Transposition of phage mu DNA

Mobile DNA II

Volumn , Issue , 2022, Pages 384-402

  Chaconas, George ^a   Harshey, Rasika M ^b  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

DNA replication; DNA supercoiling; Integration host factor (IHF); Mu DNA transposition reaction; Transesterification

Indexed keywords

EID: 85158020392     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555817954.ch17     Document Type: Chapter

References (189)

1. Adzuma, K., Mizuuchi K. 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.
2. Adzuma, K., Mizuuchi K. 1988. MuA protein-induced bending of the Mu end DNA, p. 97-104. In Olson W.K., Sarma M.H., Sarma R.H., M. Sundaralingam (ed.), Structure and Expression, vol. 3. Adenine Press, New York, N. Y.
3. Adzuma, K., Mizuuchi K. 1991. Steady-state kinetic analysis of ATP hydrolysis by the B protein of bacteriophage Mu. Involvement of protein oligomerization in the ATPase cycle. Biol J. Chem. 266:6159-6167.
4. Adzuma, K., Mizuuchi K. 1988. Target immunity of Mu transposition reflects a differential distribution of Mu B protein. Cell 53:257-266.
5. Akroyd, J. E., Symonds N. 1983. Evidence for a conservative pathway of transposition of bacteriophage Mu. Nature 303:84-86.
6. Aldaz, H., Schuster E., Baker T.A. 1996. The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis. Cell 85:257-269.
7. Allison, R. G., Chaconas G. 1992. RoleoftheAproteinbinding sites in the in vitro transposition of Mu DNA. A complex circuit of interactions involving the Mu ends and the transpositional enhancer. Biol J. Chem. 267:19963-19970.
8. Arthur, A., Sherratt D. 1979. Dissectionofthetransposition process: a transposon-encoded site-specific recombination system. Mol. Gen. Genet. 175:267-274.
9. Bainton, R., Gamas P., Craig N.L. 1991. Tn7 transposition in vitro proceeds through an excised transposon intermediate generated by staggered breaks in DNA. Cell 65: 805-816.
10. Bainton, R. J., Kubo K.M., Feng J.N., Craig N.L. 1993. Tn7 transposition: target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system. Cell 72:931-943.
11. Baker, T. A., Kremenstova E., Luo L. 1994. Complete transposition requires four active monomers in the Mu transposase tetramer. Genes Dev. 8:2416-2428.
12. Baker, T. A., Luo L. 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. USA 91:6654-6658.
13. Baker, T. A., Mizuuchi K. 1992. DNA-promoted assembly of the active tetramer of the Mu transposase. Genes Dev. 6:2221-2232.
14. Baker, T. A., Mizuuchi M., Mizuuchi K. 1991. MuB protein allosterically activates strand transfer by the transposase of phage Mu. Cell 65:1003-1013.
15. Baker, T. A., Mizuuchi M., Savilahti H., Mizuuchi K. 1993. Division of labor among monomers within the Mu transposase tetramer. Cell 74:723-733.
16. Berg, C. M., Berg D.E., Groisman E.A. 1989. Transposable elements and genetic engineering of bacteria, p. 879-925. In D.E. Berg and M.M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C.
17. Betermier, M., Alazard R., Ragueh F., Roulet E., Toussaint A., Chandler M. 1987. Phage Mu transposase: deletion of the carboxy-terminal end does not abolish DNA-binding activity. Mol. Gen. Genet. 210:77-85.
18. Bianchi, M. E. 1994. Prokaryotic HU and eukaryotic HMG1: a kinked relationship. Mol. Microbiol. 14:1-5.
19. Bujacz, G., Jaskolski M., Alexandratos J., Wlodawer A., Merkel G., Katz R.A., Skalka A.M. 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., Jaskolski M., Alexandratos J., Wlodawer A., Merkel G., Katz R.A., Skalka A.M. 1995. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. Mol J. Biol. 253:333-346.
21. Bukhari, A. I., Shapiro J.A., Adhya S.L. 1977. DNA Insertion Elements, Plasmids and Episomes. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
22. Bushman, F. D., Engelman A., Palmer I., Wingfield P., Craigie R. 1993. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc. Natl. Acad. Sci. USA 90: 3428-3432.
23. Castaing, B., Zelwer C., Laval J., Boiteux S. 1995. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. Biol J. Chem. 270: 10291-10296.
