Chapter 2 : Participating Elements in the Replication of Iteron-Containing Plasmids

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The presence of Rep-binding iterons is a hallmark, not only of many prokaryotic plasmid orfs but of chromosomal, viral (phage), and eukaryotic (5, 75, 92) as well. This chapter focuses primarily on the prokaryotic plasmid members of the Rep/iteron family, which is referred to as iteron-containing plasmids (ICPs). Several extensive reviews on a variety of aspects of plasmid biology have been written, and this review serves as an extension of the earlier works. Sequence conservation in the adjacent major and minor grooves has been demonstrated for iterons from prokaryotic and eukaryotic . It is likely, then, that a diverse set of Rep proteins can utilize the intrinsic instability of specific base pairs within iterons to bind DNA and facilitate its melting. The chapter discusses what appeared to be a rather well-understood system, λdv. It exemplifies the autorepressor model originally developed to explain the control of chromosomal replication, and discusses some of the additional DNA sequences and host proteins that likely contribute to the regulation of ICPs. The chapter discusses molecular mechanism of activation, and focuses on Rep/iteron-mediated replication of minimal ICPs in . The contributions of plasmids to the development of modern molecular biology were astutely articulated a decade ago. Currently, the need for ongoing and vigorous support of basic and applied research on plasmids continues, with an imperative to solve practical issues of fundamental societal importance. A prime example is the emergence and alarming spread of bacterial resistance to multiple antibiotics.

Citation: Krüger R, Rakowski S, Filutowiez M. 2004. Participating Elements in the Replication of Iteron-Containing Plasmids, p 23-46. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch2
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Figure 1

Schematics of ICP replication initiation. (A) The Rep protein (shaded ovals |R|) is produced from the rep gene (gray rectangle). Rep hinds in an orderly fashion to the iterons (hlack rectangle) and stimulates DNA replication (plus sign). Certain host proteins (examples in the gray box) will interact in solution with the Rep protein while others may interact with Rep bound to DNA. Host proteins also exert effects by directly binding to the DNA at multiple sites within the origin of replication (on). (B) A closer view of the protein-protein interactions model within the ori is depicted. Rep protein will interact (curved arrows) with host proteins that bind near the iterons or at distant sites (e.g., DnaA, black oval |A|). The distant sites can be brought closer by the DNA-bending ability of proteins like IHF (I), thus promoting protein interactions at different levels (Rep/host, host/host, and Rep/Rep).

Citation: Krüger R, Rakowski S, Filutowiez M. 2004. Participating Elements in the Replication of Iteron-Containing Plasmids, p 23-46. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch2
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Image of Figure 2
Figure 2

Regulation models for ICP replication. ( ) Rep dimers are able to bind to the operator/promoter region (Op/Pr) and negatively regulate Rep production (minus sign). ( ) Monomers of the replication initiator activate origin (ori) replication (plus sign). Panels 3 to 5 represent variations of the “handcuffing model.” ( ) Two layers of monomers bound to the iterons of two individual plasmids are able to bring two ori's together (curved small arrows), shutting down replication of both (minus sign). ( ) Dimers of the Rep protein bridge two plasmids by associations with monomers bound to iterons. ( ) A single layer of dimers binds the iterons of two ori's, applicable only for those systems where dimers can directly bind iterons. ( ) The “titration model” in which the presence of an extra set of iterons from a second plasmid could titrate the activator form of the Rep protein (monomers), leading to the depletion of Rep and thereby inactivating the ori.

Citation: Krüger R, Rakowski S, Filutowiez M. 2004. Participating Elements in the Replication of Iteron-Containing Plasmids, p 23-46. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch2
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Figure 3

Replication steps—a model. The replication initiator protein (Rep) recognizes the origin of replication (or/) and induces a conformational change in the plasmid (e.g., DNA bending). Then Rep protein, with or without host proteins engaging their binding sites (IHF/HU, DnaA), triggers strand separation in an A+T-rich segment of the DNA. This single-stranded region is then targeted for the loading of DNA helicase and primase. DNA helicase will further unwind the DNA helix while primase will start synthesizing short RNA molecules, which serve as primers for the initiation of DNA synthesis by “sliding” DNA polymerase.

Citation: Krüger R, Rakowski S, Filutowiez M. 2004. Participating Elements in the Replication of Iteron-Containing Plasmids, p 23-46. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch2
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1. Abeles, A. L.,, and S. J. Austin. 1991. Antiparallel plasmid-plasmid pairing may control P1 plasmid replication. Proc Natl. Acad. Sci. USA 88: 9011 9015.
2. Abeles, A. L.,, L. D. Reaves,, and S. J. Austin. 1990. A single DnaA box is sufficient for initiation from the P1 plasmid origin. J. Bacteriol. 172: 4386 4391.
3. Adhya, S.,, and S. Garges. 1990. Positive control. J. Biol. Chem. 265: 10797 10800.
4. Armstrong, K. A.,, R. Acosta,, E. Ledner,, Y. Machida,, M. Pancotto,, M. McCormick,, H. Ohtsubo,, and E. Ohtsubo. 1984. A 37 X 10(3) molecular weight plasmid-encoded protein is required for replication and copy number control in the plasmid pSC101 and its temperature-sensitive derivative pHSI.y. Mol. Biol. 175: 331 348.
5. Baker, T. A.,, and S. P, Bell. 1998. Polymerases and the replisome: machines within machines. Cell 92: 295 305.
6. Banack, T., P, D. Kim, and W. Firshein. 2000. TrfA-dependent inner membrane-associated plasmid RK2 DNA synthesis and association of TrfA with membranes of different gramnegative hosts. J. Bacteriol. 182: 4380 4383.
7.Banerjee, 5. K., B. T. Luck, H. Y. Kim, and V. N. Iyer. 1992. Three clustered origins of replication in a promiscuous-plasmid replicon and their differential use in a PolA+ strain and a delta PolA strain of Escherichia coli K-12. J. Bacteriol 174: 81398143.
8.Baumstark, B, R., K. Lowery, and J. R. Scott. 1984. Location by DNA sequence analysis of cop mutations affecting the number of plasmid copies of prophage P1. Mol. Gen. Genet. 194: 513516.
9. Blasina, A.,, B. L. Kittell,, A. E. Toukdarian,, and D. R. Helinski. 1996. Copy-up mutants of the plasmid RK2 replication initiation protein arc defective in coupling RK2 replication origins. Proc Natl Acad. Sci. USA 93: 3559 3564.
10. Bramhill, D.,, and A. Kornberg. 1988. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52: 743 755.
11. Bramhill, D.,, and A. Kornberg. 1988. A model for initiation at origins of DNA replication. Cell 54: 915 918.
12. Brendler, T.,, A. Abeles,, and S. Austin. 1991. Critical sequences in the core of the P1 plasmid replication origin. J Bacteriol. 173: 3935 3942.
13. Brendler, T.,, A. Abeles,, and S. Austin. 1995. A protein that binds to the P1 origin core and the oriC 13mer region in a meihylation-specific fashion is the product of the host seqA gene. EMBO J. 14: 4083 4089.
