Source: http://www.asmscience.org/content/book/10.1128/9781555817640.chap26
Timestamp: 2019-04-21 08:43:15+00:00

Document:
This chapter talks about four different families of transposable DNA elements and describes how transposon-mediated recombination molds the organization of the bacterial chromosome. The four families were divided based on the proteins they encode for their mobility: (i) the DDE transposons, which include the majority of the classical bacterial elements such as IS3, IS50 (Tn5), IS10 (Tn10), Tn3, and phage Mu; (ii) the rolling circle transposons, called Y2-transposons and include IS91; (iii) the Y-transposons, which include the conjugative transposon Tn916; and (iv) the Stransposons, a newly recognized family that includes IS1535, IS607, and themobilizable transposon Tn4451. The mechanisms of transposition for each of these four families are very different, although the end products may often look quite similar. Their features were summarized in order to illustrate the different ways a transposon can move from one site to another and the different types of chromosomal rearrangement they can create. It is thought that immunity plays a key role in protecting a transposon from the damaging effects of its own transposition. Immunity in Tn7 parallels that of Mu, with TnsB and TnsC playing the roles of MuA and MuB. The author has compared and contrasted four families of transposable elements found in bacteria. Each family has developed distinct ways of translocating defined segments of DNA, although there are some unifying themes and many of the end products look identical.
Comparison of the mechanisms of transposition utilized by the four transposon families. The figure highlights the major differences between transposition pathways; for specific details, see the text, Table 1, and Fig. 3 , Fig. 7 , Fig. 9 , and Fig. 10 . Heavy bar, transposon DNA; thin line, flanking donor DNA; thick line, target DNA; vertical arrows, sites of target cleavage; dashed bar, newly replicated DNA; boxed arrowhead, target duplication; circled Y or S, covalent phosphotyrosine or phosphoserine linkages of recombinase to DNA; open circles, exposed 3′-OH nucleophile. The fate of the donor DNA is not fully determined for nonreplicative transposition and is indicated by a question mark. Major differences to note are initial strand-cleavage events, transposase-DNA covalent linkages, role of DNA replication, circular intermediates, target-site duplications, and fate of the donor DNA.
Intermolecular transposition can result in a simple insertion or a cointegrate, irrespective of the transposition pathway. Shown vertically are the expected transposition products for cut-and-paste and replicative integration. Each results in a target duplication, but only the replicative pathway duplicates the transposon and fuses the donor and target replicons. The question mark in the upper product for cut-and-paste transposition indicates that the fate of the donor DNA is unclear; the double-strand gap may be repaired, or the DNA may be degraded (see text and Fig. 6d for more details). Cointegrates can be reduced to form the target with a simple insertion and the initial donor, either by site-specific resolution or by homologous recombination between each transposon copy. Homologous recombination between donor and simple insertion product can also generate cointegrates. Dimerization of the donor plasmid followed by cut-and-paste transposition of the two transposons and intervening donor DNA (a composite transposon) will also result in a cointegrate. Symbols are as described in the legend to Fig. 1 .
Comparison of DDE transposition mechanisms (see text for details). Although, for simplicity, transposons are represented as straight lines, all transposase-mediated processes occur within a complex of two transposon ends and transposase. Cleavage at the ends of Tn7 (but not of the other elements shown) also requires the presence of the target DNA. Symbols are as described in Fig. 1. A and B for the Tn7 pathway indicate the TnsA and TnsB proteins required for cleavage at the 5′ and 3′ ends of the transposon, respectively; black triangles indicate the sites of transposase-mediated hydrolysis; scissile phosphates (P in a circle) are the sites of concerted cleavage and strand joining by the indicated 3′-OH nucleophile (connecting arrows). Note that for IS911 transposition, the initial strand-transfer event generates a figure-eight molecule, which is probably resolved by replication (not shown) to regenerate the parent molecule and a transposon circle with left and right ends separated by a few nucleotides. Nicking at each transposon end then linearizes the transposon circle. Adapted from reference 69.
Intramolecular transposition. The figure shows how nonreplicative (a and b) and IS911-like (c) elements can generate adjacent deletions and inversions even though each forms an excised, linear transposon intermediate. In each case, transposition involves a composite transposon, or ends from two transposons in the sister chromosome pathway (b). Note that duplicative inversion, as shown in panel b, is not associated with any DNA loss, in contrast to deletion-inversions (a and c). Cut-and-paste transposons can also transpose to intramolecular targets if transposition is associated with replication (d). The fate of the donor is unclear (indicated by brackets). The chromosome may be degraded, or it may be rescued by gap repair using the sister chromosome as a template.
Switching from cut-and-paste transposition to replicative integration by Tn7 and IS903. Transposition of both elements is consistent with efficient cleavage of the 5′ ends of the transposon to generate an excised transposon (shown on the left), which is then integrated to form a simple insertion. TnsA mutants (B+ and A–) of Tn7 fail to cleave at the 5′ ends of Tn7 and form strand-transfer intermediates. Mutations in IS903 located either at the transposon termini (IRm) or close to the transposase active site (Tnpm) result in elevated levels of cointegrate formation consistent with formation of the strand-transfer intermediate.
Intramolecular transposition by elements that integrate replicatively generates adjacent deletions or adjacent inversions. The outcome of this event is determined simply by transposon-target strand connections. Symbols are as for Fig. 1. A, B, C, and D are four hypothetical genes used to depict the inversion event.
