Mechanistic studies of initiator-initiator interaction and replication initiation

EMBO Journal

Volumn 17, Issue 17, 1998, Pages 5192-5200

  Lu, Ya Bin ^a   Datta, Hirock J ^a   Bastia, Deepak ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

protein; DnaA; IHF; Protein protein interaction; Replication control

Indexed keywords

DNA A; INTEGRATION HOST FACTOR; PLASMID DNA;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA REPLICATION; ESCHERICHIA COLI; NONHUMAN; PLASMID; PRIORITY JOURNAL;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA HELICASES; DNA REPLICATION; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; ESCHERICHIA COLI; INTEGRATION HOST FACTORS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; PLASMIDS; PROTEIN BINDING; PROTEIN FOLDING; TRANS-ACTIVATORS;

ESCHERICHIA COLI; NEGIBACTERIA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0032167615     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/17.17.5192     Document Type: Article

References (47)

1. Ables, A.L. and Austin, S.J. (1991) Antiparallel plasmid-plasmid pairing may control P1 plasmid replication. Proc. Natl Acad. Sci. USA, 88, 9011-9015.
2. Bell, S.P. and Stillman, B. (1992) ATP-dependent recognition of eukaryotic origin of replication by a multiprotein complex. Nature, 357, 128-134.
3. Bernander, R., Krabbe, M. and Nordström, K. (1992) Mapping of the in vivo start site for leading strand DNA synthesis in plasmid R1. EMBO J., 11, 4481-4487.
4. Blasina, A., Kittel, B., Toukdarian, A.E. and Helmski, D.R. (1996) Copy-up mutants of plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins. Proc. Natl Acad. Sci. USA, 93, 3559-3564.
5. Borowicz, J.A., Zhang, L., Sasse-Dwight, S. and Gralla, J.D. (1987) DNA-supercoiling promotes formation of a bent repression loop in lac DNA. J. Mol. Biol., 196, 101-111.
6. Chattoraj, D.K. and Schneider, T.D. (1997) Replication control of plasmid P1 and its host chromosome: the common ground. Prog. Nucleic Acids Res. Mol. Biol., 57, 145-186.
7. Crosa, J.H. (1980) Three origins of DNA replication are active in vivo in Escherichia coli. J. Biol. Chem., 255, 11075-11077.
8. Crosa, J.H., Luttrop, L.K. and Falkow, S. (1976) Mode of replication of the conjugative R-plasmid R6K in Escherichia coli. J. Bacteriol., 126, 454-456.
9. Crosa, J.H., Luttrop, L. and Falkow, S. (1978) Molecular cloning of replication and incompatibility regions of the R plasmid R6K. J. Mol. Biol., 124, 443-468.
10. Filutowicz, M. and Appelt, K. (1988) The integration host factor of E.coli binds to multiple sites at plasmid R6K γ origin and is essential for replication. Nucleic Acids Res., 16, 3829-3841.
11. Filutowicz, M., Uhlenhopp, E. and Helinski, D.R. (1985) Binding of purified π initiator protein to a replication origin region of R6K. J. Mol. Biol., 187, 225-239.
12. Gaylo, P.J., Turjman, N. and Bastia, D. (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.
13. Germino, J. and Bastia, D. (1983a) Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA. Cell, 34, 125-134.
14. Germino, J. and Bastia, D. (1983b) The replication initiator protein of plasmid R6K tagged with beta-galactosidase shows sequence-specific DNA-binding. Cell, 32, 131-140.
15. Gille, H. and Messer, W. (1991) Localized DNA melting and structural perturbations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J., 10, 1579-1584.
16. Hansen, E.B. and Yarmolinsky, M.B. (1986) Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F. Proc. Natl Acad. Sci. USA, 83, 4423-4427.
17. Hasunuma, K. and Sekiguchi, M. (1977) Replication of plasmid pSC101 in Escherichia coli K12: requirement for dnaA function. Mol. Gen. Genet., 154, 225-230.
18. Hwang, D.S. and Kornberg, A. (1992) Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J. Biol. Chem., 267, 23083-23086.
19. Inuzuka, M. and Wada, Y. (1995) Single amino acid alteration in the initiator protein is responsible for the DNA overproduction phenotype of copy number mutants of plasmid R6K. EMBO J., 4, 2301-2307.
20. Jacob, E. Brenner, S. and Cuzin, F. (1964) On the regulation of DNA replication in bacteria. Cold Spring Harb. Symp. Quant. Biol., 28, 329-348.
21. Kelley, W.L. and Bastia, D. (1992) Activation in vivo of the minimal replication origin b of plasmid R6K requires a small target sequence essential for DNA looping. New Biol. 4, 569-580.
22. Kelley, W.L. and Bastia, D. (1991) Conformational changes induced by integration host factor at origin γ of R6K and copy number control. J. Biol. Chem., 266, 15924-15937.
