1887

Chapter 7 : λ Integrase and the λ Int Family

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

λ Integrase and the λ Int Family, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap07-2.gif

Abstract:

This chapter starts with Allan Campbell’s insightful proposal for the pathway by which the chromosome of bacteriophage λ is integrated into and excised from the chromosome of its host. The chapter discusses different levels of λ Int family complexity. There are presently four classes of integron integrases, IntI1 to -4, sharing approximately 50% identity. In contrast to the IntI1 integrase, which has not suggested any striking deviations from its cousins, the integron recombination targets, and , present several new variations on λ Int family themes. Recombination between sites with identical 7-bp spacer regions is not any more efficient than that for two sites differing at five positions. Recent evidence suggests that λ Int may have gone even further in evolving a dependence on arm binding. Whereas full Int binds very poorly to core-type DNA sites, C65 (lacking the N-terminal domain) binds very well. The amino acid and nucleotide residues responsible for distinction have been variously identified by genetic selections, construction of chimeric integrases (via recombination or site-directed mutagenesis), and alteration of core sites. Superimposing the crystal structure of the catalytic domain of vaccinia virus topoisomerase on the coordinates of the previously reported HP1 and Cre recombinase structures, it is apparent that the order and topology of the secondary and tertiary structural elements are strikingly similar. A unified topological mechanism of site-specific recombination by λ integrase family members has remained elusive until fairly recently, in contrast to the well-characterized mechanisms for several enzymes of the resolvase/invertase family.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7

Key Concept Ranking

Gene Expression and Regulation
0.56427073
Chromosomal DNA
0.45591334
Type 1 Fimbriae
0.4323581
DNA Synthesis
0.4252219
0.56427073
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Integrative and excisive recombination pathways. The protein binding sites for arm-type Int (○), core-type Int (⇒), IHF (□), Xis (△), and Fis (◇) are indicated by filled symbols when that site is occupied by its cognate protein to make a competent recombination partner for integrative (⇓) or excisive (⇑) recombination. Required proteins (Int, IHF, and Xis) are in boldface type, and proteins that inhibit (Xis and IHF) or enhance (Fis) the indicated reactions are in italics. The Holliday junction intermediate (square brackets) results from the reciprocal single-strand swap of the 5′ ends liberated by Int cleavage. The three bases of swapped top strands are shown just prior to ligation and formation of the fourway junction. This is followed by conformational changes that allow cleavage, swapping, and ligation of the bottom strands, i.e., resolution of the Holliday junction to yield recombinant products.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Hierarchy of λ Int family attachment sites increasing in complexity from top to bottom. The sites of the heterobivalent recombinases (P2, P22, TnL5, HP1, and λ)are not ordered on the basis of organizational complexity. Nevertheless, their arrangement captures the variability in number, spacing, orientation, and nature of different DNA binding sites within each site. Each site map (except that for topoisomerase)is centered about its respective core region, which consists of the 6- to 8-bp overlap region (i.e., the locus of catalysis and strand exchange)and flanking inverted-repeat coretype protein binding sites (open arrowheads). Topoisomerase functions as a monomer, and therefore just one core site is indicated. Cre exemplifies the simplest recombinases in that it requires only a pair of inverted core sites (per partner). Although Flp, like Cre, needs only a single pair of inverted core sites (per partner), its biological sites contain a third core site adjacent to the functional pair. An inverted pair of core sites is sometimes sufficient for XerCDmediated recombination (e.g., at sites); however, for other substrates, such as XerCD requires participation of the accessory proteins ArgR and PepA (sites not shown). The remaining maps represent the sites of recombinases that are heterobivalent and also require accessory proteins. The intrinsically asymmetric integrase arm-type sites and excisive factor binding sites (Xis or cox sites)are indicated with black arrowheads and hatched arrows, respectively, while IHF binding sites are denoted with open boxes. The Xis site of L5 has not been mapped and is not indicated. The heterobivalent integrase site maps are ordered with the P arms to the left and the P′ arms to the right of the origin, except HP1, which has been reversed. The Tnmap depicts the structure of the circular transposon intermediate postexcision and preintegration. Note that the L5 is interchangeable with the D29 and likewise the HK022 is interchangeable with the λ

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

Domain structure and selected residues of λ Int. The heights of the boxes approximate the different affinities of the three domains for their respective DNA targets. The amino-terminal domain (residues 1 to 64) binds to arm-type sites and includes a single NEM-reactive cysteine (C25). The central CB domain (residues 65 to 169) binds to core-type sites and contains residues in close proximity to DNA, as determined by DNA-sensitive pyridoxal 5′-phosphate (PLP) reactivity with Lys 103, UV zero-length cross-linking to Ala 125-Ala 126, and photoactivated cross-linkingof 4-thio-T to Lys 141. The catalytic domain (residues 170 to 356) contains the most highly conserved λ Int family residues, includingthe catalytic pentad Arg212-Lys 235-His 308-Arg311-His 333 and the activesite nucleophile Tyr342.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4.
Figure 4.

Scheme of Holliday junction formation and resolution at the core sites of (COC′) and (BOB′) during integrative recombination. (a) The core sites are shown synapsed in antiparallel within a tetrameric arrangement of λ integrases. The 5′ terminus of the top strand from each partner substrate is indicated with an open square, and the top-strand and bottomstrand cleavage sites are represented with filled and open arrowheads, respectively. The integrases poised to cleave the top strands in (i.e., bound at C and B) are displayed with hatched ovals, while the integrases poised to cleave bottom strands in (i.e., bound at C′ and B′) are displayed with open ovals. The catalytically active Ints (i.e., at C and B) (accented with triple arrowheads) cleave the top strand of each partner (a), generating a transient enzyme-Tyr-3′-phosphodiester intermediate (not shown), and permit a reciprocal swap of 5′OH-terminated single-strand segments (each approximately 3 nucleotides long that, in turn, displace the covalently bound integrases and create a recombinant joint (black bar). The resulting Holliday junction (b) most closely resembles a top-strand crossed isomer. In this structure the integrases bound to C and B are still primed for cleavage and may reverse the first strand exchange event. The transition from panel b to panel c represents the isomerization of the tetramer-Holliday junction complex required to prime the integrases bound at C′ and B′ to cleave the bottom strands: the arms of the Holliday junction shift in a scissor-like fashion so that the top strands now subtend an obtuse angle while the bottom strands subtend an acute angle, and the branch point shifts approximately one position closer to the bottom strand cleavage sites. (d) The primed integrases execute the second pair of reciprocal swaps to generate the recombinant products (COB′) and (BOC′) by a step drawn here as primarily unidirectional.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5.
Figure 5.

