN INTERACTION; SEQUENCE HOMOLOGY;

BINDING SITES; CYSTEINE; DNA NUCLEOTIDYLTRANSFERASES; DNA, SUPERHELICAL; ENHANCER ELEMENTS, GENETIC; FACTOR FOR INVERSION STIMULATION PROTEIN; MODELS, GENETIC; MUTATION; PROMOTER REGIONS, GENETIC; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RECOMBINATION, GENETIC; SALMONELLA;

EID: 67449168156     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2009.05.020     Document Type: Article

References (32)

1. Arnold P.H., Blake D.G., Grindley N.D., Boocock M.R., and Stark W.M. Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. EMBO J. 18 (1999) 1407-1414
2. Aussel L., Barre F.X., Aroyo M., Stasiak A., Stasiak A.Z., and Sherratt D. FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 108 (2002) 195-205
3. Craig N.L., Craigie R., Gellert M., and Lambowitz A.M. Mobile DNA II (2002), ASM Press, Washington, D.C.
4. Dhar G., Sanders E.R., and Johnson R.C. Architecture of the Hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands. Cell 119 (2004) 33-45
5. Grindley N.D.F. The movement of Tn3-like elements: transposition and cointegrate resolution. In: Craig N.L., Craigie R., Gellert M., and Lambowitz A.M. (Eds). Mobile DNA II (2002), ASM Press, Washington, D.C. 272-302
6. Grindley N.D., Whiteson K.L., and Rice P.A. Mechanisms of site-specific recombination. Annu. Rev. Biochem. 75 (2006) 567-605
7. Haykinson M.J., and Johnson R.C. DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J. 12 (1993) 2503-2512
8. Heichman K.A., and Johnson R.C. The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer. Science 249 (1990) 511-517
9. Heichman K.A., Moskowitz I.P., and Johnson R.C. Configuration of DNA strands and mechanism of strand exchange in the Hin invertasome as revealed by analysis of recombinant knots. Genes Dev. 5 (1991) 1622-1634
10. Huber H.E., Iida S., Arber W., and Bickle T.A. Site-specific DNA inversion is enhanced by a DNA sequence element in cis. Proc. Natl. Acad. Sci. USA 82 (1985) 3776-3780
11. Johnson R.C. Bacterial site-specific DNA inversion systems. In: Craig N.L., Craigie R., Gellert M., and Lambowitz A.M. (Eds). Mobile DNA II (2002), ASM Press, Washington, D.C. 230-271
12. Johnson R.C., and Simon M.I. Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell 41 (1985) 781-791
13. Johnson R.C., and Bruist M.F. Intermediates in Hin-mediated DNA inversion: a role for Fis and the recombinational enhancer in the strand exchange reaction. EMBO J. 8 (1989) 1581-1590
14. Kamtekar S., Ho R.S., Cocco M.J., Li W., Wenwieser S.V., Boocock M.R., Grindley N.D., and Steitz T.A. Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination. Proc. Natl. Acad. Sci. USA 103 (2006) 10642-10647
15. Kanaar R., and Cozzarelli N.R. Roles of supercoiled DNA structure in DNA transactions. Curr. Opin. Struct. Biol. 2 (1992) 369-379
16. Kanaar R., van de Putte P., and Cozzarelli N.R. Gin-mediated DNA inversion: product structure and the mechanism of strand exchange. Proc. Natl. Acad. Sci. USA 85 (1988) 752-756
17. Kanaar R., Klippel A., Shekhtman E., Dungan J.M., Kahmann R., and Cozzarelli N.R. Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62 (1990) 353-366
18. Klippel A., Kanaar R., Kahmann R., and Cozzarelli N.R. Analysis of strand exchange and DNA binding of enhancer-independent Gin recombinase mutants. EMBO J. 12 (1993) 1047-1057
19. Li W., Kamtekar S., Xiong Y., Sarkis G.J., Grindley N.D., and Steitz T.A. Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs. Science 309 (2005) 1210-1215
20. Lim H.M., and Simon M.I. The role of negative supercoiling in Hin-mediated site-specific recombination. J. Biol. Chem. 267 (1992) 11176-11182
21. Lim H.M., Lee H.J., Jaxel C., and Nadal M. Hin-mediated inversion on positively supercoiled DNA. J. Biol. Chem. 272 (1997) 18434-18439
22. Merickel S.K., and Johnson R.C. Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro. Mol. Microbiol. 51 (2004) 1143-1154
23. Nollmann M., He J., Byron O., and Stark W.M. Solution structure of the Tn3 resolvase-crossover site synaptic complex. Mol. Cell 16 (2004) 127-137
24. Osuna R., Finkel S.E., and Johnson R.C. Identification of two functional regions in Fis: the N-terminus is required to promote Hin-mediated DNA inversion but not lambda excision. EMBO J. 10 (1991) 1593-1603
25. Radman-Livaja M., Biswas T., Ellenberger T., Landy A., and Aihara H. DNA arms do the legwork to ensure the directionality of lambda site-specific recombination. Curr. Opin. Struct. Biol. 16 (2006) 42-50
26. Rodriguez A.C., and Stock D. Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J. 21 (2002) 418-426
27. Rowland S.J., Stark W.M., and Boocock M.R. Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting. Mol. Microbiol. 44 (2002) 607-619
28. Safo M.K., Yang W.Z., Corselli L., Cramton S.E., Yuan H.S., and Johnson R.C. The transactivation region of the Fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms. EMBO J. 16 (1997) 6860-6873
29. Sanders E.R., and Johnson R.C. Stepwise dissection of the Hin-catalyzed recombination reaction from synapsis to resolution. J. Mol. Biol. 340 (2004) 753-766
30. Stark W.M., Sherratt D.J., and Boocock M.R. Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58 (1989) 779-790
31. Yuan P., Gupta K., and Van Duyne G.D. Tetrameric structure of a serine integrase catalytic domain. Structure 16 (2008) 1275-1286
32. Zieg J., Silverman M., Hilmen M., and Simon M. Recombinational switch for gene expression. Science 196 (1977) 170-172