Two models for rolling circle transposition. Left, the model of Mendiola et al. ( 109 ); right, the model of Tavakoli et al. ( 166 ). See the text for details. The Y2-transposase, which binds to the ori end of the transposon, cleaves 3′ to the sequence GTTC. ter is the second site of transposase cleavage and defines the 3′ end of the ssDNA form of the transposon.
The ends of Tn916, showing binding sites for the transposition proteins. The heavy line is Tn916; the thin lines are the flanking DNA. Binding sites for the two domains of Int (the Y-transposase) are shown as arrowheads: black and white indicate sites for the C-terminal catalytic domain (the white arrowheads are the variable sites acquired from each target DNA); gray indicates sites for the N-terminal arm-site binding domain. Barred arrows indicate the Xis binding sites.
Mechanism of Y-transposon excision. The heavy lines are the transposon ends, and the thin lines are the flanking donor DNA. The dashed portions represent the coupling sequences—the 6-bp duplex segment between the cleavage sites. YOH, the free tyrosine nucleophiles; Y-, the covalent tyrosine-DNA linkages; O, free 5′ OHs positioned to attack the phosphotyrosine covalent linkages. Curved arrows show the nucleophilic attack of the YOH on the DNA cleavage site. The shaded asymmetric shapes represent the Y-transposase; dark subunits are in the active conformation, light subunits are inactive. Note the switch of both subunit activities and DNA conformations at the isomerization step. Transposon insertion involves synapsis of an excised transposon and a target site and occurs by reversal of the entire process. Adapted from reference 176 .
Mechanism of S-transposon excision. The heavy lines are the transposon ends, and the thin lines are the flanking donor DNA. The cartoon shows the two DNA duplexes separated by a tetramer of S-transposase catalytic domains, as proposed in a recent model for synapsis by Aresolvase ( 147 ). The shaded subunits are bound to the junction at the transposon&apos;s right end. SOH, the free serine nucleophiles; S-, the covalent serine-DNA linkages; O, free 3′ OHs. Curved arrows show the coordinated nucleophilic attacks of SOH on the DNA cleavage sites (top panel) or 3′ OHs on the phosphoserines (third panel). Note that in this model, strand switching is accompanied by switching of the recombinase catalytic domains, since the two are covalently linked. Transposon insertion involves synapsis of an excised transposon and a target site, and occurs by reversal of the entire process. For further details, see the text.
1. Abraham, L. J.,, and J. I. Rood. 1987. Identification of Tn 4451 and Tn 4452, chloramphenicol resistance transposons from Clostridium perfringens. J. Bacteriol. 169: 1579– 1584.
2. Adzuma, K.,, and K. Mizuuchi. 1989. Interaction of proteins located at a distance along DNA: mechanism of target immunity in the Mu DNA strand-transfer reaction. Cell 57: 41– 47.
3. Adzuma, K.,, and K. Mizuuchi. 1988. Target immunity of Mu transposition reflects a differential distribution of Mu B protein. Cell 53: 257– 266.
4. Arciszewska, L. K.,, D. Drake,, and N. L. Craig. 1989. Transposon Tn7. cis-acting sequences in transposition and transposition immunity. J. Mol. Biol. 207: 35– 52.
5. Arthur, A.,, and D. Sherratt. 1979. Dissection of the transposition process: a transposon-encoded site-specific recombination system . Mol. Gen. Genet. 175: 267– 274.
6. Azaro, M. A.,, and A. Landy,. 2002. λ integrase and the λ Int family, p. 118– 148. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
7. Bainton, R. J.,, K. M. Kubo,, J. N. Feng,, and N. L. Craig. 1993. Tn7 transposition: target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system. Cell 72: 931– 943.
8. Baker, T. A.,, and L. Luo. 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. USA 91: 6654– 6658.
9. Bannam, T. L.,, P. K. Crellin,, and J. I. Rood. 1995. Molecular genetics of the chloramphenicol-resistance transposon Tn4451 from Clostridium perfringens: the TnpX site-specific recombinase excises a circular transposon molecule. Mol. Microbiol. 16: 535– 551.
10. Bastos, M. C.,, and E. Murphy. 1988. Transposon Tn554 encodes three products required for transposition. EMBO J. 7: 2935– 2941.
11. Belfort, M.,, V. Derbyshire,, M. M. Parker,, B. Cousineau,, and A. M. Lambowitz,. 2002. Mobile introns: pathway and proteins, p. 761– 783. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
12. Berg, D. E.,, and M. M. Howe (ed.). 1989. Mobile DNA. American Society for Microbiology, Washington, D.C.
13. Bernales, I.,, M. V. Mendiola,, and F. de la Cruz. 1999. Intramolecular transposition of insertion sequence IS91 results in second-site simple insertions. Mol. Microbiol. 33: 223– 234.
14. Bhasin, A.,, I. Y. Goryshin,, and W. S. Reznikoff. 1999. Hairpin formation in Tn5 transposition. J. Biol. Chem. 274: 37021– 37029.
15. Biery, M. C.,, F. J. Stewart,, A. E. Stellwagen,, E. A. Raleigh,, and N. L. Craig. 2000. A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis. Nucleic Acids Res. 28: 1067– 1077.
16. Bilcock, D. T.,, and S. E. Halford. 1999. DNA restriction dependent on two recognition sites: activities of the SfiI restriction- modification system in Escherichia coli. Mol. Microbiol. 31: 1243– 1254.
17. Bolland, S.,, and N. Kleckner. 1996. The three chemical steps of Tn10/IS10 transposition involve repeated utilization of a single active site. Cell 84: 223– 233.