Schematic representation of active-site catalytic residues from λ Int surroundingthe scissile phosphate of a substrate DNA. This model is based on, and representative of, a synthesis of structural and functional data derived from many systems (see text for details and references). For each λ Int residue there is also indicated the correspondingresidue from vaccinia virus topoisomerase (Topo), Cre, HP1, XerD, and Flp. The homologous residues of Topo and Cre are boxed and juxtaposed to their λ counterparts since they are referred to extensively in the text. The diagrammed positions approximate the relative disposition of each amino acid to the element with which it is expected to interact. Members of the canonical Arg-His-Argtriad are Arg 212, His 308, and Arg 311. Arg 212 is shown poised to make bidentate H bonds with the nonbridging oxygens of the scissile phosphate, while His 308 and Arg311 are both oriented to make only monovalent contacts. His 333 most likely interacts with a nonbridging oxygen and probably does not act as a general acid catalyst to assist in 5′OH release. The nucleophilic Tyr 342 is accented with triple arrowheads and is shown poised to execute an inline attack of the scissile phosphate to generate a covalent Tyr-3′-phosphate linkage and a freed 5′OH. Note that the Tyr may be shifted away from its target when the catalytic site is inactive. Lys 235 is a putative general acid catalyst and is shown prepared to donate a proton to the 5′ oxygen. The chirality of the nonbridging oxygens is indicated; note that R and S become R′ and S′ in the covalent complex.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6.
Figure 6.

Differential occupancy of H′ and P′1 sites of that characterize various recombination pathways. Occupied sites are indicated by filled symbols, while vacant sites are indicated by open symbols.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817954.chap7
1. Abraham, J. M.,, C. S. Freitag,, J. R. Clements,, and B. I. Eisenstein. 1985. An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. Proc. Natl. Acad. Sci. USA 82: 5724 5727.
2. Abremski, K. E.,, and S. Gottesman. 1982. Purification of the bacteriophage λ xis gene product required for λ excisive recombination. J. Biol. Chem. 257: 9658 9662.
3. Abremski, K. E.,, and R. H. Hoess. 1992. Evidence for a second conserved arginine residue in the integrase family of recombination proteins. Protein Eng. 5: 87 91.
4. Arciszewska, L.,, I. Grainge,, and D. Sherratt. 1995. Effects of Holliday junction position on Xer-mediated recombination in vitro. EMBO J. 14: 2651 2660.
5. Arciszewska, L. K.,, I. Grainge,, and D. J. Sherratt. 1997. Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J. 16: 3731 3743.
6. Arciszewska, L. K.,, and D. J. Sherratt. 1995. Xer site-specific recombination in vitro. EMBO J. 14: 2112 2120.
7. Argos, W.,, A. Landy,, K. Abremski,, J. B. Egan,, E. Haggard- Ljungquist,, R. H. Hoess,, M. L. Kahn,, W. Kalionis,, S. V. L. Narayana,, L. S. I. Pierson,, N. Sternberg,, and J. M. Leong. 1986. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5: 433 440.
8. Auvray, F.,, M. Coddeville,, G. Espagno,, and P. Ritzenthaler. 1999. Integrative recombination of Lactobacillus delbrueckii bacteriophage mv4: functional analysis of the reaction and structure of the attP site. Mol. Gen. Genet. 262: 355 366.
9. Aviv, M. 1994. Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation. Mol. Microbiol. 14: 1021 1031.
10. Azaro, M. A.,, and A. Landy. 1997. The isomeric preference of Holliday junctions influences resolution bias by λ integrase. EMBO J. 16: 3744 3755.
11. Ball, C. A.,, and R. C. Johnson. 1991. Efficient excision of phage λ from the Escherichia coli chromosome requires the Fis protein. J. Bacteriol. 173: 4027 4031.
12. Ball, C. A.,, and R. C. Johnson. 1991. Multiple effects of Fis on integration and the control of lysogeny in phage λ. J. Bacteriol. 173: 4032 4038.
13. Ball, C. A.,, R. Osuna,, K. C. Ferguson,, and R. C. Johnson. 1992. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol. 174: 8043 8056.
14. Baum, J. A. 1995. TnpI recombinase: identification of sites within Tn 5401 required for TnpI binding and site-specific recombination. J. Bacteriol. 177: 4036 4042.
15. Baum, J. A.,, A. J. Gilmer,, and A.-M. L. Mettus. 1999. Multiple roles for TnpI recombinase in regulation of Tn 401 transposition in Bacillus thuringiensis. J. Bacteriol. 181: 6271 6277.
16. Bear, S. E.,, J. B. Clemens,, L. W. Enquist,, and R. J. Zagursky. 1987. Mutational analysis of the lambda int gene: DNA sequence of dominant mutations. J. Bacteriol. 169: 5880 5883.
17. Better, M.,, S. Wickner,, J. Auerbach,, and H. Echols. 1983. Role of the Xis protein of bacteriophage λ in a specific reactive complex at the attR prophage attachment site. Cell 32: 161 168.
18. Blakely, G.,, G. May,, R. McCulloch,, L. K. Arciszewska,, M. Burke,, S. T. Lovett,, and D. J. Sherratt. 1993. Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75: 351 361.
19. Blakely, G. W.,, and D. J. Sherratt. 1996. cis and trans in site-specific recombination. Mol. Microbiol. 20: 234 237.
20. Blomfield, I. C.,, P. J. Calie,, K. J. Eberhardt,, M. S. McClain,, and B. I. Eisenstein. 1993. Lrp stimulates phase variation of type 1 fimbriation in Escherichia coli K-12. J. Bacteriol. 175: 27 36.
21. Blomfield, I. C.,, D. H. Kulasekara,, and B. I. Eisenstein. 1997. Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli. Mol. Microbiol. 23: 705 717.
22. Breuner, A.,, L. Brondsted,, and K. Hammer. 1999. Novel organization of genes involved in prophage excision identified in the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 181: 7291 7297.
23. Bullock, P.,, J. J. Champoux,, and M. Botchan. 1985. Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination. Science 230: 954 958.
24. Burgin, A. B.,, and H. A. Nash. 1995. Suicide substrates reveal properties of the homology-dependent steps during integrative recombination of bacteriophage λ. Curr. Biol. 5: 1312 1321.
25. Burns, L. S.,, S. G. J. Smith,, and C. J. Dorman. 2000. Interaction of the FimB integrase with the fimS invertible DNA element in Escherichia coli in vivo and in vitro. J. Bacteriol. 182: 2953 2959.
26. Bushman, W.,, J. F. Thompson,, L. Vargas,, and A. Landy. 1985. Control of directionality in lambda site-specific recombination. Science 230: 906 911.
27. Bushman, W.,, S. Yin,, L. L. Thio,, and A. Landy. 1984. Determinants of directionality in lambda site-specific recombination. Cell 39: 699 706.
28. Campbell, A. M., 1962. Episomes, p. 101 145. In E. W. Caspari (ed.), Advances in Genetics, 1st ed. Academic Press, New York, N.Y.
29. Campbell, A. M. 1992. Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174: 7495 7499.
30. Cassell, G.,, M. Klemm,, C. Pinilla,, and A. Segall. 2000. Dissection of bacteriophage λ site-specific recombination usingsynthetic peptide combinatorial libraries. J. Mol. Biol. 299: 1193 1202.