14. Bussiere, D. E.,, and D. Bastia. 1999. Termination of DNA replication of bacterial and plasmid chromosomes. Mol. Microbiol. 31: 1611 1618.
15. Carr, K. M.,, and J. M. Kaguni. 2001. Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin. J. Biol. Chem. 276: 44919 44925.
16. Caspi, R.,, D. R. Helinski,, M. Pacek,, and I. Konieczny. 2000. Interactions of DnaA proteins from distantly related bacteria with the replication origin of the broad host range plasmid RK2. J. Biol. Chem. 275: 18454 18461.
17. Chattoraj, D.,, K. Cordes,, and A. Abeles. 1984. Plasmid P1 replication: negative control by repeated DNA sequences. Proc. Natl. Acad. Sci. USA 81: 6456 6460.
18. Chattoraj, D. K. 2000. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37: 467 476.
19. Chattoraj, D. K.,, R. Ghirlando,, K. Park,, J., A. Dibbens, and M. S. Lewis. 1996. Dissociation kinetics of RepA dimers: implications for mechanisms of activation of DNA binding by chapcrones. Genes Cells 1: 189 199.
20. Chattoraj, D. K.,, and T. D. Schneider. 1997. Replication control of plasmid PI and its host chromosome: the common ground. Prog. Nucleic Acid Res. Mol. Biol. 57: 145 186.
21. Chattoraj, D. K.,, K. M. Snyder,, and A. L. Abeles. 1985. P1 plasmid replication: multiple functions of RepA protein at the origin. Proc. Natl Acad. Sci. USA 82: 2588 2592.
22. Chen, D.,, J . Feng,, R. Krüger,, M. Urh,, R. B. Inman,, and M. Filutowicz. 1998. Replication of R6K γ origin in vitro: discrete start sites for DNA synthesis dependent on π and its copy-up variants. J. Mol. Biol. 282: 775 787.
23. Cohen, S. N. 1993. Bacterial plasmids: their extraordinary contribution to molecular genetics. Gene 135: 67 76.
24. Conley, D. L.,, and S. N. Cohen. 1995. Effects of the pSClOl partition (par) locus on in vivo DNA supercoiling near the plasmid replication origin. Nucleic Acids Res. 23: 701 707.
25. Crosa, J. H. 1980. Three origins of replication arc active in vivo in the R plasmid RSF1040. J. Biol. Chem. 255: 11075 11077.
26. Dasgupta, S.,, H. Masukata,, and J . Tomizawa. 1987. Multiple mechanisms for initiation of ColEl DNA replication: DNA synthesis in the presence and absence of ribonuclease H. Cell 51: 1113 1122.
27. da Silva-Tatley, F. M.,, and L. M, Steyn. 1993 , Characterization of a replicon of the moderately promiscuous plasmid, pGSH5000, with features of both the mini-replicon of pCUl and the ori-2 of F. Mol. Microbiol 7: 805 823.
28. Datta, H. J.,, G. S. Khatri,, and D. Bastia. 1999. Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSClOl. Proc. Natl. Acad. Sci. USA 96: 73 78.
29. Davey, M. J.,, and M. O'Donnell. 2000. Mechanisms of DNA replication. Curr. Opin. Chem. Biol 4: 581 586.
30. Dellis, S.,, J . Feng,, and M. Filutowicz. 1996. Replication of plasmid R6K y origin in vivo and in vitro: dependence on IHF binding to the ihfl site. J. Mol. Biol. 257: 550 560.
31. Dellis, S.,, and M. Filutowicz. 1991. Integration host factor of Escherichia coli reverses the inhibition of R6K plasmid replication by n initiator protein. J. Bacteriol 173: 1279 1286.
32. Dellis, S.,, T. Schatz,, K. Rutlin,, R. B. Inman,, and M. Filutowicz. 1992. Two alternative structures can be formed by IHF protein binding to the plasmid R6K γ origin. J. Biol. Chem. 267: 24426 24432.
33. del Solar, G.,, J . C. Alonso,, M. Espinosa,, and R. Diaz-Orejas. 1996. Broad-host-range plasmid replication: an open question. Mol. Microbiol. 21: 661 666.
34. del Solar, G.,, and M. Espinosa. 2000. Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37: 492 500.
35. del Solar, G.,, R. Giraldo,, M. J. Ruiz-Echcvarria,, M. Espinosa,, and R. Diaz-Orejas. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62: 434 464.
36. Dhavan, G. M.,, J . Lapham,, S. Yang,, and D. M. Crothers. 1999. Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR. J. Mol. Biol. 288: 659 671.
37. Díaz-López, T.,, M. Lages-Gonzalo,, A. Serrano-López,, C. Alfonso,, G. Rivas,, R. Díaz-Orejas,, and R. Giraldo. 2003. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J. Biol. Chem. 278: 18606 18616.
38. Dibbens, J. A.,, K. Muraiso,, and D. K. Chattoraj. 1997. Chaperone-mediated reduction of RepA dimerization is associated with RepA conformational change. Mol. Microbiol. 26: 185 195.
39. Doran, K. S.,, D. R. Helinski,, and l. Konieczny. 1999. A critical DnaA box directs the cooperative binding of the Escherichia coli DnaA protein to the plasmid RK2 replication origin. J. Biol. Chem. 274: 17918 17923.
40. Dove, W.,, H. Inokuchi,, and W. Stevens,. 1971. Replication control in phage λ, p. 747 771. In A. D. Hershey (ed.), The Bacteriophage Lambda. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
41. Durland, R. H.,, A. Toukdarian,, F. Fang,, and D. R. Helinski. 1990. Mutations in the trfA replication gene of the broadhost- range plasmid RK2 result in elevated plasmid copy numbers. J. Bacteriol. 172: 3859 3867.
42. Echols, H. 1986. Multiple DNA-protein interactions governing high-precision DNA transactions. Science 233: 1050 1056.
43. Eichenlaub, R.,, D. Figurski,, and D. R. Helinski. 1977. Indirection replication from a unique origin in a mini-F plasmid. Proc. Natl. Acad. Sci. USA 74: 1138 1141.
44. Fernandez-Tresguerres, M. E.,, M. Martin,, D. Garcia de Vicdma,, R. Giraldo,, and R. Diaz-Orejas. 1995. Host growth temperature and a conservative amino acid substitution in the replication protein of pPS10 influence plasmid host range. J. Bacteriol. 177: 4377 4384.
45. Filutowicz, M.,, and K. Appelt. 1988. The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K γ origin and is essential for replication. Nucleic Acids Res. 16: 3829 3843.
46. Filutowicz, M.,, G. Davis,, A. Greener,, and D. R. Helinski. 1985. Autorepressor properties of the pi-initiation protein encoded by plasmid R6K. Nucleic Acids Res. 13: 103 114.
47.Filutowicz, M,, S. Dellis, I. Levchenko, M. Urh, F. Wu, and D. York. 1994. Regulation of replication of an iteron-containing DNA molecule. Prog. Nucleic Acid Res. Mol. Biol. 48: 239273.
48. Filutowicz, M.,, and R. Inman. 1991. A compact nucleoprotein structure is produced by binding of Escherichia coli integration host factor (IHF) to the replication origin of plasmid R6K. J. Biol. Chem. 266: 24077 24083.