18. Bujacz, G.,, J. Alexandratos,, A. Wlodawer,, G. Merkel,, M. Andrake,, R. A. Katz,, and A. M. Skalka. 1997. Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. J. Biol. Chem. 272: 18161– 18168.
19. Bujacz, G.,, M. Jaskolski,, J. Alexandratos,, A. Wlodawer,, G. Merkel,, R. A. Katz,, and A. M. Skalka. 1996. The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Structure 4: 89– 96.
20. Bujacz, G.,, M. Jaskolski,, J. Alexandratos,, A. Wlodawer,, G. Merkel,, R. A. Katz,, and A. M. Skalka. 1995. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253: 333– 346.
21. Bult, C. J.,, O. White,, G. J. Olsen,, L. Zhou,, R. D. Fleischmann,, G. G. Sutton,, J. A. Blake,, L. M. FitzGerald,, R. A. Clayton,, J. D. Gocayne,, A. R. Kerlavage,, B. A. Dougherty,, J. F. Tomb,, M. D. Adams,, C. I. Reich,, R. Overbeek,, E. F. Kirkness,, K. G. Weinstock,, J. M. Merrick,, A. Glodek,, J. L. Scott,, N. S. Geoghagen,, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058– 1073.
22. Bushman, F. 2002. Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
23. Caillaud, F.,, and P. Courvalin. 1987. Nucleotide sequence of the ends of the conjugative shuttle transposon Tn1545. Mol. Gen. Genet. 209: 110– 115.
24. Caparon, M. G.,, and J. R. Scott. 1989. Excision and insertion of the conjugative transposon Tn916 involves a novel recombination mechanism. Cell 59: 1027– 1034.
25. Celli, J.,, and P. Trieu-Cuot. 1998. Circularization of Tn916 is required for expression of the transposon-encoded transfer functions: characterization of long tetracycline-inducible transcripts reading through the attachment site. Mol. Microbiol. 28: 103– 117.
26. Chaconas, G.,, and R. M. Harshey,. 2002. Transposition of phage Mu DNA, p. 384– 402. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
27. Chalmers, R.,, A. Guhathakurta,, H. Benjamin,, and N. Kleckner. 1998. IHF modulation of Tn10 transposition: sensory transduction of supercoiling status via a proposed protein/DNA molecular spring. Cell 93: 897– 908.
28. Chalmers, R. M.,, and N. Kleckner. 1996. IS10/Tn10 transposition efficiently accommodates diverse transposon end configurations. EMBO J. 15: 5112– 5122.
29. Chandler, M.,, and J. Mahillon,. 2002. Insertion sequences revisited, p. 305– 366. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington D.C.
30. Cheng, Q.,, B. J. Paszkiet,, N. B. Shoemaker,, J. F. Gardner,, and A. A. Salyers. 2000. Integration and excision of a Bacteroides conjugative transposon, CTnDOT. J. Bacteriol. 182: 4035– 4043.
31. Cheng, Q.,, Y. Sutanto,, N. B. Shoemaker,, J. F. Gardner,, and A. A. Salyers. 2001. Identification of genes required for excision of CTnDOT, a Bacteroides conjugative transposon. Mol. Microbiol. 41: 625– 632.
32. Churchward, G., 2002. Conjugative transposons and related mobile elements, p. 177– 191. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
33. Clewell, D. B.,, S. E. Flannagan,, and D. D. Jaworski. 1995. Unconstrained bacterial promiscuity: the Tn916-Tn1545 family of conjugative transposons. Trends Microbiol. 3: 229– 236.
34. Cole, S. T.,, R. Brosch,, J. Parkhill,, T. Garnier,, C. Churcher,, D. Harris,, S. V. Gordon,, K. Eiglmeier,, S. Gas,, C. E. Barry III,, F. Tekaia,, K. Badcock,, D. Basham,, D. Brown,, T. Chillingworth,, R. Connor,, R. Davies,, K. Devlin,, T. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, B. G. Barrell, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537– 544.
35. Craig, N. L. 1997. Target site selection in transposition. Annu. Rev. Biochem. 66: 437– 474.
36. Craig, N. L., 2002. Tn7, p. 423– 456. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
37. Craig, N. L., 1996. Transposition, p. 2339– 2362. 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: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
38. Craig, N. L. 1996. V(D)J recombination and transposition: closer than expected. Science 271: 1512.
39. Craig, N. L.,, R. Craigie,, M. Gellert,, and A. M. Lambowitz. 2002. Mobile DNA II. ASM Press, Washington, D.C.
40. Craigie, R.,, and K. Mizuuchi. 1985. Mechanism of transposition of bacteriophage Mu: structure of a transposition intermediate. Cell 41: 867– 876.
41. Crellin, P. K.,, and J. I. Rood. 1997. The resolvase/invertase domain of the site-specific recombinase TnpX is functional and recognizes a target sequence that resembles the junction of the circular form of the Clostridium perfringens transposon Tn4451. J. Bacteriol. 179: 5148– 5156.
41a. Curcio, M. J.,, and K. Derbyshire. 2003. The ins and outs of transposition: from Mu to Kangaroo. Nat. Rev. Mol. Cell. Biol. 4: 865– 877.
42. Davies, D. R.,, I. Y. Goryshin,, W. S. Reznikoff,, and I. Rayment. 2000. The three-dimensional structure of the Tn5 synaptic complex intermediate. Science 289: 77– 85.
43. DeBoy, R. T.,, and N. L. Craig. 2000. Target site selection by Tn7: attTn7 transcription and target activity. J. Bacteriol. 182: 3310– 3313.