31. Champoux, J. J. 1998. Domains of human topoisomerase I and associated functions. Prog. Nucleic Acid Res. 60: 111 132.
32. Chen, J.-W.,, B. R. Evans,, S.-H. Yang,, H. Araki,, Y. Oshima,, and M. Jayaram. 1992. Functional analysis of box I mutations in yeast site-specific recombinases F1p and R: pairwise complementation with recombinase variants lackingthe active- site tyrosine. Mol. Cell. Biol. 12: 3757 3765.
33. Chen, J.-W.,, J. Lee,, and M. Jayaram. 1992. DNA cleavage in trans by the active site tyrosine duringF1p recombination: switching protein partners before exchanging strands. Cell 69: 647 658.
34. Chen, J.-W.,, S.-H. Yang,, and M. Jayaram. 1993. Tests for the fractional active site model in F1p site-specific recombination: assembly of a functional recombination complex in halfsite and full-site strand transfer. J. Biol. Chem. 268: 14417 14425.
35. Chen, Y.,, U. Narendra,, L. E. Iype,, M. M. Cox,, and P. A. Rice. 2000. Crystal structure of a F1p recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell 6: 885 897.
36. Cheng, C.,, P. Kussie,, N. Pavletich,, and S. Shuman. 1998. Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92: 841 850.
37. Cheng, Q.,, B. M. Swalla,, M. Beck,, R. Alcaraz, Jr.,, R. I. Gumport,, and J. F. Gardner. 2000. Specificity determinants for bacteriophage Hong Kong 022 integrase: analysis of mutants with relaxed core-bindingspecificities. Mol. Microbiol. 36: 424 436.
38. Cho, E. H.,, C.-E. Nam,, R. Alcaraz, Jr.,, and J. F. Gardner. 1999. Site-specific recombination of bacteriophage P22 does not require integration host factor. J. Bacteriol. 181: 4245 4249.
39. Cho, E. H.,, R. Alcaraz, Jr.,, R. I. Gumport,, and J. F. Gardner. 2000. Characterization of bacteriophage lambda excisionase mutants defective in DNA binding. J. Bacteriol. 182: 5807 5812.
40. Christ, N.,, and P. Dröge. 1999. Alterations in the directionality of λ site-specific recombination catalyzed by mutant integrases in vivo. J. Mol. Biol. 288: 825 836.
41. Collis, C. M.,, M.-J. Kim,, H. W. Stokes,, and R. M. Hall. 1998. Binding of the purified integron DNA integrase IntI1, to integron- and cassette-associated recombination sites. Mol. Microbiol. 29: 477 490.
42. Colloms, S. D.,, J. Bath,, and D. J. Sherratt. 1997. Topological selectivity in xer site-specific recombination. Cell 88: 855 864.
43. Colloms, S. D.,, R. McCulloch,, K. Grant,, L. Neilson,, and D. J. Sherratt. 1996. Xer-mediated site-specific recombination in vitro. EMBO J. 15: 1172 1181.
44. Craig, N. L. 1988. The mechanism of conservative site-specific recombination. Annu. Rev. Genet. 22: 77 105.
45. Craig, N. L.,, and H. A. Nash. 1984. E. coli integration host factor binds to specific sites in DNA. Cell 39: 707 716.
46. Crisona, N. J.,, R. L. Weinberg,, B. J. Peter,, D. W. Sumners,, and N. R. Cozzarelli. 1999. The topological mechanism of phage λ integrase. J. Mol. Biol. 289: 747 775.
47. DiGabriele, A. D.,, and T. A. Steitz. 1993. A DNA dodecamer containingan adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol. 231: 1024 1039.
48. DiGabriele, A. D.,, M. R. Sanderson,, and T. A. Steitz. 1989. Crystal lattice packingis important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl. Acad. Sci. USA 86: 1816 1820.
49. Ditto, M. D.,, D. Roberts,, and R. A. Weisberg. 1994. Growth phase variation of integration host factor level in Escherichia coli. J. Bacteriol. 176: 3738 3748.
50. Dodd, I. B.,, M. R. Reed,, and J. B. Egan. 1994. The crolike Ap1 repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site. Mol. Microbiol. 10: 1139 1150.
51. Dorgai, L.,, S. Sloan,, and R. A. Weisberg. 1998. Recognition of core binding sites by bacteriophage integrases. J. Mol. Biol. 277: 1059 1070.
52. Dorgai, L.,, E. Yagil,, and R. A. Weisberg. 1995. Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J. Mol. Biol. 252: 178 188.
53. Dorman, C. J.,, and C. F. Higgins. 1987. Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases. J. Bacteriol. 169: 3840 3843.
54. Drlica, K.,, and J. Rouviere-Yaniv. 1987. Histone-like proteins of bacteria. Microbiol. Rev. 51: 301 319.
55. Duckett, D. R.,, A. I. H. Murchie,, S. Diekmann,, E. von Kitzing,, B. Kemper,, and D. M. J. Lilley. 1988. The structure of the Holliday junction, and its resolution. Cell 55: 79 89.
56. Duckett, D. R.,, A. I. H. Murchie,, and D. M. J. Lilley. 1990. The role of metal ions in the conformation of the four-way DNA junction. EMBO J. 9: 583 590.
57. Echols, H. 1970. Integrative and excisive recombination by bacteriophage λ: evidence for an excision-specific recombination protein. J. Mol. Biol. 47: 575 583.
58. Eisenstein, B. 1981. Phase variation of type 1 fimbriae in Escherichia coli is under transcriptional control. Science 214: 337 339.
59. Eisenstein, B. I.,, D. S. Sweet,, V. Vaughn,, and D. I. Friedman. 1987. Integration host factor is required for the DNA inversion that controls phase variation in Escherichia coli. Proc. Natl. Acad. Sci. USA 84: 6506 6510.
60. Enquist, L. W.,, and R. A. Weisberg. 1984. An integration proficient int mutant of bacteriophage λ. Mol. Gen. Genet. 195: 62 69.
61. Esposito, D.,, and J. J. Scocca. 1997. Purification and characterization of HP1 cox and definition of its role in controlling the direction of site-specific recombination. J. Biol. Chem. 272: 8660 8670.
62. Esposito, D.,, and J. J. Scocca. 1997. The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res. 25: 3605 3614.
63. Evans, B. R.,, J. W. Chen,, R. L. Parsons,, T. K. Bauer,, D. B. Teplow,, and M. Jayaram. 1990. Identification of the active site tyrosine of FLP recombinase. J. Biol. Chem. 265: 18504 18510.
64. Fluit, A. C.,, and F. J. Schmitz. 1999. Class 1 integrons, gene cassettes, mobility, and epidemiology. Eur. J. Clin. Microbiol. Infect. Dis. 18: 761 770.
65. Francia, M. V.,, J. C. Zabala,, F. de la Cruz,, and J. M. G. Lobo. 1999. The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site. J. Bacteriol. 181: 6844 6849.
