Participating Elements in the Replication of Iteron-Containing Plasmids

Ricardo Krüger; Sheryl A. Rakowski; Marein Filutowiez

doi:10.1128/9781555817732.ch2

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

Authors: Ricardo Krüger¹, Sheryl A. Rakowski¹, Marein Filutowiez¹

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Affiliations: 1: Department of Bacteriology, University of Wisconsin. Madison, Wl 53706

Content Type: Monograph

Publication Year: 2004

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817732

Chapter DOI: 10.1128/9781555817732.ch2

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Abstract:

The presence of Rep-binding iterons is a hallmark, not only of many prokaryotic plasmid orfs but of chromosomal, viral (phage), and eukaryotic ori’s(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 ori’s. 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 Escherichia coli 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 ori activation, and focuses on Rep/iteron-mediated replication of minimal ICPs in E. coli. 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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Participating Elements in the Replication of Iteron-Containing Plasmids

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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).

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Figure 1

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Figure 2

Regulation models for ICP replication. ( 1 ) Rep dimers are able to bind to the operator/promoter region (Op/Pr) and negatively regulate Rep production (minus sign). ( 2 ) Monomers of the replication initiator activate origin (ori) replication (plus sign). Panels 3 to 5 represent variations of the “handcuffing model.” ( 3 ) 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). ( 4 ) Dimers of the Rep protein bridge two plasmids by associations with monomers bound to iterons. ( 5 ) A single layer of dimers binds the iterons of two ori's, applicable only for those systems where dimers can directly bind iterons. ( 6 ) 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.

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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.

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References

/content/book/10.1128/9781555817732.chap2

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: 8139– 8143.

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: 513– 516.

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: 239– 273.

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: 1113– 1121.

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: 329– 348.

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: 14378– 14382.

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: 65– 68.

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: 5– 12.

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: 7552– 7557.

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: 415– 26.

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: 14986– 14995.

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: 4865– 79.

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: 6732– 6739.

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: 495– 502.

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.