44. DeBoy, R. T.,, and N. L. Craig. 1996. Tn7 transposition as a probe of cis interactions between widely separated (190 kilobases apart) DNA sites in the Escherichia coli chromosome. J. Bacteriol. 178: 6184– 6191.
45. del Solar, G.,, R. Giraldo,, M. J. Ruiz-Echevarria,, M. Espinosa,, and R. Diaz-Orejas. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62: 434– 464.
46. Derbyshire, K. M.,, and N. D. Grindley. 1986. Replicative and conservative transposition in bacteria. Cell 47: 325– 327.
47. Dyda, F.,, A. B. Hickman,, T. M. Jenkins,, A. Engelman,, R. Craigie,, and D. R. Davies. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266: 1981– 1986.
48. Engelman, A.,, and R. Craigie. 1992. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66: 6361– 6369.
49. Engels, W. R.,, D. M. Johnson-Schlitz,, W. B. Eggleston,, and J. Sved. 1990. High-frequency P element loss in Drosophila is homolog dependent. Cell 62: 515– 525.
50. Firth, N.,, K. Ippen-Ihler,, and R. A. Skurray,. 1996. Structure and function of the F factor and mechanism of conjugation, p. 2377– 2401. 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: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
51. Flannagan, S. E.,, and D. B. Clewell. 1991. Conjugative transfer of Tn916 in Enterococcus faecalis: trans activation of homologous transposons. J. Bacteriol. 173: 7136– 7141.
52. Fugmann, S. D.,, I. J. Villey,, L. M. Ptaszek,, and D. G. Schatz. 2000. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol. Cell 5: 97– 107.
53. Garcillan-Barcia, M. P.,, I. Bernales,, M. V. Mendiola,, and F. de la Cruz,. 2002. IS91 rolling-circle transposition, p. 891– 904. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
54. Garcillan-Barcia, M. P.,, I. Bernales,, M. V. Mendiola,, and F. de la Cruz. 2001. Single-stranded DNA intermediates in IS91 rolling-circle transposition. Mol. Microbiol. 39: 494– 501.
55. Gawron-Burke, C.,, and D. B. Clewell. 1982. A transposon in Streptococcus faecalis with fertility properties. Nature 300: 281– 284.
56. Gormley, N. A.,, A. L. Hillberg,, and S. E. Halford. 2001. The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of its recognition sequence. J. Biol. Chem. 29: 29.
57. Goryshin, I. Y.,, J. A. Miller,, Y. V. Kil,, V. A. Lanzov,, and W. S. Reznikoff. 1998. Tn5/IS50 target recognition. Proc. Natl. Acad. Sci. USA 95: 10716– 10721.
58. Grindley, N. D. F., 2002. The movement of Tn3-like elements: transposition and cointegrate resolution, p. 272– 302. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
59. Grindley, N. D. F., 1994. Resolvase-mediated site-specific recombination, p. 236– 267. In F. Eckstein, and D. M. J. Lilley (ed.), Nucleic Acids and Molecular Biology, vol. 8. Springer-Verlag, Berlin, Germany.
60. Grindley, N. D. F.,, and R. R. Reed. 1985. Transpositional recombination in prokaryotes. Annu. Rev. Biochem. 54: 863– 896.
61. Groth, A. C.,, E. C. Olivares,, B. Thyagarajan, andM. P. Calos. 2000. A phage integrase directs efficient site-specific integration in human cells. Proc. Natl. Acad. Sci. USA 97: 5995– 6000.
62. Guyer, M. S. 1978. The gamma delta sequence of F is an insertion sequence. J. Mol. Biol. 126: 347– 365.
63. Haapa-Paananen, S.,, H. Rita,, and H. Savilahti. 2002. DNA transposition of bacteriophage Mu: a quantitative analysis of target site selection in vitro. J. Biol. Chem. 277: 2843– 2851.
64. Hagemann, A. T.,, and N. L. Craig. 1993. Tn7 transposition creates a hotspot for homologous recombination at the transposon donor site. Genetics 133: 9– 16.
65. Hallet, B.,, and D. J. Sherratt. 1997. Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev. 21: 157– 178.
66. Halling, S. M.,, and N. Kleckner. 1982. A symmetrical six-basepair target site sequence determines Tn10 insertion specificity. Cell 28: 155– 163.
67. Hanai, R.,, and J. C. Wang. 1993. The mechanism of sequence- specific DNA cleavage and strand transfer by phi X174 gene A* protein. J. Biol. Chem. 268: 23830– 23836.
68. Haniford, D. B., 2002. Transposon Tn10, p. 457– 483. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
69. Haren, L.,, B. Ton-Hoang,, and M. Chandler. 1999. Integrating DNA: transposases and retroviral integrases. Annu. Rev. Microbiol. 53: 245– 281.
70. Harshey, R. M. 1984. Transposition without duplication of infecting bacteriophage Mu DNA. Nature 311: 580– 581.
71. Hickman, A. B.,, Y. Li,, S. V. Mathew,, E. W. May,, N. L. Craig,, and F. Dyda. 2000. Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol. Cell 5: 1025– 1034.
72. Hinerfeld, D.,, and G. Churchward. 2001. Xis protein of the conjugative transposon Tn916 plays dual opposing roles in transposon excision. Mol. Microbiol. 41: 1459– 1467.
73. Hochhut, B.,, J. Marrero,, and M. K. Waldor. 2000. Mobilization of plasmids and chromosomal DNA mediated by the SXT element, a constin found in Vibrio cholerae O139. J. Bacteriol. 182: 2043– 2047.