66. Franz, B.,, and A. Landy. 1995. The Holliday junction intermediates of λ integrative and excisive recombination respond differently to the bending proteins, IHF and Xis. EMBO J. 14: 397 406.
67. Friedman, D. I. 1988. Integration host factor: a protein for all reasons. Cell 55: 545 554.
68. Friesen, H.,, and P. D. Sadowski. 1992. Mutagenesis of a conserved region of the gene encoding the FLP recombinase of Saccharomyces cerevisiae. J. Mol. Biol. 225: 313 326.
69. Futcher, A. B. 1986. Copy number amplification of the 2 micron M circle plasmid of Saccharomyces cerevisiae. J. Theor. Biol. 119: 197 204.
70. Gally, D. L.,, J. Leathart,, and I. C. Blomfield. 1996. Interaction of FimB and FimE with the fim switch that controls the phase variation of type 1 fimbriae in Escherichia coli K-12. Mol. Microbiol. 21: 725 738.
71. Goodman, S. D.,, S. C. Nicholson,, and H. A. Nash. 1992. Deformation of DNA duringsite-specific recombination of bacteriophage λ: replacement of IHF protein by HU protein or sequence-directed bends. Proc. Natl. Acad. Sci. USA 89: 11910 11914.
72. Goodrich, J. A.,, M. L. Schwartz,, and W. R. McClure. 1990. Searchingfor and predictingthe activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18: 4993 5000.
73. Goosen, N.,, and P. van de Putte. 1995. The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16: 1 7.
74. Gopaul, D. N.,, F. Guo,, and G. D. Van Duyne. 1998. Structure of the Holliday junction intermediate in Cre- loxP site-specific recombination. EMBO J. 17: 4175 4187.
75. Granston, A. E.,, and H. A. Nash. 1993. Characterization of a set of integration host factor mutants deficient for DNA binding. J. Mol. Biol. 234: 45 59.
76. Gravel, A.,, B. Fournier,, and P. H. Roy. 1998. DNA complexes obtained with the integron integrase Intl at the att1 site. Nucleic Acids Res. 26: 4347 4355.
77. Gravel, A.,, N. Messier,, and P. H. Roy. 1998. Point mutations in the integron integrase IntI1 that affect recombination and/ or substrate recognition. J. Bacteriol. 180: 5437 5442.
78. Griffith, J. D.,, and H. A. Nash. 1985. Genetic rearrangement of DNA induces knots with a unique topology: implication for the mechanism of synapsis and crossing-over. Proc. Natl. Acad. Sci. USA 82: 3124 3128.
79. Guo, F.,, D. N. Gopaul,, and G. D. Van Duyne. 1997. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389: 40 46.
80. Guo, F.,, D. N. Gopaul,, and G. D. Van Duyne. 1999. Asymmetric DNA-bendingin the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA 96: 7143 7148.
81. Haffter, P.,, and T. A. Bickle. 1987. Purification and DNA-binding properties of FIS and CIN, two proteins required for the bacteriophage P1 site-specific recombination system, cin. J. Mol. Biol. 198: 579 587.
82. Hakimi, J. M.,, and J. J. Scocca. 1994. Bindingsites for bacteriophage HP1 integrase on its DNA substrates. J. Biol. Chem. 269: 21340 21345.
83. Hales, L. M.,, R. I. Gumport,, and J. F. Gardner. 1996. Examiningthe contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes. Nucleic Acids Res. 24: 1780 1786.
84. Hallet, B.,, and D. J. Sherratt. 1997. Transposition and sites-pecific recombination: adaptingDNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev. 21: 157 178.
85. Han, Y. W.,, R. I. Gumport,, and J. F. Gardner. 1993. Complementation of bacteriophage lambda integrase mutants: evidence for an intersubunit active site. EMBO J. 12: 4577 4584.
86. Han, Y. W.,, R. I. Gumport,, and J. F. Gardner. 1994. Mapping the functional domains of bacteriophage lambda integrase protein. J. Mol. Biol. 235: 908 925.
87. Hansson, K.,, O. Skold,, and L. Sundstrom. 1997. Non-palindromic att1 sites of integrons are capable of site-specific recombination with one another and with secondary targets. Mol. Microbiol. 26: 441 453.
88. Henderson, I. R.,, P. Owen,, and J. P. Nataro. 1999. Molecular switches—the ON and OFF bacterial phase variation. Mol. Microbiol. 33: 919 932.
89. Hendrix, R. W.,, J. W. Roberts,, F. W. Stahl,, and R. A. Weisberg (ed.). 1983. Lambda II. Cold SpringHarbor Laboratory, Cold SpringHarbor, N.Y.
90. Hengen, P. N.,, S. L. Bartram,, L. E. Stewart,, and T. D. Schneider. 1997. Information analysis of Fis binding sites. Nucleic Acids Res. 25: 4994 5002.
91. Hershey, A. D. (ed.). 1971. The Bacteriophage Lambda. Cold SpringHarbor Laboratory, Cold SpringHarbor, N.Y.
92. Hickman, A. B.,, S. Waninger,, J. J. Scocca,, and F. Dyda. 1997. Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 Å resolution. Cell 89: 227 237.
93. Hubner, P.,, and W. Arber. 1989. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 8: 577 585.
94. Hwang, E. S.,, and J. J. Scocca. 1990. Interaction of integration host factor from Escherichia coli with the integration region of the Haemophilus influenzae bacteriophage HP1. J. Bacteriol. 172: 4852 4860.
95. Jaxel, C.,, G. Capranico,, D. Kerrigan,, K. W. Kohn,, and Y. Pommier. 1991. Effect of localDNAsequence on topoisomerase I cleavage in the presence or absence of camptothecin. J. Biol. Chem. 266: 20418 20423.
96. Jayaram, M. 1997. The cis-trans paradox of integrase. Science 276: 49 51.
97. Jia, Y.,, and G. Churchward. 1999. Interactions of the integrase protein of the conjugative transposon Tn 916 with its specific DNA binding sites. J. Bacteriol. 181: 6114 6123.
98. Johnson, R. C.,, M. F. Bruist,, and M. I. Simon. 1986. Host protein requirements for in vitro site-specific DNA inversion. Cell 46: 531 539.
99. Kanaar, R.,, A. Klippel,, E. Shekhtman,, J. M. Dungan,, R. Kahmann,, and N. R. Cozzarelli. 1990. Processive recombination by the phageMu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62: 353 366.
100. Kikuchi, A.,, E. Flamm,, and R. A. Weisberg. 1985. An Escherichia coli mutant unable to support site-specific recombination of bacteriophage λ. J. Mol. Biol. 183: 129 140.
101. Kikuchi, Y.,, and H. A. Nash. 1978. The bacteriophage λ int gene product. J. Biol. Chem. 253: 7149 7157.
102. Kim, S.,, L. Moitoso de Vargas,, S. E. Nunes-Düby,, and A. Landy. 1990. Mappingof a higher order protein-DNA complex: two kinds of long-range interactions in λ attL. Cell 63: 773 781.