24. Castilho, B. A., Casadaban M.J. 1991. Specificity of mini-Mu bacteriophage insertions in a small plasmid. Bactenol J. 173:1339-1343.
25. Chaconas, G. 1999. Studies on a ''jumping gene machine'': higher-order nucleoprotein complexes in Mu DNA transposition. Biochem. Cell Biol. 77:487-491.
26. Chaconas, G. 1987. Transposition of bacteriophage Mu DNA in vivo, p. 137-158. In Symonds N., Toussaint A., Van de Putte P., M. M. Howe (ed.), Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
27. Chaconas, G., Giddens E.B., Miller J.L., Gloor G. 1985. A truncated form of the bacteriophage Mu B protein promotes conservative integration, but not replicative transposition, of Mu DNA. Cell 41:857-865.
28. Chaconas, G., Harshey R.M., Sarvetnick N., Bukhari A.I. 1981. Predominant end-products of prophage Mu DNA transposition during the lytic cycle are replicon fusions. Mol J. Biol. 150:341-359.
29. Chaconas, G., Lavoie B.D., Watson M.A. 1996. DNA transposition: jumping gene machine, some assembly required. Curr. Biol. 6:817-820.
30. Chaconas, G., Surette M.G. 1988. Mechanism of Mu DNA transposition. BioEssays 9:205-208.
31. Chow, S. A., Vincent K.A., Ellison V., Brown P.O. 1992. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science 255: 723-726.
32. Clubb, R. T., Mizuuchi M., Huth J.R., Omichinski J.G., Savilahti H., Mizuuchi K., Clore G.M., Gronenborn A.M. 1996. The wing of the enhancer-binding domain of phage Mu transposase is flexible and is essential for efficient transposition. Proc. Natl. Acad. Sci. USA 93:1146-1150.
33. Clubb, R. T., Omichinski J.G., Savilahti H., Mizuuchi K., Gronenborn A.M., Clore G.M. 1994. A novel class of winged helix-turn-helix protein: the DNA binding domain of Mu transposase. Structure 2:1041-1048.
34. Clubb, R. T., Schumacher S., Mizuuchi K., Gronenborn A.M., Clore G.M. 1997. Solution structure of the Iy subdomain of the Mu end DNA-binding domain of phage Mu transposase. Mol J. Biol. 273:19-25.
35. Colloms, S. D., Bath J., Sherratt D.J. 1997. Topological selectivity in Xer site-specific recombination. Cell 88: 855-864.
36. Craigie, R. 1996. Quality control in Mu DNA transposition. Cell 85:137-140.
37. Craigie, R., Arndt-Jovin D.J., Mizuuchi K. 1985. A defined system for the DNA strand-transfer reaction at the initiation of bacteriophage Mu transposition: protein and DNA substrate requirements. Proc. Natl. Acad. Sci. USA 82: 7570-7574.
38. Craigie, R., Mizuuchi K. 1985. Mechanismoftransposition of bacteriophage Mu: structure of a transposition intermediate. Cell 41:867-876.
39. Craigie, R., Mizuuchi K. 1986. Role of DNA topology in Mu transposition: mechanism of sensing the relative orientation of two DNA segments. Cell 45:793-800.
40. Craigie, R., Mizuuchi K. 1987. Transposition of Mu DNA: joining of Mu to target DNA can be uncoupled from cleavage at the ends of Mu. Cell 51:493-501.
41. Craigie, R., Mizuuchi M., Mizuuchi K. 1984. Site-specific recognition of the bacteriophage Mu ends by the Mu A protein. Cell 39:387-394.
42. Darzins, A., Kent N.E., Buckwalter M.S., Casadaban M.J. 1988. Bacteriophage Mu sites required for transposition immunity. Proc. Natl. Acad. Sci. USA 85:6826-6830.
43. Davies, D. R., Braam L.M., Reznikoff W.S., Rayment I. 1999. The three-dimensional structure of a Tn5 transposaserelated protein determined to2.9-A resolution. Biol J. Chem. 274:11904-11913.
44. Ding, Z. M., Harshey R.M., Hurley L.H. 1993. (+)CC-1065 as a structural probe of Mu transposase-induced bending ofDNA: overcoming limitations ofhydroxyl-radical footprinting. Nucleic Acids Res. 21:4281-4287.