74. Hochhut, B.,, and M. K. Waldor. 1999. Site-specific integration of the conjugal Vibrio cholerae SXT element into prfC. Mol. Microbiol. 32: 99– 110.
75. Hosking, S. L.,, M. E. Deadman,, E. R. Moxon,, J. F. Peden,, N. J. Saunders,, and N. J. High. 1998. An in silico evaluation of Tn916 as a tool for generalized mutagenesis in Haemophilus influenzae Rd. Microbiology 144: 2525– 2530.
76. Hu, W.-Y.,, and K. M. Derbyshire. 1998. Target choice and orientation preference of the insertion sequence IS903. J. Bacteriol. 180: 3039– 3048.
77. Hu, W. Y.,, W. Thompson,, C. E. Lawrence,, and K. M. Derbyshire. 2001. Anatomy of a preferred target site for the bacterial insertion sequence IS903. J. Mol. Biol. 306: 403– 416.
78. Iida, S.,, and R. Hiestand-Nauer. 1986. Localized conversion at the crossover sequences in the site-specific DNA inversion system of bacteriophage P1. Cell 45: 71– 79.
79. Jilk, R. A.,, J. C. Makris,, L. Borchardt,, and W. S. Reznikoff. 1993. Implications of Tn5-associated adjacent deletions. J. Bacteriol. 175: 1264– 1271.
80. Johnson, R. C., 2002. Bacterial site-specific DNA inversion systems, p. 230– 271. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
81. Johnson, R. C.,, and M. F. Bruist. 1989. Intermediates in Hin-mediated DNA inversion: a role for Fis and the recombinational enhancer in the strand exchange reaction. EMBO J. 8: 1581– 1590.
82. Joyce, C. M.,, and T. A. Steitz. 1994. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63: 777– 822.
83. Junop, M. S.,, and D. B. Haniford. 1997. Factors responsible for target site selection in Tn10 transposition: a role for the DDE motif in target DNA capture. EMBO J. 16: 2646– 2655.
84. Kapitonov, V. V.,, and J. Jurka. 2001. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. USA 98: 8714– 8719.
85. Kennedy, A. K.,, A. Guhathakurta,, N. Kleckner,, and D. B. Haniford. 1998. Tn10 transposition via a DNA hairpin intermediate. Cell 95: 125– 134.
86. Kennedy, A. K.,, D. B. Haniford,, and K. Mizuuchi. 2000. Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity. Cell 101: 295– 305.
87. Kersulyte, D.,, A. K. Mukhopadhyay,, M. Shirai,, T. Nakazawa,, and D. E. Berg. 2000. Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J. Bacteriol. 182: 5300– 5308.
88. Kim, D. R.,, Y. Dai,, C. L. Mundy,, W. Yang,, and M. A. Oettinger. 1999. Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13: 3070– 3080.
89. Kim, K.,, S. Y. Namgoong,, M. Jayaram,, and R. M. Harshey. 1995. Step-arrest mutants of phage Mu transposase. Implications in DNA-protein assembly, Mu end cleavage, and strand transfer. J. Biol. Chem. 270: 1472– 1479.
90. Kitts, P. A.,, and H. A. Nash. 1987. Homology-dependent interactions in phage lambda site-specific recombination. Nature 329: 346– 348.
91. Kleckner, N. 1981. Transposable elements in prokaryotes. Annu. Rev. Genet. 15: 341– 404.
92. Kuduvalli, P. N.,, J. E. Rao,, and N. L. Craig. 2001. Target DNA structure plays a critical role in Tn7 transposition. EMBO J. 20: 924– 932.
93. Kulkosky, J.,, K. S. Jones,, R. A. Katz,, J. P. Mack,, and A. M. Skalka. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12: 2331– 2338.
94. Landree, M. A.,, J. A. Wibbenmeyer,, and D. B. Roth. 1999. Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev. 13: 3059– 3069.
95. Landy, A. 1989. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58: 913– 949.
96. Lanka, E.,, and B. M. Wilkins. 1995. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64: 141– 169.
97. Lewis, L. A.,, and N. D. Grindley. 1997. Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway. Mol. Microbiol. 25: 517– 529.
98. Lodge, J. K.,, and D. E. Berg. 1990. Mutations that affect Tn5 insertion into pBR322: importance of local DNA supercoiling. J. Bacteriol. 172: 5956– 5960.
99. Lovell, S.,, I. Y. Goryshin,, W. R. Reznikoff,, and I. Rayment. 2002. Two-metal active site binding of a Tn5 transposase synaptic complex. Nat. Struct. Biol. 9: 278– 281.
100. Lu, F.,, and G. Churchward. 1994. Conjugative transposition: Tn916 integrase contains two independent DNA binding domains that recognize different DNA sequences. EMBO J. 13: 1541– 1548.
101. Lyras, D.,, and J. I. Rood. 2000. Transposition of Tn4451 and Tn4453 involves a circular intermediate that forms a promoter for the large resolvase, TnpX. Mol. Microbiol. 38: 588– 601.
102. Mahillon, J.,, and M. Chandler. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62: 725– 774.
103. Manna, D.,, and N. P. Higgins. 1999. Phage Mu transposition immunity reflects supercoil domain structure of the chromosome. Mol. Microbiol. 32: 595– 606.
104. Manna, D.,, X. Wang,, and N. P. Higgins. 2001. Mu and IS1 transpositions exhibit strong orientation bias at the Escherichia coli bgl locus. J. Bacteriol. 183: 3328– 3335.