103. Kim, S.-H.,, and A. Landy. 1992. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science 256: 198 203.
104. Klemm, M.,, C. Cheng,, G. Cassell,, S. Shuman,, and A. M. Segall. 2000. Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases. J. Mol. Biol. 299: 1203 1216.
105. Klemm, P. 1986. Two regulatory fim genes, fimB and fimE, control the phase variation of type 1 fimbriae in Escherichia coli. EMBO J. 5: 1389 1393.
106. Koch, C.,, and R. Kahmann. 1986. Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu. J. Biol. Chem. 261: 15673 15678.
107. Koch, C.,, O. Ninnemann,, H. Fuss,, and R. Kahmann. 1991. The N-terminal part of the E. coli DNA binding protein FIS is essential for stimulating site-specific DNA inversion but is not required for specific DNA binding. Nucleic Acids Res. 19: 5915 5922.
108. Kostrewa, D.,, J. Granzin,, C. Koch,, H.-W. Choe,, J. Labahn,, R. Kahmann,, and W. Saenger. 1991. Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature 349: 178 180.
109. Krogh, B. O.,, and S. Shuman. 2000. Catalytic mechanism of DNA topoisomerase IB. Mol. Cell 5: 1035 1041.
110. Kuhstoss, S.,, and R. N. Rao. 1991. Analysis of the integration function of the streptomycete bacteriophage phi C31. J. Mol. Biol. 222: 897 908.
111. Kulasekara, H. D.,, and I. C. Blomfield. 1999. The molecular basis for the specificity of fimE in the phase variation of type 1 fimbriae of Escherichia coli K-12. Mol. Microbiol. 31: 1171 1181.
112. Kwon, H. J.,, R. S. Tirumalai,, A. Landy,, and T. Ellenberger. 1997. Flexibility in DNA recombination: structure of the λ integrase catalytic core. Science 276: 126 131.
113. Landy, A. 1989. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58: 913 949.
114. Landy, A. 1993. Mechanistic and structural complexity in the site-specific recombination pathways of Int and FLP. Curr. Biol. 3: 699 707.
115. Landy, A.,, and W. Ross. 1977. Viral integration and excision: structure of the lambda att sites. Science 197: 1147 1160.
116. Lee, J.,, and M. Jayaram. 1993. Mechanism of site-specific recombination: logic of assembling recombinase catalytic site from fractional active sites. J. Biol. Chem. 268: 17564 17570.
117. Lee, J.,, and M. Jayaram. 1995. Functional roles of individual recombinase monomers in strand breakage and strand union during site-specific DNA recombination. J. Biol. Chem. 270: 23203 23211.
118. Lee, J.,, and M. Jayaram. 1995. Junction mobility and resolution of Holliday structures by Flp site-specific recombinase. J. Biol. Chem. 270: 19086 19092.
119. Lee, J.,, and M. Jayaram. 1995. Role of partner homology in DNA recombination. J. Biol. Chem. 270: 4042 4052.
120. Lee, J.,, M. C. Serre,, S.-H. Yang,, I. Whang,, H. Araki,, Y. Oshima,, and M. Jayaram. 1992. Functional analysis of box II mutations in yeast site-specific recombinases FLP and R. J. Mol. Biol. 228: 1091 1103.
121. Leffers, G. G., Jr.,, and S. Gottesman. 1998. Lambda Xis degradation in vivo by Lon and FtsH. J. Bacteriol. 180: 1573 1577.
122. Leong, J.,, S. Nunes-Düby,, C. Lesser,, P. Youderian,, M. M. Susskind,, and A. Landy. 1985. Primary structure of the ϕ and P22 attachment sites and their interactions with E. coli integration host factor. J. Biol. Chem. 260: 4468 4477.
123. Lewis, J. A.,, and G. F. Hatfull. 2000. Identification and characterization of mycobacteriophage L5 excisionase. Mol. Microbiol. 35: 350 360.
124. Lilley, D. M. J.,, and R. M. Clegg. 1994. The structure of the four-way junction in DNA. Annu. Rev. Biophys. Biomol. Struct. 22: 299 328.
125. Lorenz, M.,, A. Hillisch,, S. D. Goodman,, and S. Diekmann. 1999. Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer. Nucleic Acids Res. 27: 4619 4625.
126. MacWilliams, M. P.,, R. I. Gumport,, and J. F. Gardner. 1996. Genetic analysis of the bacteriophage λ attL nucleoprotein complex. Genetics 143: 1069 1079.
127. Mahillon, J.,, and D. Lereclus. 1988. Structural and functional analysis of Tn 4430: identification of an integrase-like protein involved in the co-integrate-resolution process. EMBO J. 7: 1515 1526.
128. Matsuura, M.,, T. Noguchi,, D. Yamaguchi,, T. Aida,, M. Asayama,, H. Takahashi,, and M. Shirai. 1996. The sre gene (ORF469) encodes a site-specific recombinase responsible for integration of the R4 phage genome. J. Bacteriol. 178: 3374 3376.
129. Mazel, D.,, B. Dychinco,, V. A. Webb,, and J. Davies. 1998. A distinctive class of integron in the Vibrio cholerae genome. Science 280: 605 608.
130. McClain, M. S.,, I. C. Blomfield,, and B. I. Eisenstein. 1991. Roles of fimB and fimE in site-specific DNA inversion associated with phase variation of type 1 fimbriae in Escherichia coli. J. Bacteriol. 173: 5308 5314.
131. McCulloch, R.,, L. W. Coggins,, S. D. Colloms,, and D. J. Sherratt. 1994. Xer-mediated site-specific recombination at cer generates Holliday junctions in vitro. EMBO J. 13: 1844 1855.
132. Mechulam, Y.,, S. Blanquet,, and G. Fayat. 1987. Dual level control of the Escherichia coli pheST-himA operon expression. J. Mol. Biol. 197: 453 470.
133. Miller, H. I.,, A. Kikuchi,, H. A. Nash,, R. A. Weisberg,, and D. I. Friedman. 1979. Site-specific recombination of bacteriophage?: the role of host gene products. Cold Spring Harbor Symp. Quant. Biol. 43: 1121 1126.
134. Miller, H. I.,, M. Kirk,, and H. Echols. 1981. SOS induction and autoregulation of the himA gene for site-specific recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 78: 6754 6758.
135. Miller, H. I.,, and H. A. Nash. 1981. Direct role of the himA gene product in phage λ integration. Nature 290: 523 526.
136. Mizuuchi, K. 1992. Polynucleotidyl transfer reactions in transpositional DNA recombination. J. Biol. Chem. 267: 21273 21276.
137. Mizuuchi, K.,, M. Gellert,, R. A. Weisberg,, and H. A. Nash. 1980. Catenation and supercoilingin the products of bacteriophage λ integrative recombination in vitro. J. Mol. Biol. 141: 485 495.
138. Moitoso de Vargas, L.,, S. Kim,, and A. Landy. 1989. DNA looping generated by the DNA-bendingprotein IHF and the two domains of lambda integrase. Science 244: 1457 1461.