49. Filutowicz, M.,, M. McEachern,, A. Greener,, P. Mukhopadhyay,, E. Uhlcnhopp,, R. Durland,, and D. Helinski. 1985. Role of the n initiation protein and direct nucleotide sequence repeats in the regulation of plasmid R6K replication. Basic Life Sci. 30: 125 140.
50. Filutowicz, M.,, M. J. McEachern,, and D. R. Helinski. 1986. Positive and negative roles of an initiator protein at an origin of replication. Proc. Natl. Acad. Sci. USA 83: 9645 9649.
51. Filutowicz, M.,, and S. A. Rakowski. 1998. Regulatory implications of protein assemblies at the y origin of plasmid R6K— a review, Gene 223: 195 204.
52. Filutowicz, M.,, and J. Roll. 1990. The requirement of IHF protein for extrachromosomal replication of the Escherichia coli oriC in a mutant deficient in DNA polymerase I activity. New Biol. 2: 818 827.
53. Filutowicz, M.,, W. Ross,, J . Wild,, and R. L, Gourse. 1992. Involvement of Fis protein in replication of the Escherichia coli chromosome. J. Bacteriol. 174: 398 407.
54. Filutowicz, M.,, D. York,, and I. Levchenko. 1994. Cooperative binding of initiator protein to replication origin conferred by single amino acid substitution. Nucleic Acids Res. 22: 4211 4215.
55. Firshein, W.,, and P. Kim. 1997. Plasmid replication and partition in Escherichia coli: is the cell membrane the key? Mol. Microbiol. 23: 1 10.
56. Forest, K. T., and M, S. Filutowicz. 2003. Remodeling of replication initiator proteins. Nat. Struct. Biol. 10: 496 498.
57. Frey, J.,, M. Chandler,, and L. Caro. 1979. The effects of an Escherichia coli dnaAts mutation on the replication of the plasmids colE1 pSC101, R 100.1 and RTF-TC. Mol. Gen. Genet. 174: 117 126.
58. Friedman, D. I. 1988. Integration host factor: a protein for all reasons. Cell 55: 545 554.
59. Gammie, A. E.,, and J. H, Crosa. 1991. Co-operative autoregulation of a replication protein gene. Mol. Microbiol. 5: 3015 3023.
60. Garcia de Viedma, D.,, R. Giraldo,, G. Rivas,, E. Fernandez- Tresguerres,, and R. Diaz-Orejas. 1996. A leucine zipper motif determines different functions in a DNA replication protein. EMBO. J. 15: 925 934.
61. Gaylo, P. J.,, N. Turjman,, and D. Bastia. 1987. DnaA protein is required for replication of the minimal replicon of the broad-host-range plasmid RK2 in Escherichia coli. J. Bacteriol. 169: 4703 4709.
62. Georgopoulos, C. P. 1977. A new bacterial gene ( groPC) which affects λ DNA replication. Mol Gen. Genet. 151: 35 39.
63. Germino, J.,, and D. Bastia. 1983. Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA. Cell 34: 125 134.
64. Germino, J.,, and D. Bastia. 1984. Rapid purification of a cloned gene product by genetic fusion and site-specific proteolysis. Proc. Natl. Acad. Sci. USA 81: 4692 4696.
65. Gilbride, K. A.,, and J. L. Brumon. 1990. Identification and characterization of a new replication region in the Neisseria gonorrhoeae beta-lactamasc plasmid pFA3. J. Bacteriol. 172: 2439 2446.
66. Giraldo, R.,, J. M. Andreu,, and R. Diaz-Orejas. 1998. Protein domains and conformational changes in the activation of RepA, a DNA replication initiator. EMBO J. 17: 4511 1526.
67. Giraldo, R.,, and R. Diaz-Orejas. 2001. Similarities between the DNA replication initiators of gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaca (Cdc6p). Proc. Natl. Acad. Sci. USA 98: 4938 4943.
68. Giraldo, R.,, C. Fernandez-Tornero,, P. R. Evans,, R. Diaz- Orejas,, and A. Romero. 2003. A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nat. Struct. Biol. 10: 565 571.
69.Gordon, G, S., D. Sitnikov, C. D. Webb, A. Teleman, A. Straight, R. Losick, A. W. Murray, and A. Wright. 1997. Chromosome and low copy plasmid segregation in E. coli: visual evidence for distinct mechanisms. Cell 90: 11131121.
70. Gordon, G. S.,, and A. Wright. 2000. DNA segregation in bacteria. Annu. Rev. Microbiol. 54: 681 708.
71. Hansen, E. B.,, and M. B. Yarmolinsky. 1986. Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from PI and F. Proc. Natl. Acad. Sci. USA 83: 4423 4427.
72. Hasunuma, K.,, and M. Sekiguchi 1977. Replication of plasmid pSC101 in Escherichia coli K12: requirement for dnaA function. Mol Gen. Genet. 154: 225 230.
73. Haugan, K.,, P. Karunakaran,, A. Tondervik,, and S. Valla. 1995. The host range of RK2 minimal replicon copy-up mutants is limited by species-specific differences in the maximum tolerable copy number. Plasmid 33: 27 39.
74. Helinski, D. R.,, A. E. Toukdarian,, and R. P. Novick,. 1996. Replication control and other stable maintenance mechanisms of plasmids, p. 2295 2324. 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..
75. Hickey, R. J.,, and L. H. Malkas. 1997. Mammalian cell DNA replication. Crit. Rev. Eukaryot. Gene Expr. 7: 125 157.
76. Highlander, S. K.,, and R. P. Novick. 1987. Plasmid repopulation kinetics in Staphylococcus aureus. Plasmid 17: 210 221.
77. Hiraga, S. 2000. Dynamic localization of bacterial and plasmid chromosomes. Annu. Rev. Genet. 34: 21 59.
78. Ho, T. Q.,, Z. Zhong,, S. Aung,, and J. Pogliano. 2002. Compatible bacterial plasmids are targeted to independent cellular locations in Escherichia coli. EMBO J. 21: 1864 1872.
79. Hwang, D. S.,, and A. Kornberg. 1990. A novel protein binds a key origin sequence to block replication of an E. coli minichromosome. Cell 63: 325 331.
80. Ingmer, H.,, and S. N. Cohen. 1993. Excess intracellular concentration of the pSC101 RepA protein interferes with both plasmid DNA replication and partitioning. J. Bacteriol 175: 7834 7841.
81. Ingmer, H.,, E. L. Fong,, and S. N. Cohen. 1995. Monomerdimcr equilibrium of the pSClOl RepA protein. J. Mol. Biol. 250: 309 314.
82. Inuzuka, M. 1997. [Replication control of iteron-containing plasmids—role of initiator protein-mediated DNA looping|. Seikagaku 69: 1272 1277.
83. Inuzuka, N.,, M. Inuzuka,, and D. R, Helinski. 1980. Activity in vitro of three replication origins of the antibiotic resistance plasmid RSF1040. J. Biol Chem. 255: 11071 11074.
84. Irani, M. H.,, L. Orosz,, and S. Adhya. 1983. A control element within a structural gene: the gal operon of Escherichia coli. Cell 32: 783 788.