45. DuBow, M. S. 1987. Transposable Mu-like phages, p. 201-213. In Symonds N., Toussaint A., Van de Putte P., M. M. Howe (ed.), Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
46. Dyda, F., Hickman A.B., Jenkins T.M., Engelman A., Craigie R., Davies D.R. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266:1981-1986.
47. Echols, H. 1990. Nucleoprotein structures initiating DNA replication, transcription, site-specific recombination. Biol J. Chem. 265:14697-14700.
48. Engelman, A., Mizuuchi K., Craigie R. 1991. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67:1211-1221.
49. Falconi, M., Mc-Govern V., Gualerzi C., Hillyard D., Higgins N.P. 1991. Mutations altering chromosomal protein H-NS induce mini-Mu transposition. New Biol. 3:615-625.
50. Gama, M. J., Toussaint A., Pato M.L. 1990. Instability of bacteriophage Mu transposase and the role of host Hfl protein. Mol. Microbiol. 4:1891-1897.
51. Gellert, M., Nash H. 1987. Communication between segments of DNA during site-specific recombination. Nature 325:401-404.
52. Geuskens, V., Mhammedi-Alaoui A., Desmet L., Toussaint A. 1992. Virulence in bacteriophage Mu: a case of trans-dominant proteolysis by the Escherichia coli Clp serine protease. EMBO J. 11:5121-5127.
53. Gloor, G., Chaconas G. 1986. The bacteriophage Mu N gene encodes the 64-kDa virion protein which is injected with, circularizes, infectingMuBiol DNA.Chem J. 261: 16682-16688.
54. Goosen, N., van de Putte P. 1987. Regulation of transcription, p. 41 -52. In Symonds N., Toussaint A., Van de Putte P., M. M. Howe (ed.), Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
55. Grainge, I., Jayaram M. 1999. The integrase family of recombinase: organization and function of the active site. Mol. Microbiol. 33:449-456.
56. Grindley, N. D. 1983. Transposition of Tn3 and related transposons. Cell 32:3-5.
57. 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. SpringerVerlag, Berlin, Germany.
58. Groenen, M. A., van de Putte P. 1986. Analysis of the ends of bacteriophage Mu using site-directed mutagenesis. Mol J. Biol. 189:597-602.
59. Groenen, M. A., van de Putte P. 1985. Mapping of a site for packaging of bacteriophage Mu DNA. Virology 144: 520-522.
60. Groenen, M. A., van de Putte P. 1987. The requirements for a high level of transposition of bacteriophage Mu. J. Cell Sci. Suppl. 7:41-50.
61. Grosschedl, R. 1995. Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr. Opin. Cell Biol. 7:362-370.
62. Haapa, S., Suomalainen S., Eerikainen S., Airaksinen M., Paulin L., Savilahti H. 1999. An efficient DNA sequencing strategy based on the bacteriophage Mu in vitro DNA transposition reaction. Genome Res. 9:308-315.
63. Haapa, S., Taira S., Heikkinen E., Savilahti H. 1999. An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications. Nucleic Acids Res. 27: 2777-2784.
64. Hallet, B., Sherratt D.J. 1997. Transposition and sitespecific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev. 21:157-178.
65. Haniford, D. B., Chaconas G. 1992. Mechanistic aspects of DNA transposition. Curr. Opin. Genet. Dev. 2:698-704.
66. Harel, J., Duplessis L., Kahn J.S., M. S. DuBow. 1990. The cis-acting DNA sequences required in vivo for bacteriophage Mu helper-mediated transposition and packaging. Arch. Microbiol. 154:67-72.
67. Haren, L., Ton-Hoang B., Chandler M. 1999. Integrating DNA: transposases and retroviral integrases. Annu. Rev. Microbiol. 53:245-281.
68. Harshey, R. M. 1987. Integration of infecting Mu DNA, p. 111-135. In Symonds N., Toussaint A., Van de Putte P., M. M. Howe (ed.), Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
69. Harshey, R. M. 1984. Transposition without duplication of infecting bacteriophage Mu DNA. Nature 311:580-581.
70. Harshey, R. M., Bukharl A.I. 1983. Infecting bacteriophage Mu DNA forms a circular DNA-protein complex. Mol J. Biol. 167:427-441.