139. Moitoso de Vargas, L.,, and A. Landy. 1991. A switch in the formation of alternative DNA loops modulates λ site-specific recombination. Proc. Natl. Acad. Sci. USA 88: 588 592.
140. Montanez, C.,, J. Bueno,, U. Schmeissner,, D. L. Court,, and G. Guarneros. 1986. Mutations of bacteriophage lambda that define independent but overlappingRNA processingand transcription termination sites. J. Mol. Biol. 191: 29 37.
141. Murtin, C.,, M. Engelhorn,, J. Geiselmann,, and F. Boccard. 1998. A quantitative UV laser footprintinganalysis of the interaction of IHF with specific bindingsites: re-evaluation of the effective concentration of IHF in the cell. J. Mol. Biol. 284: 949 961.
142. Nagaraja, R.,, and R. A. Weisberg. 1990. Specificity determinants in the attachment sites of bacteriophage HK022 and λ. J. Bacteriol. 172: 6540 6550.
143. Nash, H. A. 1975. Integrative recombination of bacteriophage lambda DNA in vitro. Proc. Natl. Acad. Sci. USA 72: 1072 1076.
144. Nash, H. A. 1981. Integration and excision of bacteriophage lambda: the mechanism of conservative site-specific recombination. Annu. Rev. Genet. 15: 143 167.
145. Nash, H. A. 1990. Bendingand supercoilingof DNA at the attachment site of bacteriophage lambda. Trends Biochem. Sci. 15: 222 227.
146. Nash, H. A., 1996. Site-specific recombination: integration, excision, resolution, and inversion of defined DNA segments, p. 2363 2376. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium, 2nd ed. ASM Press, Washington, D.C.
147. Nash, H. A., 1996. The HU and IHF proteins: accessory factors for complex protein-DNA assemblies, p. 149 179. In E. C. C. Lin, and A. S. Lynch (ed.), Regulation of Gene Expression in Escherichia coli. R. G. Landes Company, Austin, Tex.
148. Nash, H. A.,, and T. J. Pollock. 1983. Site-specific recombination of bacteriophage lambda: the change in topological linkingnumber associated with exchange of DNA strands. J. Mol. Biol. 170: 19 38.
149. Nash, H. A.,, and C. A. Robertson. 1981. Purification and properties of the Escherichia coli protein factor required for λ integrative recombination. J. Biol. Chem. 256: 9246 9253.
150. Nash, H. A.,, C. A. Robertson,, E. Flamm,, R. A. Weisberg,, and H. I. Miller. 1987. Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J. Bacteriol. 169: 4124 4127.
151. Nelson, H. C. M.,, J. T. Finch,, F. L. Bonaventura,, and A. Klug. 1987. The structure of an oligo(dA) oligo(dT) tract and its biological implications. Nature 330: 221 226.
152. Nilsson, L.,, H. Verbeek,, E. Vijgenboom,, C. van Drunen,, A. Vanet,, and L. Bosch. 1992. FIS-dependent trans activation of stable RNA operons of Escherichia coli under various growth conditions. J. Bacteriol. 174: 921 929.
153. Numrych, T. E.,, R. I. Gumport,, and J. F. Gardner. 1992. Characterization of the bacteriophage lambda excisionase (Xis) protein: the C-terminus is required for Xis-integrase cooperativity but not for DNA binding. EMBO J. 11: 3797 3806.
154. Nunes-Düby, S.,, M. A. Azaro,, and A. Landy. 1995. Swapping DNA strands and sensing homology without branch migration in λ site-specific recombination. Curr. Biol. 5: 139 148.
155. Nunes-Düby, S.,, R. S. Tirumalai,, H. J. Kwon,, T. Ellenberger,, and A. Landy. 1998. Similarities and differences among105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26: 391 406.
156. Nunes-Düby, S. E.,, L. I. Smith-Mungo,, and A. Landy. 1995. Single base-pair precision and structural rigidity in a small IHF-induced DNA loop. J. Mol. Biol. 253: 228 242.
157. Nunes-Düby, S. E.,, R. S. Tirumalai,, L. Dorgai,, R. Yagil,, R. Weisberg,, and A. Landy. 1994. λ Integrase cleaves DNA in cis. EMBO J. 13: 4421 4430.
158. Nystrom, T. 1995. Glucose starvation stimulon of Escherichia coli: role of integration host factor in starvation survival and growth phase-dependent protein synthesis. J. Bacteriol. 177: 5707 5710.
159. Osuna, R.,, S. E. Finkel,, and R. C. Johnson. 1991. Identification of two functional regions in Fis: the N-terminus is required to promote Hin-mediated DNA inversion but not λ excision. EMBO J. 10: 1593 1603.
160. Ouellette, M.,, and P. H. Roy. 1987. Homology of ORFs from Tn 2603 and from R46 to site-specific recombinases. Nucleic Acids Res. 15: 10055.
161. Pan, C. Q.,, J. A. Feng,, S. E. Finkel,, R. Landgraf,, D. Sigman,, and R. C. Johnson. 1994. Structure of the Escherichia coli Fis-DNA complex probed by protein conjugated with 1,10- phenanthroline copper(I) complex. Proc. Natl. Acad. Sci. USA 91: 1721 1725.
162. Pan, C. Q.,, S. E. Finkel,, S. E. Cramton,, J. -A. Feng,, D. S. Sigman,, and R. C. Johnson. 1996. Variable structures of Fis- DNA complexes determined by flankingDNA-protein contacts. J. Mol. Biol. 264: 675 695.
163. Pargellis, C. A.,, S. E. Nunes-Düby,, L. Moitoso de Vargas,, and A. Landy. 1988. Suicide recombination substrates yield covalent λ integrase-DNA complexes and lead to identification of the active site tyrosine. J. Biol. Chem. 263: 7678 7685.
164. Parsons, R. L.,, B. R. Evans,, L. Zheng,, and M. Jayaram. 1990. Functional analysis of Arg-308 mutants of Flp recombinase. Possible role of Arg-308 in coupling substrate binding to catalysis. J. Biol. Chem. 265: 4527 4533.
165. Parsons, R. L.,, P. V. Prasad,, R. M. Harshey,, and M. Jayaram. 1988. Step-arrest mutants of FLP recombinase: implications for the catalytic mechanism of DNA recombination. Mol. Cell. Biol. 8: 3303 3310.
166. Partridge, S. R.,, G. D. Recchia,, C. Scaramuzzi,, C. M. Collis,, H. W. Stokes,, and R. M. Hall. 2000. Definition of the attI1 site of class 1 integrons. Microbiology 146: 2855 2864.
167. Pedulla, M. L.,, M. H. Lee,, D. C. Lever,, and G. F. Hatfull. 1996. A novel host factor for integration of mycobacteriophage L5. Proc. Natl. Acad. Sci. USA 93: 15411 15416.