85. Ishiai, M.,, C. Wada,, Y. Kawasaki,, and T. Yura. 1994. Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor). Proc. Natl. Acad. Sci. USA 91: 3839 3843.
86.Jacob. F. S. Brenner, and F, Cuzin. 1963. On the regulation of DNA replication in bacteria. Cold Spring Harbor Symp. Quant. Biol. 28: 329348.
87. Kaguni, J. M. 1997. Escherichia coli DnaA protein: the replication initiator. Mol. Cells 7: 145 157.
88. Kamio, Y.,, Y. Itoh,, and Y. Terawaki. 1988. Purification of Rts1 RepA protein and binding of the protein to mini- Rts1 DNA. J. Bacteriol 170: 4411 4414.
89. Karunakaran, P.,, J . M. Blatny,, H. Ertcsvag,, and S. Valla. 1998. Species-dependent phenorypes of replication-temperature-sensitive trfA mutants of plasmid RK2: a codon-neutral base substitution stimulates temperature sensitivity by leading to reduced levels of trfA expression. J. Bacteriol 180: 3793 3798.
90. Katayama, T., T, Kubota, K. Kurokawa, E. Crookc, and K. Sckimizu. 1998. The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E. coli chromosomal replicase. Cell 94: 61 71.
91. Kawasaki, Y.,, F. Matsunaga,, Y. Kano,, T. Yura,, and C. Wada. 1996. The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli. Mol. Gen. Genet. 253: 42 49,
92. 92 Keck, J. L.,, and J. M. Berger. 2000. DNA replication at high resolution. Chem. Biol. 7: R63 R7I.
93. Kelley, W.,, and D. Bastia. 1985. Replication initiator protein of plasmid R6K autoregulates its own synthesis at the transcriptional step. Proc. Natl. Acad. Sci. USA 82: 2574 2578.
94. Kelley, W. L.,, and D. Bastia. 1991. Conformational changes induced by integration host factor at origin γ of R6K and copy number control. J. Biol. Chem. 266: 15924 15937.
95. Kelley, W. L.,, I. Patel,, and D. Bastia. 1992. Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin y of plasmid R6K. Proc. Natl. Acad. Sci. USA 89: 5078 5082.
96. Kim, H. Y.,, S. K. Banerjee,, and V. N. Iyer. 1994. The incN plasmid replicon: two pathways of DNA polymerase I-independent replication. J. Bacteriol 176: 7735 7739.
97. Kim, K.,, and R. J. Meyer. 1985. Copy number of the broad host-range plasmid R1 162 is determined by the amounts of essential plasmid-encoded proteins. J. Mol. Biol. 185: 755 767.
98. Kim, P. D.,, and W. Firshcin. 2000. Isolation of an inner membrane-derived subfraction that supports in vitro replication of a mini-RK2 plasmid in Escherichia coli. J. Bacteriol 182: 1757 1760.
99. Kim, P. D.,, T. M. Roschc,, and W. Firshein. 2000. Identification of a potential membrane-targeting region of the replication initiator protein (TrfA) of broad-host-range plasmid RK2. Plasmid 43: 214 222.
100. Kim, Y. J.,, and R. J. Meyer. 1991. An essential iteron-binding protein required for plasmid Rl 162 replication induces localized melting within the origin at a specific site in AT-rich DNA. J. Bacteriol 173: 5539 5545.
101. Kittell, B. U and D. R. Helinski. 1991. Iteron inhibition of plasmid RK2 replication in vitro: evidence for intermolecular coupling of replication origins as a mechanism for RK2 replication control. Proc. Natl. Acad. Sci. USA 88: 1389 1393.
102. Kittell, B. L.,, and D. R. Helinski,. 1992. Plasmid incompatibility and replication control, p. 223 242. In D. B. Clewell (ed.), Bacterial Conjugation. Plenum Press, New York, N.Y..
103. Kline, B. C. 1988. Aspects of plasmid F maintenance in Escherichia coli. Can. J. Microbiol. 34: 526 535.
104. Kline, B. C.,, T. Kogoma,, J. E. Tarn,, and M. S. Shields. 1986. Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance. J. Bacteriol 168: 440 443.
105. Kogoma, T. 1997. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol Biol Rev. 61: 212 238.
106. Kogoma, T.,, and K. G. Lark. 1975. Characterization of the replication of Escherichia coli DNA in the absence of protein synthesis: stable DNA replication. J. Mol. Biol. 94: 243 256.
107. Kolter, R.,, and D. R. Helinski. 1982. Plasmid R6K DNA replication. II. Direct nucleotide sequence repeats are required for an active γ-origin. J. Mol. Biol. 161: 45 56.
108. Komori, H.,, F. Matsunaga,, Y. Higuchi,, M. Ishiai,, C. Wada,, and K. Miki. 1999. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J. 18: 4597 4607.
109. Kong, X. P.,, R. Onrust,, M. O'Donnell,, and J . Kuriyan. 1992. Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzymc: a sliding DNA clamp. Cell 69: 425 437.
110.. Konieczny,, L. K. S. Doran,, D. R. Helinski,, and A. Blasina. 1997. Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J. Biol. Chem. 272: 20173 20178.
111.Konieczny, L, and D. R. Helinski. 1997. The replication initiation protein of the broad-host-range plasmid RK2 is activated by the CIpX chaperone. Proc. Natl. Acad. Sci. USA 94: 1437814382.
112. Kornberg, A.,, and T. A. Baker. 1992. DNA Replication, 2nd ed. W.H. Freeman and Company, New York, N.Y..
113. Kowalski, D.,, and M. J . Eddy. 1989. The DNA unwinding clement: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 8: 4335 344.
114. Kowalski, D.,, D. A. Natale,, and M. J. Eddy. 1988. Stable DNA unwinding, not "breathing," accounts for single-strand- specific nuclease hypersensitivity of specific A+T-rich sequences. Proc Natl. Acad. Sci. USA 85: 9464 9488.
115. Krishnan, B. R.,, P. R, Fobert, U. Seitzer, and V. N. Iyer. 1990. Mutations within the replicon of the IncN plasmid pCUl that affect its Escherichia coli polA-independence but not its autonomous replication ability. Gene 91: 1 7.
116. Krishnan, B. R.,, and V. N. Iyer. 1990. IncN plasmid replicon. A deletion and subcloning analysis. J. Mol. Biol. 213: 777 788.
117. Krüger, R.,, and M. Filutowicz. 2000. Dimers of γ protein bind the A+T-rich region of the R6K γ origin near the leading- strand synthesis start sites: regulatory implications. J. Bacteriol. 182: 2461 2467.
118. Krüger, R.,, I. Konieczny,, and M. Filutowicz. 2001. Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin. J. Mol Biol. 306: 945 955.
119. Kues, U.,, and U. Stahl. 1989. Replication of plasmids in gram-negative bacteria. Microbiol. Rev. 53: 491 516.
120. Kurokawa, K.,, S. Nishida,, A. Emoto,, K. Sekimizu,, and T. Katayama. 1999. Replication cycle-coordinated change of the adenine nucleotide-bound forms of DnaA protein in Escherichia coli. EMBO J. 18: 6642 6652.
121. Lemon, K. P.,, and A. D, Grossman. 2000. Movement of replicating DNA through a stationary replisome. Mol. Cell. 6: 1321 1330.