23. Kelley, W.L., Patel, I. and Bastia, D. (1992) Structural and functional analysis of a replication enhancer: separation of enhancer activity from origin function by mutational dissection of the replication origin γ of plasmid R6K. Proc. Natl Acad. Sci. USA, 89, 5078-5082.
24. Kittel, B.L. and Helinski, D.R. (1991) Iteron inhibition of plasmid RK2 in vitro: evidence for intermolecular coupling of replication origins as a mechanism of RK2 replication control., Proc. Natl Acad. Sci. USA, 88, 1389-1393.
25. Kolter, R. and Helinski, D.R. (1978) Construction of plasmid R6K derivatives in vitro: characterization of the R6K replication region. Plasmid, 1, 571-580.
26. Kolter, R., Stalker, D.M., Thomas, C.M. and Helinski, D.R. (1982) Plasmid R6K DNA replication II: direct nucleotide sequence repeats are required for an active γ origin. J. Mol. Biol., 161, 45-56.
27. Konieczny, I., Doran, K.S., Helinski, D.R. and Blasina, A. (1997) Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication the broad host range plasmid RK2. J. Biol. Chem., 272, 20173-20178.
28. Lovett, M., Sparks, R.A. and Helinski, D.R. (1975) Bidirectional replication of plasmid R6K DNA in E.coli: Correspondence between origin of replication and a single strand break in relaxed complexes. Proc. Natl Acad. Sci. USA, 72, 2905-2909.
29. Macrina, F., Weatherly, G.G. and Curtis, R. (1974) R6K plasmid replication: influence of chromosomal genotypes in mini cell producing strains of E.coli. J. Bacteriol., 120, 1387-1400.
30. MacAllister, T., Kelley, W., Miron, A., Stenzel, T. and Bastia, D. (1991) Replication of plasmid R6K γ origin in vitro: dependence on dual initiator proteins and inhibition by transcription. J. Biol. Chem., 266, 16056-16062.
31. Masai, H., Nomura, N. and Arai, K.-I. (1990) The ABC primosome system. J. Biol. Chem., 265, 15134-15144.
32. McEachern, M., Bott, M.A., Tooker, P.A. and Helinski, D.R. (1989) Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins. Proc. Natl Acad. Sci. USA, 86, 7942-7946.
33. Miron, A., Mukherjee, S. and Bastia, D. (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, 1205-1211.
34. Mizushima, T., Nishida, S., Kurokawa, K., Katayama, T., Miki, T. and Sekimizu, K. (1997) Negative control of DNA replication by hydrolysis of ATP-bound DnaA protein, the initiation of chromosomal DNA replication of Escherichia coli. EMBO J., 16, 3724-3730.
35. Mukherjee, S., Erickson, H. and Bastia, D. (1988a) Detection of DNA looping due to simultaneous interaction of a DNA-binding protein with two spatially separated binding sites on DNA. Pror. Natl Acad. Sci. USA, 85, 6287-6291.
36. Mukherjee, S., Erickson, H. and Bastia, D. (1988b) Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell, 52, 375-383.
37. Mukhopadhyay, G., Carr, K.M., Kaguni, J.M. and Chattoraj, D.K. (1993) Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J., 12, 4547-4554.
38. Nash, H., Robertson, C.A., Flamm, E., Weisberg, R.A. and Miller, H.I. (1987) Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J. Bacteriol., 169, 4124-4127.
39. Nordstrom, K. (1991) Control of plasmid replication - how do DNA iterons set the replication frequency. Cell, 63, 1121-1124.
40. Pal, S.K. and Chattoraj, D.K. (1988) P1 plasmid replication initiator sequestration is inadequate to explain control by initiator binding sites. J. Bacteriol., 170, 3554-3560.
41. Ratnakar, P.V.A.L., Mohanty, B.K., Lobert, M. and Bastia, D. (1986) The replicator initiator protein II of plasmid R6K physically interacts with the replicative helicase DnaB. Proc. Natl Acad. Sci. USA, 93, 5522-5526.
42. Sekimizu, K., Bramhill, D., Kornberg, A., Baker, T.A., Funnell, B.E. and Kornberg, A. (1987) ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E.coli chromosome. Cell, 50, 259-265.
43. Shon, M., Germino, J. and Bastia, D. (1982) The nucleotide sequence of the replication origin beta of the plasmid R6K. J. Biol. Chem., 257, 13823-13827.
44. Stalker, D.M., Kolter, R., Tolun, A. and Helinski, D.R. (1982a) Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment: Separation of the minimal replication region of the F plasmid into a replication origin segment and a trans-acting segment. J. Mol. Biol., 161, 33-43.
45. Stalker, D.M., Thomas, C.M. and Helinski, D.R. (1982b) Plasmid R6K DNA replication. II. Direct nucleotide sequence repeats are required for an active γ-origin. J. Mol. Biol., 161, 45-56.
46. Stenzel, T.T., MacAllister, T. and Bastia, D. (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.
47. von Meyenburg, K., Hansen, F.G., Riise, E., Bergman, H.E.N., Meijer, M. and Messer, W. (1979) Origin of replication oriC of Escherichia coli K12: genetic mapping and minichromosome replication. Cold Spring Harbor Symp. Quant. Biol., 43, 121-128.