Relating primary structure to function in the Escherichia coli XerD site-specific recombinase

Molecular Microbiology

Volumn 24, Issue 5, 1997, Pages 1071-1082

  Spiers, Andrew J ^a   Sherratt, David J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RECOMBINASE;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CHROMOSOME PAIRING; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE DELETION; GENETIC RECOMBINATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING;

ESCHERICHIA COLI;

EID: 0030832562     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1997.4171784.x     Document Type: Article

References (46)

1. Abremski, K.E., and Hoess, R.H. (1992) Evidence for a second conserved arginine residue in the integrase family of recombination proteins. Prot Eng 5: 87-91.
2. Amin, A.A., and Sadowski, P.D. (1989) Synthesis of an enzymatically active Flp recombinase in vitro: search for a DNA-binding domain. Mol Cell Biol 9: 1987-1995.
3. Arciszewska, L.K., and Sherratt, D.J. (1995) Xer site-specific recombination in vitro. EMBO J 14: 2112-2120.
4. Argos, P., Landy, A., Abremski, K., Egan, J.B., Haggard-Ljungquist, E., Hoess, R.H., Kahn, K.L., Kalionis, B., Narayana, S.V.L., Pierson, L.S., Sternberg, N., and Leong, J.M. (1986) The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J 5: 433-440.
5. Blakely, G.W., and Sherratt, D.J. (1994) Interactions of the site-specific recombinases XerC and XerD with the recombination site dif. Nucleic Acids Res 22: 5613-5620.
6. Blakely, G., and Sherratt, D. (1996) Determinants of selectivity in Xer site-specific recombination. Genes Dev 10: 762-773.
7. 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.
8. Blakely, G., May, G., McCulloch, R., Arciszewska, L.K., Burke, M., Lovett, S.T., and Sherratt, D.J. (1993) Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75: 351-361.
9. Blakely, G.W., Davidson, A.O., and Sherratt, D.J. (1997) Binding and cleavage of nicked substrates by site-specific recombinases XerC and XerD. J Mol Biol 265: 30-39.
10. Chen, J-W., Evans, B.R., Yang, S.-H., Araki, H., Oshima, Y., and Yayaram, M. (1992) Functional analysis of box I mutations in yeast site-specific recombinases Flp and R: pair-wise complementation with recombinase variants lacking the active-site tyrosine. Mol Cell Biol 12: 3757-3765.
11. Colloms, S.D., Sykora, P., Szatmari, G., and Sherratt, D.J. (1990) Recombination at ColE1 requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases. J Bacteriol 172: 6973-6980.
12. 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.
13. Cornet, F., Mortier, I., Patte, J., and Louarn, J.-M. (1994) Plasmid pSC101 harbors a recombination site, psi, which is able to resolve plasmid multimers and to substitute for the analogous chromosomal Escherichia coli site dif. J Bacteriol 176: 3188-3195.
14. Crothers, D.M., Gartenberg, M.R., and Shrader, T.E. (1991) DNA-bending in protein-DNA complexes. Methods Enzymol 208: 118-146.
15. Dorgai, L., Yagil, E., and Weisberg, R.A. (1995) Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J Mol Biol 252: 178-188.
16. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
17. Friesen, H., and Sadowski, P.D. (1992) Mutagenesis of a conserved region of the gene encoding the Flp recombinase of Saccharomyces cerevisiae. J Mol Biol 225: 313-326.
18. Han, Y.W., Gumport, R.I., and Gardner, J.F. (1994) Mapping the functional domains of bacteriophage lambda integrase protein. J Mol Biol 235: 908-925.
19. Hayes, F., and Sherratt, D.J. (1997) Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. J Mol Biol 266: 525-537.
20. Hiraga, S.-I., Sugiyama, T., and Itoh, T. (1994) Comparative analysis of the replicon regions of eleven ColE2-related plasmids. J Bacteriol 176: 7233-7243.
21. Hoess, R.H., Abremski, K., Irwin, S., Kendall, M., and Mack, A. (1990) DNA specificity of the Cre recombinase resides in the 25kDa carboxyl domain of the protein. J Mol Biol 216: 873-882.