122. Levchenko,, L., and M. Filutowicz. 1996. Initiator protein it can bind independently to two domains of the y origin core of plasmid R6K: the direct repeats and the A+T-rich segment. Nucleic Acids Res. 24: 1936 1942.
123. Levchenko, I.,, R. B. Inman,, and M. Filutowicz. 1997. Replication of the R6K y origin in vitro: dependence on wt n and hyperactive piS87N protein variant. Gene 193: 97 103.
124.Levchenko, L, D. York, and M. Filutowicz. 1994. The dimerization domain of R6K plasmid replication initiator protein it revealed by analysis of a truncated protein. Gene 145: 6568.
125. Lilley, D. M. 1988. DNA opens up—supcrcoiling and heavy breathing. Trends Genet. 4: 111 114.
126. Linder, P.,, G. Churchward,, G. X. Xia,, Y. Y. Yu,, and L. Caro. 1985. An essential replication gene, rep A, of plasmid pSClOl isautoregulated. J. Mol. Biol. 181: 383 393.
127. Lobner-Olesen, A.,, K. Skarstad,, F. G. Hansen,, K. von Mcycnburg,, and E. Boyc. 1989. The DnaA protein determines the initiation mass of Escherichia coli K-12. Cell 57: 881 889.
128. Lu, Y. B.,, H. J . Datta,, and D. Bastia. 1998. Mechanistic studies of initiator-initiator interaction and replication initiation. EMBO J. 17: 5192 5200.
129. Lyakhov, I. G.,, P. N. Hengcn,, D. Rubens,, and T. D. Schneider. 2001. The PI phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping. Nucleic Acids Res. 29: 4892 4900.
130. Macrina, F. L.,, G. G. Weatherly,, and R. D. Curtiss. 1974. R6K plasmid replication: influence of chromosomal genotype in minicell-producing strains of Escherichia coli K-12. J. Bacteriol. 120: 1387 1400.
131. Mancn, D.,, L. C. Upcgui-Gonzalez,, and L. Caro. 1992. Monomers and dimers of the RepA protein in plasmid pSClOl replication: domains in RepA. Proc. Natl. Acad. Sci. USA 89: 8923 8927.
132. Marians, K. J . 1992. Prokaryotic DNA replication. Annu. Rev. Biochem. 61: 673 719.
133. Marszalek, J.,, and J. M. Kaguni. 1994. DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli. J. Biol. Chem. 269: 4883 4890.
134. Masai, H.,, and K. Arai. 1987. RepA and DnaA proteins are required for initiation of Rl plasmid replication in vitro and interact with the oriR sequence. Proc. Natl. Acad. Sci. USA 84: 4781 4785.
135. Matsubara, K. 1981. Replication control system in Xdv. Plasmid 5: 32 52.
136. Matsunaga, F.,, M. Ishiai,, G. Kobayashi,, H. Uga,, T. Yura,, and C. Wada. 1997. The central region of RepE initiator protein of mini-F plasmid plays a crucial role in dimerization required for negative replication control. J. Mol. Biol. 274: 27 38.
137. Mazel, D.,, and J . Davics. 1999. Antibiotic resistance in microbes. Cell. Mol. Life. Sci. 56: 742 754.
138.McEachern, M, J., 1987. Regulation of plasmid replication by the interaction of an initiator protein with multiple DNA binding sites. Ph.D. thesis. University of California-San Diego, Lajolla, Calif..
139. McEachern, M. J. , M. A. Bott, P. A. Tooker, and D. R. Helinski. 1989. Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins. Proc. Natl. Acad. Sci. USA 86: 7942 7946.
140. McEachern, M. J.M. Filutowicz, and D. R. Helinski. 1985. Mutations in direct repeat sequences and in a conserved sequence adjacent to the repeats result in a defective replication origin in plasmid R6K. Proc. Natl. Acad. Sci. USA 82: 1480 1484.
141. McEachern, M. J.,, M. Filutowicz,, S. Yang,, A. Greener,, P. Mukhopadhyay,, and D. R. Helinski,. 1986. Elements involved in the copy control regulation of the antibiotic resistance plasmid R6K, p. 195 207. In S. B. Levy, and R. P. Novick (ed.), Banbury Report 24: Antibiotic Resistance Genes: Ecology, Transfer, and Expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y..
142. Mcnsa-Wilmot, K.,, K. Carroll,, and R. McMackcn. 1989. Transcriptional activation of bacteriophage X DNA replication in vitro: regulatory role of histone-like protein HU of Escherichia coli. EMBO. J. 8: 2393 2402.
143. Mensa-Wilmot, K.,, R. Seaby,, C. Alfano, M, C, Wold, B. Gomes, and R. McMackcn. 1989. Reconstitution of a nineprotein system that initiates bacteriophage λ DNA replication. J. Biol. Chem. 264: 2853 2861.
144.Messer, W,, F. Blaesing, D. Jakimowicz, M. Krausc, J . Majka, J . Nardmann, S. Schaper, H. Seitz, C. Speck, C. Weigel, G. Wcgrzyn, M. Welzeck, and J . Zakrzewska- Czcrwinska. 2001. Bacterial replication initiator DnaA. Rules for DnaA binding and roles of DnaA in origin unwinding and helicase loading. Biochimie 83: 512.
145. Miao, D. M.,, H. Sakai,, S. Okamoto,, K. Tanaka,, M. Okuda,, Y. Honda,, T. Komano,, and M. Bagdasarian. 1995. The interaction of RepC initiator with iterons in the replication of the broad host-range plasmid RSF1010. Nucleic Acids Res. 23: 3295 3300.
146.Miller, C , and S, N. Cohen. 1999. Separate roles of Escherichia coli replication proteins in synthesis and partitioning of pSClOl plasmid DNA. J. Bacteriol 181: 75527557.
147. Miller, C. A.,, H. Ingmer,, and S. N. Cohen. 1995. Boundaries of the pSC101 minimal replicon are conditional. J. Bacteriol. 177: 4865 871.
148. Miron, A.,, S. Mukherjee, and D. Bastia. 1992. Activation of distant replication origins in vivo by DNA looping as revealed by a novel mutant form of an initiator protein defective in cooperativity at a distance. EMBO J. 11: 1205 1216. ( Erratum, 11:2002.)
149. Miron, A.,, I. Patel,, and D. Bastia. 1994. Multiple pathways of copy control of y replicon of R6K: mechanisms both dependent on and independent of cooperativity of interaction of tau protein with DNA affect the copy number. Proc. Natl. Acad. Sci. USA 91: 6438 6442.
150. Mizushima, T.,, S. Nishida,, K. Kurokawa, T, Katayama, T. Miki, and K. Sckimizu. 1997. Negative control of DNA replication by hydrolysis of ATP bound to DnaA protein, the initiator of chromosomal DNA replication in Escherichia coli. EMBO J. 16: 3724 3730.
151. Moore, D. D.,, K. Denniston-Thompson,, K. E. Kruger,, M. E. Furth,, B. G. Williams,, D. L. Daniels,, and F. R. Blattner. 1979. Dissection and comparative anatomy of the origins of replication of lambdoid phages. Cold Spring Harbor Symp. Quant. Biol. 43: 155 163.