71. Harshey, R. M., Cuneo S.D. 1986. Carboxyl-terminal mutants of phage Mu transposase. Genet J. 65:159-174.
72. Harshey, R. M., Getzoff E.D., Baldwin D.L., Miller J.L., Chaconas G. 1985. Primary structure of phage Mu transposase: homology to Mu repressor. Proc. Natl. Acad. Sci. USA 82:7676-7680.
73. Higgins, N. P., Collier D.A., Kilpatrick M.W., Krause H.M. 1989. Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage Mu. Biol J. Chem. 264: 3035-3042.
74. Huisman, O., Faelen M., Girard D., Jaffe A., Toussaint A., J. Rouvlere-Yaniv. 1989. Multiple defects in Escherichia coli mutants lacking HU protein. Bacteriol J. 171: 3704-3712.
75. Jiang, H., Yang J.Y., Harshey R.M. 1999. Criss-crossed interactions between the enhancer and the att sites of phage Mu during DNA transposition. EMBO J. 18:3845-3855.
76. Jones, J. M., Nakai H. 1999. Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. Mol J. Biol. 289:503-516.
77. Jones, J. M., Nakai H. 1997. The ΦX174-type primosome promotes replisome assembly at the site of recombination in bacteriophage Mu transposition. EMBO J. 16: 6886-6895.
78. Jones, J. M., Nakai H. 2000. PriA and phage T4 gp59: factors that promote DNA replication on forked DNA substrates. Mol. Microbiol. 36:519-527.
79. Jones, J. M., D.Welty J., Nakai H. 1998. Versatileaction of Escherichia coli ClpXP as protease or molecular chaperone for bacteriophage Mu transposition. Biol J. Chem. 273: 459-465.
80. Kanaar, R., Cozzarelli N.R. 1992. Roles of supercoiled DNA structure in DNAtransactions. Curr. Opin. Struct. Biol. 2:369-379.
81. Kanaar, R., Klippel A., Shekhtman E., Dungan J.M., Kahmann R., Cozzarelli N.R. 1990. Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, enhancer action. Cell 62:353-366.
82. Kennedy, A. K., Haniford D.B., Mizuuchi K. 2000. Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity. Cell 101:295-305.
83. Kim, K., Harshey R.M. 1995. Mutational analysis of the att DNA-binding domain of phage Mu transposase. Nucleic Acids Res. 23:3937-3943.
84. Kim, K., Namgoong S.Y., Jayaram M., Harshey R.M. 1995. Step-arrest mutants of phage Mu transposase. Implications in DNA-protein assembly, Mu end cleavage, strand transfer. Biol J. Chem. 270:1472-1479.
85. Kobryn, K., Lavoie B.D., Chaconas G. 1999. Supercoiling-dependent site-specific binding of HU to naked Mu Mol DNA.Biol J. 289:777-784.
86. Krause, H. M., Rothwell M.R., Higgins N.P. 1983. The early promoter of bacteriophage Mu: definition of the site of transcript initiation. Nucleic Acids Res. 11: 5483-5495.
87. Krementsova, E., Giffin M.J., Pincus D., Baker T.A. 1998. Mutational analysis of the Mu transposase. Contributions of two distinct regions of domain II to recombination. Biol J. Chem. 273:31358-31365.
88. Kruklitis, R., Nakai H. 1994. Participation of the bacteriophage Mu A protein and host factors in the initiation of Mu DNA synthesis in vitro. Biol J. Chem. 269: 16469-16477.
89. Kruklitis, R., Welty D.J., Nakai H. 1996. Clpx protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. EMBO J. 15:935-944.
90. Kuo, C. F., Zou A.H., Jayaram M., Getzoff E., Harshey R. 1991. DNA-protein complexes during attachment-site synapsis in MuDNAtransposition. EMBO J. 10:1585-1591.
91. Lamrani, S., Ranquet C., Gama M.J., Nakai H., Shapiro J.A., Toussaint A., G. Maenhaut-Michel. 1999. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol. Microbiol. 32: 327-343.
92. Lavoie, B. D., Chaconas G. 1990. Immunoelectron microscopic analysis of the A, B, HU protein content of bacteriophage Mu transpososomes. Biol J. Chem. 265: 1623-1627.
93. Lavoie, B. D., Chaconas G. 1994. A second high affinity HU binding site in the phage Mu transpososome. Biol J. Chem. 269:15571-15576.