22. Hofte, M., Dong, Q., Kourambas, S., Krishnapillai, V., Sherratt, D., and Mergeay, M. (1994) The sss gene product, which affects pyoverdin production in Pseudomonas aeruginosa 7NSK2, is a site-specific recombinase. Mol Microbiol 14: 1011-1020.
23. Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K., and Pease, L.R. (1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77: 61-68.
24. Kim, J., Zwieb, C., Wu, C., and Adhya, S. (1989) Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene 85: 15-23.
25. Kuempel, P.L., Henson, J.M., Dircks, L., Tecklenburg, M., and Lim, D.F. (1991) dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli. New Biol 3: 799-811.
26. Landy, A. (1993) Mechanistic and structural complexity in the site-specific recombination pathways of Int and Flp. Curr Opin Genet Develop 3: 699-707.
27. Lane, D., Prentki, P., and Chandler, M. (1992) Use of gel retardation to analyse protein-nucleic acid interactions. Microbiol Rev 56: 509-528.
28. LeBowitz, J.H., Clerc, R.G., Brenowitz, M., and Sharp, P.A. (1989) The Oct-2 protein binds cooperatively to adjacent octamer sites. Genes Dev 3: 1625-1638.
29. Lovett, S.T., and Kolodner, R.D. (1991) Nucleotide sequence of the Escherichia coli recJ chromosomal region and construction of RecJ-overexpression plasmids. J Bacteriol 173: 353-364.
30. McCulloch, R., Burke, M.E., and Sherratt, D.J. (1994a) Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination. Mol Microbiol 12: 241-251.
31. McCulloch, R., Coggins, L.W., Colloms, S.D., and Sherratt, D.J. (1994b) Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo. EMBO J 13: 1844-1855.
32. Pan, G., and Sadowski, P.D. (1993) Identification of the functional domains of the Flp recombinase. Separation of the non-specific and specific DNA-binding, cleavage, and ligation domains. J Biol Chem 268: 22546-22551.
33. 2- and COOH-terminal domains of the Flp recombinase with the Flp recognition target sequence. J Biol Chem 269: 10940-10945.
34. Prentki, P., and Krisch, H.M. (1984) In vitro insertional mutagenesis with a selectable DNA fragment. Gene 29: 303-313.
35. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
36. Sherratt, D.J. (1993) Site-specific recombination and the segregation of circular chromosomes. Nucleic Acids Mol Biol 7: 203-216.
37. Sirois, S., and Szatmari, G. (1995) Detection of XerC and XerD recombinases in Gram-negative bacteria of the family Enterobacteriaceae. J Bacteriol 177: 4183-4186.
38. Slack, F.J., Serror, P., Joyce, E., and Sonenshein, A.L. (1995) A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol Microbiol 15: 689-702.
39. Stark, W.M., Boocock, M.R., and Sherratt, D.J. (1992) Catalysis by site-specific recombinases. Trends Genet 8: 432-439.
40. Summers, D.K., and Sherratt, D.J. (1984) Multimerization of high copy number plasmids causes instability: ColE1 encodes a determinant essential for plasmid monomerization and stability. Cell 36: 1097-1103.
41. Summers, D.K., and Sherratt, D.J. (1988) Resolution of ColE1 dimers requires DNA sequences implicated in the three dimensional organisation of the cer site. EMBO J 7: 851-858.
42. de Vargas, M.L., Pargellis, C.A., Hasan, N.M., Bushman, E.W., and Landy, A. (1988) Autonomous DNA binding domains of lambda integrase recognise two different sequence families. Cell 54: 923-929.
43. Vossen, K.M., Stickle, D.F., and Fried, M.G. (1996) The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter. J Mol Biol 255: 44-54.
44. Wierzbicki, A., Kendall, M., Abremski, K., and Hoess, R.H. (1987) A mutational analysis of the bacteriophage P1 recombinase Cre. J Mol Biol 195: 785-794.
45. Yagil, E., Dorgai, L., and Weisberg, R.A. (1995) Identifying determinants of recombination specificity: construction and characterization of chimeric bacteriophage integrases. J Mol Biol 252: 162-177.
46. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119.