152. Mosig, G.,, N. Colowick,, M. E. Gruidl,, A. Chang,, and A. J. Harvey. 1995. Multiple initiation mechanisms adapt phage T4 DNA replication to physiological changes during T4's development. FEMS Microbiol. Rev. 17: 83 98.
153. Mukherjee, S.,, H. Erickson,, and D. Bastia. 1988. Detection of DNA looping due to simultaneous interaction of a DNA-binding protein with two spatially separated binding sites on DNA. Proc. Natl. Acad. Sci. USA 85: 6287 6291.
154. Mukherjee, S.,, H. Erickson,, and D. Bastia. 1988. Enhancer origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52: 375 383.
155. Mukherjee, S.,, I. Patel,, and D. Bastia. 1985. Conformational changes in a replication origin induced by an initiator protein. Cell 43: 189 197.
156. Mukhopadhyay, G.,, K. M. Carr,, J . M. Kaguni,, and D. K. Chattoraj. 1993. Open-complex formation by the host initiator, DnaA, at the origin of PI plasmid replication. EMBO J. 12: 4547 4554.
157. Mukhopadhyay, G.,, and D. K. Chattoraj. 1993. Conformation of the origin of PI plasmid replication. Initiator protein induced wrapping and intrinsic unstacking. J. Mol. Biol. 231: 19 28.
158. Mukhopadhyay, G.,, S. Sozhamannan,, and D. K. Chattoraj. 1994. Relaxation of replication control in chaperone-independent initiator mutants of plasmid PI EMBO J. 13: 2089 2096.
159. Mukhopadhyay, S.,, and D. K. Chattoraj. 2000. Replication induced transcription of an autorepressed gene: the replication initiator gene of plasmid PI. Proc. Natl. Acad. Sci. USA 97: 7142 7147.
160. Murakami, Y.,, H. Ohmori,, T. Yura, and T, Nagata. 1987. Requirement of the Escherichia coli dnaA gene function for ori-2-dependent mini-F plasmid replication. J. Bacteriol. 169: 1724 1730.
161. Murchie, A. I.,, R. Bowater,, F. Aboul-ela,, and D. M. Lilley. 1992. Helix opening transitions in supercoiled DNA. Biochim. Biophys. Acta 1131: 1 15.
162. Murotsu, T.,, and K. Matsubara. 1980. Role of an autorepression system in the control of λdv plasmid copy number and incompatibility. Mol. Gen. Genet. 179: 509 519.
163. Murotsu, T.,, K. Matsubara,, H. Sugisaki,, and M. Takanami. 1981. Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid. Gene 15: 257 271.
164.Nieto, C , R. Giraldo, E. Fernandez-Tresguerres, and R. Diaz. 1992. Genetic and functional analysis of the basic replicon of pPSlO, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae pathovar savastanoi. J. Mol. Biol. 223: 41526.
165. Niki, H.,, and S. Hiraga. 1997. Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli. Cell 90: 951 957.
166.Nishida, S.K. Fujimitsu, K. Sekimizu, T. Ohmura, T. Ueda, and T. Katayama. 2002. A nucleotide switch in the Escherichia coli DnaA protein initiates chromosomal replication: evidence from a mutant DnaA protein defective in regulatory ATP hydrolysis in vitro and in vivo. J. Biol. Chem. 277: 1498614995.
167. Nordstrom, K. 1985. Control of plasmid replication: theoretical considerations and practical solutions. Basic Life Sci. 30: 189 214.
168. Nordstrom, K. 1990. Control of plasmid replication—how do DNA iterons set the replication frequency? Cell 63: 1121 1124.
169. Nordstrom, K.,, and S. J. Austin. 1989. Mechanisms that contribute to the stable segregation of plasmids. Annu. Rev. Genet. 23: 37 69.
170. Nordstrom, K.,, S. Molin,, and J. Light. 1984. Control of replication of bacterial plasmids: genetics, molecular biology, and physiology of the plasmid R1 system. Plasmid 12: 71 90.
171. Novick, R. P. 1987. Plasmid incompatibility. Microbiol. Rev. 51: 381 395.
172.Ortega, S,, E, Lanka, and R. Diaz. 1986. The involvement of host replication proteins and of specific origin sequences in the in vitro replication of miniplasmid Rl DNA. Nucleic Acids Res. 14: 486579.
173. Pak, M.,, and S. Wickner, 1997. Mechanism of protein remodeling by ClpA chaperonc. Proc. Natl. Acad. Sci. USA 94: 4901 4906.
174. Pal, S. K.,, and D. K, Chattoraj. 1988. PI plasmid replication: initiator sequestration is inadequate to explain control by initiator-binding sites. J. Bacteriol. 170: 3554 3560.
175. Pal, S. K.,, R . J . Mason,, and D. K. Chattoraj. 1986. PI plasmid replication. Role of initiator titration in copy number control. J. Mol. Biol. 192: 275 285.
176. Panayotatos, N.,, and R. D. Wells. 1981. Cruciform structures in supercoiled DNA. Nature 289: 466 470.
177. Papp, P. P., D, K. Chattoraj, and T. D. Schneider. 1993. Information analysis of sequences that bind the replication initiator RepA. Mol Biol. 233: 219 230.
178. Papp, P. P.,, and V. N. Iyer. 1995. Determination of the binding sites of RepA, a replication initiator protein of the basic replicon of the IncN group plasmid pCU1. J. Mol Biol. 246: 595 608.
179. Papp, P. P.,, G. Mukhopadhyay,, and D. K, Chattoraj. 1994. Negative control of plasmid DNA replication by iterons. Correlation with initiator binding affinity. J. Biol. Chem. 269: 23563 23568.
180. Park, K.,, and D. K. Chattoraj, 2001. DnaA boxes in the PI plasmid origin: the effect of their position on the directionality of replication and plasmid copy number, J. Mol. Biol. 310: 69 81.
181. Park, K.,, E. Han,, J . Paulsson,, and D. K. Chattoraj. 2001. Origin pairing ('handcuffing') as a mode of negative control of Pi plasmid copy number. EMBO J. 20: 7323 7332.
182. Park, K.,, S. Mukhopadhyay,, and D. K. Chattoraj. 1998. Requirements for and regulation of origin opening of plasmid PI J. Biol. Chem. 273: 24906 24911.
183. Perez-Casal, J. F.,, A. E. Gammie,, and J. H. Crosa. 1989. Nucleotide sequence analysis and expression of the minimum REPI replication region and incompatibility determinants of pColV-K30. J. Bacteriol. 171: 2195 2201. ( Erratum, 173:2409, 1991.)
184. Perri, S.,, D. R. Helinski,, and A. Toukdarian. 1991. Interactions of plasmid-cncoded replication initiation proteins with the origin of DNA replication in the broad host range plasmid RK2. J. Biol. Chem. 266: 12536 12543.
185. Persson, C.,, E. G. Wagner,, and K. Nordstrom. 1990. Control of replication of plasmid Rl: structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT. EMBO J. 9: 3767 3775.
186. Pogliano, J. T . Q. Ho, Z, Zhong, and D. R. Helinski. 2001. Multicopy plasmids are clustered and localized in Escherichia coli. Proc. Natl. Acad. Sci. USA 98: 4486 4491.