94. Lavoie, B. D., Chaconas G. 1993. Site-specific HU binding in the Mu transpososome: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev. 7:2510-2519.
95. Lavoie, B. D., Chaconas G. 1995. Transposition of phage Mu Curr DNA. Top. Microbiol. Immunol. 204: 83-99.
96. Lavoie, B. D., Chan B.S., Allison R.G., Chaconas G. 1991. Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 10: 3051-3059.
97. Lavoie, B. D., Shaw G.S., Millner A., Chaconas G. 1996. Anatomy of a flexer-DNA complex inside a higherorder transposition intermediate. Cell 85:761-771.
98. Leung, P. C., Harshey R.M. 1991. Two mutations of phage Mu transposase that affect strand transfer or interactions with B protein lie in distinct polypeptide domains. Mol J. Biol. 219:189-199.
99. Leung, P. C., Teplow D.B., Harshey R.M. 1989. Interaction of distinct domains in Mu transposase with Mu DNA ends and an internal transpositional enhancer. Nature 338: 656-658.
100. Levchenko, I., Luo L., Baker T.A. 1995. Disassembly of the Mu transposase tetramer by the Clpx chaperone. Genes Dev. 9:2399-2408.
101. Levchenko, I., Yamauchi M., Baker T.A. 1997. ClpX and MuB interact with overlapping regions of Mu transposase: implications for control of the transposition pathway. Genes Dev. 11:1561-1572.
102. Liebart, J. C., Ghelardini P., Paolozzi L. 1982. Conservative integration of bacteriophage Mu DNA into pBR322 plasmid. Proc. Natl. Acad. Sci. USA 79:4362-4366.
103. Mahillon, J., Chandler M. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62: 725-774.
104. Manna, D., Higgins N.P. 1999. Phage Mu transposition immunity reflects supercoil domain structure of the chromosome. Mol. Microbiol. 32:595-606.
105. Maxwell, A., Craigie R., Mizuuchi K. 1987. Bproteinof bacteriophage mu is an ATPase that preferentially stimulates intermolecular DNA strand transfer. Proc. Natl. Acad. Sci. USA 84:699-703.
106. Merickel, S. K., Haykinson M.J., Johnson R.C. 1998. Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed sitespecific DNA inversion. Genes Dev. 12:2803-2816.
107. Mhammedi-Alaoui, A., Pato M., Gama M.J., Toussaint A. 1994. A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. Mol. Microbiol. 11:1109-1116.
108. Miller, J. L., Anderson S.K., Fujita D.J., Chaconas G., Baldwin D.L., Harshey R.M. 1984. The nucleotide sequence of the B gene of bacteriophage Mu. Nucleic Acids Res. 12:8627-8638.
109. Miller, J. L., Chaconas G. 1986. Electron microscopic analysis of in vitro transposition intermediates of bacteriophage Mu DNA. Gene 48:101-108.
110. Millner, A., Chaconas G. 1998. Disruption of target DNA binding in Mu DNA transposition by alteration of position 99 in the Mu B protein. Mol J. Biol. 275:233-243.
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. 1997. Polynucleotidyl transfer reactions in sitespecific DNA recombination. Genes Cells 2:1-12.
113. Mizuuchi, K. 1992. Polynucleotidyl transfer reactions in transpositional DNA recombination. Biol J. Chem. 267: 21273-21276.
114. Mizuuchi, K. 1992. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61:1011-1051.
115. Mizuuchi, K., Adzuma K. 1991. Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: evidence for a one-step transesterification mechanism. Cell 66:129-140.
116. Mizuuchi, K., Craigie R. 1986. Mechanism of bacteriophage Mu transposition. Annu. Rev. Genet. 20:385-429.
117. Mizuuchi, K., Nobbs T.J., Halford S.E., Adzuma K., Qin J. 1999. A new method for determining the stereochemistry of DNA cleavage reactions: application to the Sfil and Hpall restriction endonucleases and to the MuA transposase. Biochemistry 38:4640-4648.
118. Mizuuchi, M., Baker T.A., Mizuuchi K. 1995. Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds. Cell 83:375-385.
119. Mizuuchi, M., Baker T.A., Mizuuchi K. 1992. Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70:303-311.
120. Mizuuchi, M., Baker T.A., Mizuuchi K. 1991. DNase protection analysis of the stable synaptic complexes involved in Mu transposition. Proc. Natl. Acad. Sci. USA 88: 9031-9035.