105. Marra, D.,, and J. R. Scott. 1999. Regulation of excision of the conjugative transposon Tn916. Mol. Microbiol. 31: 609– 621.
106. 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.
107. May, E. W.,, and N. L. Craig. 1996. Switching from cut-and- paste to replicative Tn7 transposition. Science 272: 401– 404.
108. McBlane, J. F.,, D. C. van Gent,, D. A. Ramsden,, C. Romeo,, C. A. Cuomo,, M. Gellert,, M. A. Oettinger,, G. Bujacz,, J. Alexandratos,, A. Wlodawer,, G. Merkel,, M. Andrake,, R. A. Katz,, and A. M. Skalka. 1995. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83: 387– 395.
109. Mendiola, M. V.,, I. Bernales,, and F. de la Cruz. 1994. Differential roles of the transposon termini in IS91 transposition. Proc. Natl. Acad. Sci. USA 91: 1922– 1926.
110. Mendiola, M. V.,, and F. de la Cruz. 1992. IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids. Nucleic Acids Res. 20: 3521.
111. Mizuuchi, K. 1983. In vitro transposition of bacteriophage Mu: a biochemical approach to a novel replication reaction. Cell 35: 785– 794.
112. Mizuuchi, K. 1984. Mechanism of transposition of bacteriophage Mu: polarity of the strand transfer reaction at the initiation of transposition. Cell 39: 395– 404.
112a. Mizuuchi, K.,, and T. A. Baker,. 2002. Chemical mechanisms for mobilizing DNA, p. 12– 23. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
113. Mizuuchi, M.,, T. A. Baker,, and K. Mizuuchi. 1992. Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70: 303– 311.
114. Mizuuchi, M.,, and K. Mizuuchi. 1993. Target site selection in transposition of phage Mu. Cold Spring Harbor Symp. Quant. Biol. 58: 515– 523.
115. Moitoso de Vargas, L.,, C. A. Pargellis,, N. M. Hasan,, E. W. Bushman,, and A. Landy. 1988. Autonomous DNA binding domains of l integrase recognize two different sequence families. Cell 54: 923– 929.
116. Mullany, P.,, M. Wilks,, I. Lamb,, C. Clayton,, B. Wren,, and S. Tabaqchali. 1990. Genetic analysis of a tetracycline resistance element from Clostridium difficile and its conjugal transfer to and from Bacillus subtilis. J. Gen. Microbiol. 136: 1343– 1349.
117. Nakai, H.,, and R. Kruklitis. 1995. Disassembly of the bacteriophage Mu transposase for the initiation of Mu DNA replication. J. Biol. Chem. 270: 19591– 19598.
118. Nash, H. A. 1981. Integration and excision of bacteriophage l: the mechanism of conservative site specific recombination. Annu. Rev. Genet. 15: 143– 167.
119. 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: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
120. Naumann, T. A.,, and W. S. Reznikoff. 2000. Trans catalysis in Tn5 transposition. Proc. Natl. Acad. Sci. USA 97: 8944– 8949.
121. Nunes-Duby, S. E.,, D. Yu,, and A. Landy. 1997. Sensing homology at the strand-swapping step in lambda excisive recombination. J. Mol. Biol. 272: 493– 508.
122. O’Keeffe, T.,, C. Hill,, and R. P. Ross. 1999. In situ inversion of the conjugative transposon Tn916 in Enterococcus faecium DPC3675. FEMS Microbiol. Lett. 173: 265– 271.
123. Peters, J. E.,, and N. L. Craig. 2001. Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev. 15: 737– 747.
124. Peters, J. E.,, and N. L. Craig. 2000. Tn7 transposes proximal to DNA double-strand breaks and into regions where chromosomal DNA replication terminates. Mol. Cell 6: 573– 582.
125. Plasterk, R. H.,, and J. T. Groenen. 1992. Targeted alterations of the Caenorhabditis elegans genome by transgene instructed DNA double strand break repair following Tc1 excision. EMBO J. 11: 287– 290.
126. Polard, P.,, B. Ton-Hoang,, L. Haren,, M. Betermier,, R. Walczak,, and M. Chandler. 1996. IS911-mediated transpositional recombination in vitro. J. Mol. Biol. 264: 68– 81.
127. 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.
128. Pribil, P. A.,, and D. B. Haniford. 2000. Substrate recognition and induced DNA deformation by transposase at the target-capture stage of Tn10 transposition. J. Mol. Biol. 303: 145– 159.
129. Reynolds, A. E.,, J. Felton,, and A. Wright. 1981. Insertion of DNA activates the cryptic bgl operon in E. coli K12. Nature 293: 625– 629.
130. Reznikoff, W. S., 2002. Tn5 transposition, p. 403– 422. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
131. Rezsohazy, R.,, B. Hallet,, J. Delcour,, and J. Mahillon. 1993. The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol. Microbiol. 9: 1283– 1295.
132. Rice, P.,, and K. Mizuuchi. 1995. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82: 209– 220.
133. Rice, P. A.,, and T. A. Baker. 2001. Comparative architecture of transposase and integrase complexes. Nat. Struct. Biol. 8: 302– 307.
134. Rice, P. A.,, R. Craigie,, and D. R. Davies. 1996. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6: 76– 83.
135. Richet, E.,, P. Abcarian,, and H. A. Nash. 1988. Synapsis of attachment sites during lambda integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell 52: 9– 17.