187. Polaczek, P. 1990. Bending of the origin of replication of E. coli by binding of IHF at a specific site. New Biol. 2: 265 271.
188. Prentki, P., M, Chandler, and D. J. Galas. 1987. Escherichia coli integration host factor bends the DNA at the ends of IS 1 and in an insertion hotspot with multiple IHF binding sites. EMBO J. 6: 2479 2487.
189. Pritchard, R. H., 1978. Control of DNA replication in bacteria, p, 1 22, In I. Molineux, and M. Kohiyama (ed,), DNA Synthesis: Present and Future. Plenum Press, New York, N.Y.
190. Pritchard, R. H.,, P. T. Barth,, and J. Collins,. 1969. Control of DNA synthesis in bacteria, p. 263 297. In P. Meadow, and S. J. Pirt (ed) Microbial Growth: Nineteenth Symposium of the Society for General Microbiology. University Press, London, United Kingdom.
191. Ptashne, M. 1987. A Genetic Switch. Cell Press and Blackwell Scientific Publications, Cambridge, Mass.
192. Ratnakar, P. V.,, B. K. Mohanty,, M. Lobert,, and D. Bastia. 1996. The replication initiator protein n of the plasmid R6K specifically interacts with the host-encoded helicase DnaB. Proc. Natl. Acad. Sci. USA 93: 5522 5526.
193. Rice, P. A. 1997. Making DNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol 7: 86 93.
194. Rice, P. A.,, S. 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.
195. Rippe, K. 2001. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26: 733 740.
196. Roberts, R . J . 1995. On base flipping. Cell 82: 9 12.
197. Sakai, H.,, and T. Komano. 1996. DNA replication of IncQ broad-host-range plasmids in gram-negative bacteria. Biosci. Biotechnol. Biochem. 60: 377 382.
198. Sakakibara, Y. 1988. The dnaK gene of Escherichia coli functions in initiation of chromosome replication. J. Bacteriol 170: 972 979.
199. Scherzinger, E.,, G. Zicgelin,, M. Barccna,, J . M. Carazo,, R. Lurz,, and E. Lanka. 1997. The RepA protein of plasmid RSF1010 is a replicative DNA helicase. J. Biol. Chem. 272: 30228 30236.
200. Schleif, R. 1992. DNA looping. Annu. Rev. Biochem. 61: 199 223.
201. Schmidhauser, T. J., M, Filutowicz, and D. R. Helinski. 1983. Replication of derivatives of the broad host range plasmid RK2 in two distantly related bacteria. Plasmid 9: 325 330.
202. Schneider, T. D. 2001. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res. 29: 4881 4891.
203. Schnos, M.,, K. Zahn,, R. B. Inman,, and F. R. Blattncr. 1988. Initiation protein induced helix destabilization at the λ origin: a prepriming step in DNA replication. Cell 52: 385 395.
204. Seeman, N. C.,, J. M. Rosenberg,, and A. Rich. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Set. USA 73: 804 808.
205. Shafferman, A.,, R. Kolter,, D. Stalker,, and D. R. Helinski. 1982. Plasmid R6K DNA replication. III. Regulator properties of the π initiation protein. J. Mol. Biol. 161: 57 76.
206. Sharma, R.,, A. Kachroo,, and D. Bastia. 2001. Mechanistic aspects of DnaA-RepA interaction as revealed by yeast forward and reverse two-hybrid analysis. EMBO J. 20: 4577 4587.
207. Singleton, C. K. J. Klysik, S. M, Stirdivant, and R. D. Wells. 1982. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature 299: 312 316.
208. Skarstad, K.,, T. A. Baker,, and A. Kornbcrg. 1990. Strand separation required for initiation of replication at the chromosomal origin of E. coli is facilitated by a distant RNA— DNA hybrid. EMBO J. 9: 2341 2348.
209. Skovgaard, O.,, K. Olesen,, and A. Wright. 1998. The central lysine in the P-loop motif of the Escherichia coli DnaA protein is essential for initiating DNA replication from the chromosomal origin, oriC, and the F factor origin, oriS, but is dispensable for initiation from the PI plasmid origin, oriK. Plasmid 40: 91 99.
210. Slater, S.,, S. Wold,, M. Lu,, E. Boye,, K. Skarstad,, and N. Kleckner. 1995. E. coli SeqA protein binds or/C in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82: 927 936.
211. Sompayrac, L.,, and O. Maaloc. 1973. Autorepressor model for control of DNA replication. Nat. New Biol 241: 133 135.
212. Speck, C.,, and W. Messer. 2001. Mechanism of origin unwinding: sequential binding of DnaA to double- and single- stranded DNA. EMBO. J. 20: 1469 1476.
213. Stalker, D. M.,, M. Filutowicz,, and D. R. Helinski. 1983. Release of initiation control by a mutational alteration in the R6K n protein required for plasmid DNA replication. Proc. Natl. Acad. Sci. USA 80: 5500 5504.
214. Stalker, D. M.,, R. Kolter, and D, R. Helinski. 1982. Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment. J. Mol. Biol 161: 33 43,
215. Stenzel, T. T.,, T. MacAllister,, and D. Bastia. 1991. Cooperativity at a distance promoted by the combined action of two replication initiator proteins and a DNA bending protein at the replication origin of pSC101. Genes Dev. 5: 1453 1463. ( Erratum, 5:2362.)
216. Stenzel, T. T.,, P. Patel,, and D. Bastia. 1987. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell 49: 709 717.
217. Sugiura, S.,, M. Tanaka,, Y. Masamune,, and K. Yamaguchi. 1990. DNA binding properties of purified replication initiator protein (Rep) encoded by plasmid pSClOl J. Biochem. (Tokyo) 107: 369 376.
218. Sullivan, K. M.,, and D. M. Lilley. 1986. A dominant influence of flanking sequences on a local structural transition in DNA. Cell 47: 817 827.
219. Sullivan, K. M.,, and D. M. Lilley. 1988. Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules. Nucleic Acids Res. 16: 1079 1093.
220. Swack, J.,, A., S. K. Pal, R. J. Mason, A. L. Abeles, and D. K. Chattoraj. 1987. PI plasmid replication: measurement of initiator protein concentration in vivo. J. Bacteriol 169: 3737 3742.
221. Tamm, J.,, and B. Polisky. 1985. Characterization of the ColEl primcr-RNAl complex: analysis of a domain of ColE1 RNA1 necessary for its interaction with primer RNA. Proc. Natl. Acad. Sci. USA 82: 2257 2261.
222. Terawaki, Y.,, and Y. Itoh. 1985. Copy mutant of mini-Rts 1: lowered binding affinity of mutated RepA protein to direct repeats. J. Bacteriol 162: 72 77.
223. Thompson, J. F.,, and A. Landy. 1988. Empirical estimation of protein-induced DNA bending angles: applications to X site-specific recombination complexes. Nucleic Acids Res. 16: 9687 9705.
224. Tomizawa, J. 1984. Control of ColEl plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38: 861 870.
225. Tomizawa, J.,, and T. Som. 1984. Control of ColE1 plasmid replication: enhancement of binding of RNA 1 to the primer transcript by the Rom protein. Cell 38: 871 878.