121. Mizuuchi, M., Mizuuchi K. 1989. EfficientMutransposition requires interaction of transposase with a DNA sequence at the Mu operator: implications for regulation. Cell 58:399-408.
122. Mizuuchi, M., Mizuuchi K. 1993. Target site selection in transposition of phage Mu. Cold Spring Harbor Symp. Quant. Biol. 58:515-523.
123. Mizuuchi, M., Weisberg R.A., Mizuuchi K. 1986. DNA sequence of the control region of phage D108: the N-terminal amino acid sequences of repressor and transposase are similar both in phage D108 and in its relative, phage Mu. Nucleic Acids Res. 14:3813-3825.
124. Naigamwalla, D. Z., Chaconas G. 1997. A new set of Mu DNA transposition intermediates: alternate pathways of target capture preceding strand transfer. EMBO J. 16: 5227-5234.
125. Naigamwalla, D. Z., Coros C.J., Wu Z., Chaconas G. 1998. Mutations in domain IIIo. of the Mu transposase: evidence suggesting an active site component which interacts with the Mu-host junction. Mol J. Biol. 282:265-274.
126. Nakai, H. 1993. Amplification of bacteriophage Mu DNA by rolling circle DNA replication in vitro. Biol J. Chem. 268: 23997-24004.
127. Nakai, H., Kruklitis R. 1995. Disassembly of the bacteriophage Mu transposase for the initiation of Mu DNA replication. Biol J. Chem. 270:19591-19598.
128. Nakayama, C., Teplow D.B., Harshey R.M. 1987. Structural domains in phage Mu transposase: identification of the site-specific DNA-binding domain. Proc. Natl. Acad. Sci. USA 84:1809-1813.
129. Namgoong, S. Y., Harshey R.M. 1998. The same two monomers within a MuA tetramer provide the DDE domains for the strand cleavage and strand transfer steps of transposition. EMBO J. 17:3775-3785.
130. Namgoong, S. Y., Jayaram M., Kim K., Harshey R.M. 1994. DNA-protein cooperativity in the assembly and stabilization of Mu strand transfer complex. Relevance of DNA phasing and att site cleavage. Mol J. Biol. 238:514-527.
131. Namgoong, S. Y., Kim K., Saxena P., Yang J.Y., Jayaram M., Giedroc D.P., Harshey R.M. 1998. Mutational analysis of domain II£ of bacteriophage Mu transposase: domains IIo. and Iip belong to different catalytic complementation groups. Mol J. Biol. 275:221-232.
132. Namgoong, S. Y., Sankaralingam S., Harshey R.M. 1998. Altering the DNA-binding specificity of Mu transposase in vitro. Nucleic Acids Res. 26:3521-3527.
133. Nash, H. A. 1990. Bending and supercoiling of DNA at the attachment site of bacteriophage lambda. Trends Biochem. Sci. 15:222-227.
134. 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.
135. Pato, M. 1989. Bacteriophage Mu, p. 23-52. In D.E. Berg and M.M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington D.C.
136. Pato, M. L. 1994. Central location of the Mu strong gyrase binding site is obligatory for optimal rates of replicative transposition. Proc. Natl. Acad. Sci. USA 91:7056-7060.
137. Pato, M. L., Benerjee M. 1996. The Mu strong gyrasebinding site promotes efficient synapsis of the prophage termini. Mol. Microbiol. 22:283-292.
138. Pato, M. L., Banerjee M. 1999. Replacement of the bacteriophage Mu strong gyrase site and effect on Mu DNA replication. Bacteriol J. 181:5783-5789.
139. Pato, M. L., Howe M.M., Higgins N.P. 1990. A DNA gyrase-binding site at the center of the bacteriophage Mu genome is required for efficient replicative transposition. Proc. Natl. Acad. Sci. USA 87:8716-8720.
140. Pato, M. L., Karlok M., Wall C., Higgins N.P. 1995. Characterization of Mu prophage lacking the central strong gyrase binding site: localization of the block in replication. Bacteriol J. 177:5937-5942.
141. Pato, M. L., Reich C. 1982. Instability of transposase activity: evidence from bacteriophage Mu DNA replication. Cell 29:219-225.
142. Pinson, V., Takahashi M., J. Rouviere-Yaniv. 1999. Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform Mol DNA.Biol J. 287:485-497.