168. Pena, C. E. A.,, M. Kahlenberg,, and G. F. Hatfull. 2000. Assembly and activation of site-specific recombination complexes. Proc. Natl. Acad. Sci. USA 97: 7760 7765.
169. Perkins-Balding, D.,, D. P. Dias,, and A. C. Glasgow. 1997. Location, degree, and direction of DNA bending associated with the Him recombinational enhancer sequence and Fisenhancer complex. J. Bacteriol. 179: 4747 4753.
170. Pollock, T. J.,, and K. Abremski. 1979. DNA without supertwists can be an in vitro substrate for site-specific recombination of bacteriophage λ. J. Mol. Biol. 131: 651 654.
171. Pollock, T. J.,, and H. A. Nash. 1983. Knottingof DNA caused by a genetic rearrangement: evidence for a nucleosome- like structure in site-specific recombination for bacteriophage lambda. J. Mol. Biol. 170: 1 18.
172. Poyart-Salmeron, C.,, P. Trieu-Cuot,, C. Carlier,, and P. Courvalin. 1989. Molecular characterization of two proteins involved in the excision of the conjugative transposon Tn1545: homologies with other site-specific recombinases. EMBO J. 8: 2425 2433.
173. Recchia, G. D.,, and R. M. Hall. 1997. Origins of the mobile gene cassettes found in integrons. Trends Genet. 5: 389 394.
174. Redinbo, M. R.,, J. J. Champoux,, and W. G. J. Hol. 2000. Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Biochemistry 39: 6832 6840.
175. Redinbo, M. R.,, L. Stewart,, P. Kuhn,, J. J. Champoux,, and W. G. J. Hol. 1998. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279: 1504 1513.
176. Reiter, W. D.,, P. Palm,, and S. Yeats. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17: 1907 1914.
177. Rice, P. A. 1997. MakingDNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol. 7: 86 93.
178. Rice, P. A.,, S.-W. Yang,, K. Mizuuchi,, and H. A. Nash. 1996. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87: 1295 1306.
179. Richet, E.,, P. Abcarian,, and H. A. Nash. 1986. The interaction of recombination proteins with supercoiled DNA: definingthe role of supercoilingin lambda integrative recombination. Cell 46: 1011 1021.
180. Richet, E.,, P. Abcarian,, and H. A. Nash. 1988. Synapsis of attachment sites duringlambda integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell 52: 9 17.
181. Ross, W.,, and A. Landy. 1983. Patterns of λ Int recognition in the regions of strand exchange. Cell 33: 261 272.
182. Rowe-Magnus, D. A.,, and D. Mazel. 1999. Resistance gene capture. Curr. Opin. Microbiol. 2: 483 488.
183. Rudy, C. K.,, J. R. Scott,, and G. Churchward. 1997. DNA bindingby the Xis protein of the conjugative transposon Tn 916. J. Bacteriol. 179: 2567 2572.
184. Sadowski, P. D. 1993. Site-specific genetic recombination: hops, flips and flops. FASEB J. 7: 760 767.
185. Safo, M. K.,, W.-Z. Yang,, L. Corselli,, S. E. Cramton,, H. S. Yuan,, and R. C. Johnson. 1997. The transactivation region of the Fis protein that controls site-specific DNA inversion contains extended mobile β-hairpin arms. EMBO J. 16: 6860 6873.
186. Salyers, A.,, N. Shoemaker,, G. Bonheyo,, and J. Frias,. 1999. Conjugative transposons: transmissible resistance islands, p. 331 345. In J. B. Kaper, and J. Hacker (ed.), Pathogenicity Islands and Other Mobile Virulence Elements. American Society for Microbiology, Washington, D.C.
187. Salyers, A. A.,, N. B. Shoemaker,, A. M. Stevens,, and L.-Y. Li. 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59: 579 590.
188. Sandmann, C. 1996. Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures. Proteins 25: 486 500.
189. Sarkar, D.,, M. Radman-Livaja,, and A. Landy. 2001. The small DNA bindingdomain of λ integrase is a context-sensitive modulator of recombinase functions. EMBO J. 20: 1203 1212.
190. Scott, J. R.,, and G. G. Churchward. 1995. Conjugative transposition. Annu. Rev. Microbiol. 49: 367 397.
191. Seeman, N. C.,, and N. R. Kallenbach. 1994. DNA branched junctions. Annu. Rev. Biophys. Biomol. Struct. 23: 53 86.
192. Segall, A. M.,, S. D. Goodman,, and H. A. Nash. 1994. Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA bindingproteins. EMBO J. 13: 4536 4548.
193. Segall, A. M.,, and H. A. Nash. 1993. Synaptic intermediates in bacteriophage lambda site-specific recombination: integrase can align pairs of attachment sites. EMBO J. 12: 4567 4576.
194. Shaikh, A. C.,, and P. D. Sadowski. 1997. The Cre recombinase cleaves the lox site in trans. J. Biol. Chem. 272: 5695 5702.
195. Shaikh, A. C.,, and P. D. Sadowski. 2000. Chimeras of the Flp and Cre recombinases: tests of the mode of cleavage by Flp and Cre. J. Mol. Biol. 302: 27 48.
196. Shuman, S. 1989. Vaccinia DNA topoisomerase I promotes illegitimate recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 86: 3489 3493.
197. Shuman, S. 1991. Site-specific interaction of vaccinia topoisomerase I with duplex DNA. Minimal DNA substrate for strand cleavage in vitro. J. Biol. Chem. 266: 11372 11379.
198. Shuman, S. 1998. Vaccinia virus DNA topoisomerase: a model eukaryotic type IB enzyme. Biochim. Biophys. Acta 1400: 321 337.
199. Shuman, S.,, E. M. Kane,, and S. G. Morham. 1989. Mapping the active-site tyrosine of vaccinia virus DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 86: 9793 9797.
200. Smith-Mungo, L.,, I. T. Chan,, and A. Landy. 1994. Structure of the P22 att site: conservation and divergence in the lambda motif of recombinogenic complexes. J. Biol. Chem. 269: 20798 20805.
201. Spengler, S. J.,, A. Stasiak,, and N. R. Cozzarelli. 1985. The stereostructure of knots and catenanes produced by phage λ integrative recombination: implications for mechanism and DNA structure. Cell 42: 325 334.
202. Stark, W. M.,, and M. R. Boocock. 1995. Gatecrashers at the catalytic party. Trends Genet. 11: 121 123.
203. Stark, W. M.,, and M. R. Boocock,. 1995. Topological selectivity in site-specific recombination, p. 101 129. In D. Sherratt (ed.), Mobile Genetic Elements. Oxford University Press, New York, N.Y.
204. Stark, W. M.,, M. R. Boocock,, and D. J. Sherratt. 1989. Sitespecific recombination by Tn3 resolvase. Trends Genet. 5: 304 309.
205. Stark, W. M.,, M. R. Boocock,, and D. J. Sherratt. 1992. Catalysis by site-specific recombinases. Trends Genet. 8: 432 439.
206. Stark, W. M.,, D. J. Sherratt,, and M. R. Boocock. 1989. Sitespecific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58: 779 790.