136. Roberts, D.,, B. C. Hoopes,, W. R. McClure,, and N. Kleckner. 1985. IS10 transposition is regulated by DNA adenine methylation. Cell 43: 117– 130.
137. Roberts, D. E.,, D. Ascherman,, and N. Kleckner. 1991. IS10 promotes adjacent deletions at low frequency. Genetics 128: 37– 43.
138. Roberts, R. J.,, and D. Macelis. 2001. REBASE—restriction enzymes and methylases. Nucleic Acids Res. 29: 268– 269.
139. Roth, D. B.,, and N. L. Craig. 1998. VDJ recombination: a transposase goes to work. Cell 94: 411– 414.
140. Roth, J. R.,, N. Benson,, T. Galitski,, K. Haack,, J. G. Lawrence,, and L. Miesel,. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 2256– 2276. 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:Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
141. Rousseau, P.,, C. Normand,, C. Loot,, C. Turlan,, R. Alazard,, G. Duval-Valentin,, and M. Chandler,. 2002. Transposition of IS911, p. 367– 383. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
142. Rudy, C.,, K. L. Taylor,, D. Hinerfeld,, J. R. Scott,, and G. Churchward. 1997. Excision of a conjugative transposon in vitro by the Int and Xis proteins of Tn916. Nucleic Acids Res. 25: 4061– 4066.
143. Rudy, C. K.,, and J. R. Scott. 1994. Length of the coupling sequence of Tn916. J. Bacteriol. 176: 3386– 3388.
144. Rudy, C. K.,, J. R. Scott,, and G. Churchward. 1997. DNA binding by the Xis protein of the conjugative transposon Tn916. J. Bacteriol. 179: 2567– 2572.
145. Sakai, J.,, R. M. Chalmers,, and N. Kleckner. 1995. Identification and characterization of a pre-cleavage synaptic complex that is an early intermediate in Tn10 transposition. EMBO J. 14: 4374– 4383.
146. Sarkar, D.,, M. Radman-Livaja,, and A. Landy. 2001. The small DNA binding domain of lambda integrase is a context-sensitive modulator of recombinase functions. EMBO J. 20: 1203– 1212.
147. Sarkis, G. J.,, L. L. Murley,, A. E. Leschziner,, M. R. Boocock,, W. M. Stark,, and N. D. Grindley. 2001. A model for the gamma delta resolvase synaptic complex. Mol. Cell 8: 623– 631.
148. Sarnovsky, R. J.,, E. W. May,, and N. L. Craig. 1996. The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products. EMBO J. 15: 6348– 6361.
149. Sato, T.,, Y. Samori,, and Y. Kobayashi. 1990. The cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologous to a site-specific recombinase. J. Bacteriol. 172: 1092– 1098.
150. Scott, J. R.,, F. Bringel,, D. Marra,, G. Van Alstine,, and C. K. Rudy. 1994. Conjugative transposition of Tn916: preferred targets and evidence for conjugative transfer of a single strand and for a double-stranded circular intermediate. Mol. Microbiol. 11: 1099– 1108.
151. Scott, J. R.,, P. A. Kirchman,, and M. G. Caparon. 1988. An intermediate in transposition of the conjugative transposon Tn916. Proc. Natl. Acad. Sci. USA 85: 4809– 4813.
152. Sekine, Y.,, K. Aihara,, and E. Ohtsubo. 1999. Linearization and transposition of circular molecules of insertion sequence IS3. J. Mol. Biol. 294: 21– 34.
153. Shapiro, J. A. 1997. Genome organization, natural genetic engineering and adaptive mutation. Trends Genet. 13: 98– 104.
154. Shapiro, J. A. 1979. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc. Natl. Acad. Sci. USA 76: 1933– 1937.
155. Shapiro, J. A.,, and N. P. Higgins. 1989. Differential activity of a transposable element in Escherichia coli colonies. J. Bacteriol. 171: 5975– 5986.
156. She, Q.,, R. K. Singh,, F. Confalonieri,, Y. Zivanovic,, G. Allard,, M. J. Awayez,, C. C. Chan-Weiher,, I. G. Clausen,, B. A. Curtis,, A. De Moors,, G. Erauso,, C. Fletcher,, P. M. Gordon,, I. Heikamp-de Jong,, A. C. Jeffries,, C. J. Kozera,, N. Medina,, X. Peng,, H. P. Thi-Ngoc,, P. Redder,, M. E. Schenk,, C. Theriault,, N. Tolstrup,, R. L. Charlebois,, W. F. Doolittle,, M. Duguet,, T. Gaasterland,, R. A. Garrett,, M. A. Ragan,, C. W. Sensen,, and J. Van der Oost. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98: 7835– 7840.
157. Sherratt, D. J.,, and D. B. Wigley. 1998. Conserved themes but novel activities in recombinases and topoisomerases. Cell 93: 149– 152.
158. Shoemaker, N. B.,, G. R. Wang,, and A. A. Salyers. 2000. Multiple gene products and sequences required for excision of the mobilizable integrated Bacteroides element NBU1. J. Bacteriol. 182: 928– 936.
159. Shoemaker, N. B.,, G. R. Wang,, and A. A. Salyers. 1996. NBU1, a mobilizable site-specific integrated element from Bacteroides spp., can integrate nonspecifically in Escherichia coli. J. Bacteriol. 178: 3601– 3607.
160. Signon, L.,, and N. Kleckner. 1995. Negative and positive regulation of Tn10/IS10-promoted recombination by IHF: two distinguishable processes inhibit transposition off of multicopy plasmid replicons and activate chromosomal events that favor evolution of new transposons. Genes Dev. 9: 1123– 1136.