143. Pontiggia, A., Negri A., Beltrame M., Blanchi M.E. 1993. Protein HU binds specifically to kinked Mol DNA. Microbiol. 7:343-350.
144. Reich, C., Waggoner B.T., Pato M.L. 1984. Synchronization of bacteriophage Mu DNA replicative transposition: analysis of the first round after induction. EMBO J. 3: 1507-1511.
145. Rice, P., Craigie R., Davies D.R. 1996. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6:76-83.
146. Rice, P., Mizuuchi K. 1995. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82: 209-220.
147. Rice, P. A. 1997. Making DNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol. 7:86-93.
148. Rice, P. A., Yang S., Mizuuchi K., Nash H.A. 1996. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87:1295-1306.
149. Sakai, J., Kleckner N. 1997. The Tn10 synaptic complex can capture a target DNA only after transposon excision. Cell 89:205-214.
150. Savilahti, H., Mizuuchi K. 1996. Mu transpositional recombination-donor DNA cleavage and strand transfer in trans by the Mu transposase. Cell 85:271-280.
151. Savilahti, H., Rice P.A., Mizuuchi K. 1995. The Phage Mu transpososome core-DNA requirements for assembly and function. EMBO J. 14:4893-4903.
152. Schumacher, S., Clubb R.T., Cal M., Mizuuchi K., Clore G.M., Gronenborn A.M. 1997. Solution structure of the Mu end DNA-binding I£ subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J. 16:7532-7541.
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. 1984. The use of Mudlac transposons as tools for vital staining to visualize clonal and non-clonal patterns of organization in bacterial growth on agar surfaces. Gen J. Microbiol. 130:1169-1181.
156. Stark, W. M., Boocock M.R., Sherratt D.J. 1992. Catalysis by site-specific recombinases. Trends Genet. 8:432-439.
157. Surette, M. G., Buch S.J., Chaconas G. 1987. Transpososomes: stable protein-DNA complexes involved in the in vitro transposition of bacteriophage Mu DNA. Cell 49: 253-262.
158. Surette, M. G., Chaconas G. 1992. The Mu transpositional enhancer can function in trans: requirement of the enhancer for synapsis but not strand cleavage. Cell 68: 1101-1108.
159. Surette, M. G., Chaconas G. 1989. A protein factor which reduces the negative supercoiling requirement in the Mu DNA strand transfer reaction is Escherichia coli integration host factor. Biol J. Chem. 264:3028-3034.
160. Surette, M. G., Chaconas G. 1991. Stimulation of the Mu DNA strand cleavage and intramolecular strand transfer reactions by the Mu B protein is independent of stable binding of the Mu B protein to Biol DNA.Chem J. 266: 17306-17313.
161. Surette, M. G., Harkness T., Chaconas G. 1991. Stimulation of the Mu A protein-mediated strand cleavage reaction by the Mu B protein, the requirement of DNA nicking for stable type 1 transpososome formation. In vitro transposition characteristics of mini-Mu plasmids carrying terminal base pair mutations. Biol J. Chem. 266:3118-3124.
162. Surette, M. G., Lavoie B.D., Chaconas G. 1989. Action at a distance in Mu DNA transposition: an enhancer-like element is the site of action of supercoiling relief activity by integration host factor (IHF). EMBO J. 8:3483-3489.
163. Symonds, N., Toussaint A., Van de Putte P., Howe M.M. 1987. Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
164. Taylor, A. L. 1963. Bacteriophage-induced mutations in E. coli. Proc. Natl. Acad. Sci. USA 50:1043-1051.
165. Teplow, D. B., Nakayama C., Leung P.C., Harshey R.M. 1988. Structure-function relationships in the transposition protein B of bacteriophage Mu. Biol J. Chem. 263: 10851-10857.
166. van Ulsen, P., Hillebrand M., Kainz M., Collard R., Zullanello L., van de Putte P., Gourse R.L., Goosen N. 1997. Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and integration host factor-mediated activation of the early promoter of bacteriophage Mu. Bacteriol J. 179:530-537.
167. van Ulsen, P., Hillebrand M., Zulianello L., van de Putte P., Goosen N. 1997. The integration host factor-DNA complex upstream of the early promoter of bacteriophage Mu is functionally symmetric. Bacteriol J. 179:3073-3075.