226. Toukdarian, A. E.,, and D. R. Helinski. 1998. TrfA dimers play a role in copy-number control of RK2 replication. Gene 223: 205 211.
227. Toukdarian, A. E.,, D. R. Helinski,, and S. Perri. 1996. The plasmid RK2 initiation protein binds to the origin of replica- 243. tion as a monomer. J. Biol. Chem. 271: 7072 7078.
228. Trawick, J. D.,, and B. C. Kline. 1985. A two-stage molecular model for control of mini-F replication. Plasmid 13: 59 69.
229. Tsurimoto, T.,, and K. Matsubara. 1981. Purified bacteriophage λO protein binds to four repeating sequences at the λ replication origin. Nucleic Acids Res. 9: 1789 1799.
230. Uga, H.,, F. Matsunaga,, and C. Wada. 1999. Regulation of DNA replication by iterons: an interaction between the ori2 245. and incC regions mediated by RcpE-bound iterons inhibits DNA replication of mini-F plasmid in Escherichia coli. EMBO J. 18: 3856 3867.
231.Urh, M.Y. Flashner, A. Shaffcrman, and M. Filutowicz, 1995. Altered (copy-up) forms of initiator protein n suppress the point mutations inactivating the y origin of plasmid R6K. Bacteriol. 177: 67326739.
232. Urh, M.,, J. Wu,, K. Forest,, R. B. Inman,, and M. Filutowicz. 1998. Assemblies of replication initiator protein on symmetric and asymmetric DNA sequences depend on multiple 248. protein oligomerization surfaces. J. Mol. Biol 283: 619 631.
233. Urh, M.,, D. York,, and M. Filutowicz. 1995. Buffer composition mediates a switch between cooperative and independent binding of an initiator protein to DNA. Gene 164: 1 7.
234.Vocke, C , and D. Bastia. 1983. DNA-protein interaction at the origin of DNA replication of the plasmid pSC101. Cell 35: 495502.
235. Wegrzyn, A.,, and G. Wegrzyn. 2001. Inheritance of the replication complex: a unique or common phenomenon in the control of DNA replication? Arch. Microbiol 175: 86 93.
236. Wegrzyn, A.,, and G. Wegrzyn. 1998. Random inheritance of 251. the replication complex by one of two daughter X plasmid copies after a replication round in Escherichia coli. Biochem. Biophys. Res. Commun. 246: 634 639.
237. Wegrzyn, G.,, and K. Taylor. 1992. Inheritance of the replica- 252. tion complex by one of two daughter copies during X plasmid replication in Escherichia coli. J. Mol. Biol 226: 681 688.
238. Wei, T.,, and R. Bcrnander. 1996. Interaction of the Ici A protein with AT-rich regions in plasmid replication origins. Nucleic Acids Res. 24: 1865 1872.
239. Wickner, S.,, J. Hoskins,, D. Chattoraj,, and K. McKcnncy. 1990. Deletion analysis of the mini-IM plasmid origin of replication and the role of Escherichia coli DnaA protein. J. Biol. Chem. 265: 11622 11627.
240. Wickner, S.,, J. Hoskins,, and K. McKenney. 1991. Monomerization of RepA dimers by heat shock proteins 255, activates binding to DNA replication origin. Proc. Natl. Acad. Set. USA 88: 7903 7907.
241. Wickner, S.,, D. Skowyra,, J . Hoskins,, and K. McKenney. 1992. DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. USA 89: 10345 10349.
242. Wickner, S. H. 1990. Three Escherichia coli heat shock proteins are required for PI plasmid DNA replication: formation of an active complex between E. coli DnaJ protein and the PI initiator protein. Proc. Natl. Acad. Sci. USA 87: 2690 2694.
243. Wickner, S. H.,, and D. K. Chattoraj. 1987. Replication of mini-Pi plasmid DNA in vitro requires two initiation proteins, encoded by the repA gene of phage PI and the dnaA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 84: 3668 3672.
244. Wold, M. S.,, J. B. Mallory,, J. D. Roberts,, J. H. LeBowitz,, and R. McMacken. 1982. Initiation of bacteriophage λ DNA replication in vitro with purified λ replication proteins. Proc. Natl. Acad. Sci. USA 79: 6176 6180.
245. Wu, F.,, I. Goldberg,, and M. Filutowicz. 1992. Roles of a 106-bp origin enhancer and Escherichia coli DnaA protein in replication of plasmid R6K. Nucleic Acids Res. 20: 811 817.
246. Wu, F.,, I. Levchenko,, and M. Filutowicz. 1994. Binding of DnaA protein to a replication enhancer counteracts the inhibition of plasmid R6K γ origin replication mediated by elevated levels of R6K π protein. J. Bacteriol. 176: 6795 6801.
247. Wu, F.,, I. Levchenko,, and M. Filutowicz. 1995. A DNA segment conferring stable maintenance on R6K γ-origin core replicons. J. Bacteriol 177: 6338 6345
248. Wu, F.,, J. Wu,, J. Ehley,, and M. Filutowicz. 1996. Preponderance of Fis-binding sites in the R6K y origin and the curious effect of the penicillin resistance marker on replication of this origin in the absence of Fis. J. Bacteriol. 178: 4965 4974. ( Erratum, 179:2464, 1997.)
249. Tsuchimoto, S., and E Ohstubo. 1989. Effect of the pem system on stable maintenance of plasmid R100 in various Escherichia coli hosts. Mol. Gen. Genet. 215: 463 468.
250. Xia, G.,, D. Mancn,, Y. Yu,, and L. Caro. 1993. In vivo and in vitro studies of a copy number mutation of the RepA replication protein of plasmid pSC101. J. Bacteriol. 175: 4165 4175.
251. 0Yamamoto, T.,, J. Mclntyrc,, S. M. Sell,, C. Georgopoulos,, D. Skowyra,, and M. Zylicz. 1987. Enzymology of the pre-priming steps in Xdv DNA replication in vitro. J. Biol. Chem. 262: 7996 7999.
252. Yoshimoto, H.,, and M. Yoshikawa. 1975. Chromosome plasmid interaction in Escherichia coli K-12 carrying a thermo sensitive plasmid, Rtsl, in autonomous and in integrated states. J. Bacteriol. 124: 661 667.
253. Yoshimura, S. H.,, R. L. Ohniwa,, M. H. Sato,, F. Matsunaga,, G. Kobayashi,, H. Uga, C Wada, and K. Takeyasu. 2000. DNA phase transition promoted by replication initiator. Biochemistry 39: 9139 9145.
254. Yung, B. Y.,, and A. Kornbcrg. 1989. The dnaA initiator protein binds separate domains in the replication origin of Escherichia coli. J. Biol. Chem. 264: 6146 6150.
255. Zahn, K.,, and F. R. Blattner. 1987. Direct evidence for DNA bending at the X replication origin. Science 236: 416 422.
256. Zylicz, M.,, D. Ang,, K. Liberek,, and C. Georgopoulos. 1989. Initiation of X DNA replication with purified host- and bacteriophage- encoded proteins: the role of the dnaK, dnaJ and grpE heat shock proteins. EMBO J. 8: 1601 1608.

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