161. Stark, W. M.,, and M. R. Boocock,. 1995. Topological selectivity in site-specific recombination, p. 101– 129. In D. J. Sherratt (ed.), Mobile Genetic Elements. Oxford University Press, Oxford, United Kingdom.
162. Stark, W. M.,, M. R. Boocock,, and D. J. Sherratt. 1992. Catalysis by site-specific recombinases. Trends Genet. 8: 432– 439.
163. Stark, W. M.,, N. D. Grindley,, G. F. Hatfull,, and M. R. Boocock. 1991. Resolvase-catalysed reactions between res sites differing in the central dinucleotide of subsite I. EMBO J. 10: 3541– 3548.
164. Stellwagen, A. E.,, and N. L. Craig. 1997. Avoiding self: two Tn7-encoded proteins mediate target immunity in Tn7 transposition. EMBO J. 16: 6823– 6834.
165. Storrs, M. J.,, C. Poyart-Salmeron,, P. Trieu-Cuot,, and P. Courvalin. 1991. Conjugative transposition of Tn916 requires the excisive and integrative activities of the transposon- encoded integrase. J. Bacteriol. 173: 4347– 4352.
166. Tavakoli, N.,, A. Comanducci,, H. M. Dodd,, M. C. Lett,, B. Albiger,, and P. Bennett. 2000. IS1294, a DNA element that transposes by RC transposition. Plasmid 44: 66– 84.
167. Tavakoli, N. P.,, and K. M. Derbyshire. 1999. IS903 transposase mutants that suppress defective inverted repeats. Mol. Microbiol. 31: 1183– 1195.
168. Tavakoli, N. P.,, and K. M. Derbyshire. 2001. Tipping the balance between replicative and simple transposition. EMBO J. 20: 2923– 2930.
169. Taylor, K. L.,, and G. Churchward. 1997. Specific DNA cleavage mediated by the integrase of conjugative transposon Tn916. J. Bacteriol. 179: 1117– 1125.
170. Thorpe, H. M.,, and M. C. 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.
171. Tribble, G. D.,, A. C. Parker,, and C. J. Smith. 1997. The Bacteroides mobilizable transposon Tn4555 integrates by a site-specific recombination mechanism similar to that of the gram-positive bacterial element Tn916. J. Bacteriol. 179: 2731– 2739.
172. Tribble, G. D.,, A. C. Parker,, and C. J. Smith. 1999. Transposition genes of the Bacteroides mobilizable transposon Tn4555: role of a novel targeting gene. Mol. Microbiol. 34: 385– 394.
173. Trieu-Cuot, P.,, C. Poyart-Salmeron,, C. Carlier,, and P. Courvalin. 1993. Sequence requirements for target activity in site-specific recombination mediated by the Int protein of transposon Tn1545. Mol. Microbiol. 8: 179– 185.
174. Turlan, C.,, and M. Chandler. 2000. Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA. Trends Microbiol. 8: 268– 274.
175. Turlan, C.,, B. Ton-Hoang,, and M. Chandler. 2000. The role of tandem IS dimers in IS911 transposition. Mol. Microbiol. 35: 1312– 1325.
176. Van Duyne, G. D. 2001. A structural view of Cre-loxP site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30: 87– 104.
177. van Gent, D. C.,, A. A. Groeneger,, and R. H. Plasterk. 1992. Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. USA 89: 9598– 9602.
178. van Gent, D. C.,, J. F. McBlane,, D. A. Ramsden,, M. J. Sadofsky,, J. E. Hesse,, and M. Gellert. 1995. Initiation of V(D)J recombination in a cell-free system. Cell 81: 925– 934.
179. Wang, H.,, and P. Mullany. 2000. The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. J. Bacteriol. 182: 6577– 6583.
180. Wang, H.,, A. P. Roberts,, D. Lyras,, J. I. Rood,, M. Wilks,, and P. Mullany. 2000. Characterization of the ends and target sites of the novel conjugative transposon Tn5397 from Clostridium difficile: excision and circularization is mediated by the large resolvase, TndX. J. Bacteriol. 182: 3775– 3783.
181. Wang, H.,, A. P. Roberts,, and P. Mullany. 2000. DNA sequence of the insertional hot spot of Tn916 in the Clostridium difficile genome and discovery of a Tn916-like element in an environmental isolate integrated in the same hot spot. FEMS Microbiol. Lett. 192: 15– 20.
182. Watson, M. A.,, and G. Chaconas. 1996. Three-site synapsis during Mu DNA transposition: a critical intermediate preceding engagement of the active site. Cell 85: 435– 445.
183. Weinert, T. A.,, K. M. Derbyshire,, F. M. Hughson,, and N. D. Grindley. 1984. Replicative and conservative transpositional recombination of insertion sequences. Cold Spring Harbor Symp. Quant. Biol. 49: 251– 260.
184. Weisberg, R. A.,, 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 Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
185. Wentzell, L. M.,, T. J. Nobbs,, and S. E. Halford. 1995. The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248: 581– 595.
186. Willetts, N. S.,, C. Crowther,, and B. W. Holloway. 1981. The insertion sequence IS21 of R68.45 and the molecular basis for mobilization of the bacterial chromosome. Plasmid 6: 30– 52.
187. Wolkow, C. A.,, R. T. DeBoy,, and N. L. Craig. 1996. Conjugating plasmids are preferred targets for Tn7. Genes Dev. 10: 2145– 2157.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.