168. Vologodskii, A., Cozzarelli N.R. 1996. Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophys. J. 70:2548-2556.
169. Vologodskii, A. V., Cozzarelli N.R. 1994. Conformational and thermodynamic properties of supercoiled Annu DNA. Rev. Biophys. Biomol. Struct. 23:609-643.
170. Vologodskii, A. V., Cozzarelli N.R. 1993. Monte Carlo analysis of the conformation ofDNA catenanes. Mol J. Biol. 232:1130-1140.
171. Vologodskii, A. V., Levene S.D., Klenin K.V., Frank-Kamenetskii M., Cozzarelli N.R. 1992. Conformational and thermodynamic properties of supercoiled Mol DNA.Biol J. 227:1224-1243.
172. Wang, X., Higgins N.P. 1994. 'Muprints' of the lac operon demonstrate physiological control over the randomness of in vivo transposition. Mol. Microbiol. 12:665-677.
173. Wang, Z., Harshey R.M. 1994. Crucial role for DNA supercoiling in Mu transposition: a kinetic study. Proc. Natl. Acad. Sci. USA 91:699-703.
174. Wang, Z., Namgoong S.-Y., Zhang X., Harshey R.M. 1996. Kinetic and structural probing of the pre-cleavage synaptic complex (type 0) formed during phage Mu transposition: action of metal ions and reagents specific to single stranded Biol DNA.Chem J. 271:9619-9626.
175. Watson, M. A., Chaconas G. 1996. Three-site synapsis during Mu DNA transposition: a critical intermediate preceding engagement of the active site. Cell 85:435-445.
176. Wei, S. Q., Mizuuchi K., Craigie R. 1998. Footprints on the viral DNA ends in moloney murine leukemia virus preintegration complexes reflect a specific association with integrase. Proc. Natl. Acad. Sci. USA 95:10535-10540.
177. Wei, S. Q., Mizuuchi K., Craigie R. 1997. A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration. EMBO J. 16:7511-7520.
178. Welty, D. J., Jones J.M., Nakai H. 1997. Communication of ClpXP protease hypersensitivity to bacteriophage Mu repressor isoforms. Mol J. Biol. 272:31-41.
179. Williams, T. L., Jackson E.L., Carritte A., Baker T.A. 1999. Organization and dynamics of the Mu transpososome: recombination by communication between two active sites. Genes Dev. 13:2725-2737.
180. Wu, Z., Chaconas G. 1994. Characterization of a region in phage Mu transposase that is involved in interaction with the Mu B protein. Biol J. Chem. 269:28829-28833.
181. Wu, Z., Chaconas G. 1992. Flanking host sequences can exert an inhibitory effect on the cleavage step of the in vitro Mu DNA strand transfer reaction. Biol J. Chem. 267: 9552-9558.
182. Wu, Z., Chaconas G. 1997. The Mu transposase tetramer is inactive in unassisted strand transfer: an auto-allosteric effect of Mu A promotes the reaction in the absence of Mu Mol B.Biol J. 267:132-141.
183. Wu, Z., Chaconas G. 1995. A novel DNA binding and nuclease activity in domain III of Mu transposase: evidence for a catalytic region involved in donor cleavage. EMBO J. 14:3835-3843.
184. Yamauchi, M., Baker T.A. 1998. An ATP-ADP switch in MuB controls progression of the Mu transposition pathway. EMBO J. 17:5509-5518.
185. Yang, J. Y., Jayaram M., Harshey R.M. 1995. Enhancer-independent variants of phage Mu transposase: enhancerspecific stimulation of catalytic activity by a partner transposase. Genes Dev. 9:2545-2555.
186. Yang, J. Y., Kim K., Jayaram M., Harshey R.M. 1995. Domain sharing model for active site assembly within the Mu a tetramer during transposition: the enhancer may specify domain contributions. EMBO J. 14:2374-2384.
187. Yang, J.-Y., Jayaram M., Harshey R.M. 1996. Positional information within the Mu transposase tetramer: catalytic contributions of individual monomers. Cell 85: 447-455.
188. Yang, W., Steitz T.A. 1995. Recombining the structures of HIV integrase, RuvC and RNase H. Structure 3:131134.
189. Zou, A. H., Leung P.C., Harshey R.M. 1991. Transposase contacts with Mu DNA ends. Biol J. Chem. 266: 20476-20482.