207. Stewart, L.,, M. R. Redinbo,, X. Qiu,, W. G. J. Hol,, and J. J. Champoux. 1998. A model for the mechanism of human topoisomerase I. Science 279: 1534 1541.
208. Stokes, H. W.,, D. B. O’Gorman,, G. D. Recchia,, M. Parsekhian,, and R. M. Hall. 1997. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol. Microbiol. 26: 731 745.
209. Su, Y. A.,, and D. B. Clewell. 1993. Characterization of the left 4kb of conjugative transposon Tn916: determinants involved in excision. Plasmid 30: 234 250.
210. Subramanya, H. S.,, L. K. Arciszewska,, R. A. Baker,, L. E. Bird,, D. J. Sherratt,, and D. B. Wigley. 1997. Crystal structure of the site-specific recombinase, XerD. EMBO J. 16: 5178 5187.
211. Tanaka, I.,, K. Appelt,, J. Dijk,, S. W. White,, and K. S. Wilson. 1984. 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature 310: 376 381.
212. Thompson, J. F.,, and A. Landy. 1988. Empirical estimation of protein-induced DNA bendingang les: applications to λ site-specific recombination complexes. Nucleic Acids Res. 16: 9687 9705.
213. Thompson, J. F.,, L. Moitoso de Vargas,, C. Koch,, R. Kahmann,, and A. Landy. 1987. Cellular factors couple recombination with growth phase: characterization of a new component in the λ site-specific recombination pathway. Cell 50: 901 908.
214. Thompson, J. F.,, L. Moitoso de Vargas,, S. E. Skinner,, and A. Landy. 1987. Protein-protein interactions in a higher-order structure direct lambda site-specific recombination. J. Mol. Biol. 195: 481 493.
215. Thompson, J. F.,, D. Waechter-Brulla,, R. I. Gumport,, J. F. Gardner,, L. Moitoso de Vargas,, and A. Landy. 1986. Mutations in an integration host factor-binding site: effect on lambda site-specific recombination and regulatory implications. J. Bacteriol. 168: 1343 1351.
216. Thorpe, H. M.,, and M. C. M. Smith. 1998. In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proc. Natl. Acad. Sci. USA 95: 5505 5510.
217. Tirumalai, R. S.,, E. Healey,, and A. Landy. 1997. The catalytic domain of λ site-specific recombinase. Proc. Natl. Acad. Sci. USA 94: 6104 6109.
218. Tirumalai, R. S.,, H. Kwon,, E. Cardente,, T. Ellenberger,, and A. Landy. 1998. The recognition of core-type DNA sites by λ integrase. J. Mol. Biol. 279: 513 527.
219. Travers, A. 1997. DNA-protein interactions: IHF—the master bender. Curr. Biol. 7: R252 R254.
220. Trieu-Cuot, P.,, C. Poyart-Salmeron,, C. Carlier,, and P. Courvalin. 1994. Sequence requirements for target activity in site specific recombination mediated by the Int protein of transposon Tn 1545. Mol. Microbiol. 8: 179 185.
221. Volkert, F. C.,, and J. R. Broach. 1986. Site-specific recombination promotes plasmid amplification in yeast. Cell 46: 541 550.
222. Wang, J. C. 1996. DNA topoisomerases. Annu. Rev. Biochem. 65: 635 692.
223. Wasserman, S. A.,, J. M. Dungan,, and N. R. Cozzarelli. 1985. Discovery of a predicted DNA knot substantiates a model for site-specific recombination. Science 229: 171 174.
224. Weisberg, R.,, and A. Landy,. 1983. Site-specific recombination in phage lambda, p. 211 250. In R. W. Hendrix,, J. W. Roberts,, F. W. Stahl,, and R. A. Weisberg(ed.), Lambda II. Cold SpringHarbor Laboratory, Cold SpringHarbor, N.Y.
225. Weisberg, R. A.,, and M. E. Gottesman,. 1971. The stability of Int and Xis functions, p. 489 500. In A. D. Hershey (ed.), The Bacteriophage Lambda. Cold SpringHarbor Laboratory, Cold SpringHarbor, N.Y.
226. Weisberg, R. A.,, M. E. Gottesman,, R. W. Hendrix,, and J. W. Little. 1999. Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022. Annu. Rev. Genet. 33: 565 602.
227. White, S. W.,, K. Appelt,, K. S. Wilson,, and I. Tanaka. 1989. A protein structural motif that bends DNA. Proteins 5: 281 288.
228. Wierzbicki, A.,, M. Kendall,, K. Abremski,, and R. Hoess. 1987. A mutational analysis of the bacteriophage P1 recombinase Cre. J. Mol. Biol. 195: 785 794.
229. Wittschieben, J.,, and S. Shuman. 1997. Mechanism of DNA transesterification by vaccinia topoisomerase: catalytic contributions of essential residues Arg-130, Gly-132, Tyr-136 and Lys-167. Nucleic Acids Res. 25: 3001 3008.
230. Woodfield, G.,, C. Cheng,, S. Shuman,, and A. B. Burgin. 2000. Vaccinia topoisomerase and Cre recombinase catalyze direct ligation of activated DNA substrates containing a 3′- paranitrophenyl phosphate ester. Nucleic Acids Res. 28: 3323 3331.
231. Wu, Z.,, R. I. Gumport,, and J. F. Gardner. 1998. Defining the structural and functional roles of the carboxyl region of the bacteriophage lambda excisionase (Xis) protein. J. Mol. Biol. 281: 651 661.
232. Yagil, E.,, L. Dorgai,, and R. Weisberg. 1995. Identifying determinants of recombination specificity: construction and characterization of chimeric bacteriophage integrases. J. Mol. Biol. 252: 163 177.
233. Yang, C.-C.,, and H. A. Nash. 1989. The interaction of E. coli IHF protein with its specific bindingsites. Cell 57: 869 880.
234. Yang, S.,, and H. A. Nash. 1995. Comparison of protein bindingto DNA in vivo and in vitro: definingan effective intracellular target. EMBO J. 14: 6292 6300.
235. Yin, S.,, W. Bushman,, and A. Landy. 1985. Interaction of λ site-specific recombination protein Xis with attachment site DNA. Proc. Natl. Acad. Sci. USA 82: 1040 1044.
236. Yu, A.,, and E. Haggaård-Ljungquist. 1993. Characterization of the bindingsites of two proteins involved in the bacteriophage P2 site-specific recombination system. J. Bacteriol. 175: 1239 1249.
237. Yu, A.,, and E. Haggård-Ljungquist. 1993. The Cox protein is a modulator of directionality in bacteriophage P2 site-specific recombination. J. Bacteriol. 175: 7848 7855.
238. Yuan, H. S.,, S. E. Finkel,, J.-A. Feng,, M. Kaczor-Grzeskowiak,, R. C. Johnson,, and R. E. Dickerson. 1991. The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. Proc. Natl. Acad. Sci. USA 88: 9558 9562.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error