Regulatory implications of protein assemblies at the γ origin of plasmid R6K - A review

Gene

Volumn 223, Issue 1-2, 1998, Pages 195-204

  Filutowicz, Marcin ^a   Rakowski, Sheryl A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Direct repeat; Handcuffing; Initiator protein; Inverted half repeat; Iteron; Protein oligomerization; Replication origin

Indexed keywords

DNA; INITIATION FACTOR;

CONFERENCE PAPER; DNA REPLICATION ORIGIN; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE TARGETING; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN POLYMERIZATION; PROTEIN STRUCTURE;

BASE SEQUENCE; BINDING SITES; DNA HELICASES; DNA REPLICATION; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; PLASMIDS; REGULATORY SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; TRANS-ACTIVATORS;

ESCHERICHIA COLI;

EID: 0032570060     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(98)00367-9     Document Type: Conference Paper

References (90)

1. Alfano C., McMacken R. Ordered assembly of nucleoprotein structures at the bacteriophage l replication origin during the initiation of DNA replication. J. Biol. Chem. 264:1989;10699-10708.
2. Baker T.A., Sekimizu K., Funnell B.E., Kornberg A. Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the origin of the Escherichia coli chromosome. Cell. 45:1986;53-64.
3. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collardo-Vides J., Glasner J.D., Rode C.K., Mayhew G., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M., Rose D., Mau R., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462.
4. Bramhill D., Kornberg A. A model for initiation at origins of DNA replication. Cell. 54:1988;915-918.
5. Carra J.H., Schleif R.F. Formation of AraC-DNA sandwiches. Nucleic Acids Res. 21:1993;435-438.
6. Carra J.H., Schleif R.F. Variation of half-site organization and DNA looping by AraC protein. EMBO J. 12:1993;35-44.
7. Chattoraj D.K., Ghirlando R., Park K., Dibbens J.A., Lewis M.S. Dissociation kinetics of RepA dimers: implicatons for mechanisms of activation of DNA binding by chaperones. Genes Cells. 1:1996;189-199.
8. Chen D., Feng J., Urh M., Inman R.B., Filutowicz M. Replication of R6K γ origin in vitro: discrete start sites for DNA synthesis dependent on π and its copy-up variants. J. Mol. Biol. 282:1998;775-787.
9. Corton J., Johnston S. Altering DNA-binding specificity of GAL4 requires sequences adjacent to the zinc finger. Nature. 340:1989;724-727.
10. DasGupta S., Mukhopadhyay G., Papp P.P., Lewis M.S., Chattoraj D.K. Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK. J. Mol. Biol. 232:1993;23-34.
11. Dellis S., Filutowicz M. Integration host factor of Escherichia coli reverses the inhibition of R6K plasmid replication by π initiator protein. J. Bacteriol. 173:1991;1279-1286.
12. Dellis S., Feng J., Filutowicz M. Replication of plasmid R6K γ origin in vivo and in vitro: dependence on IHF binding to the ihf1 site. J. Mol. Biol. 257:1996;550-560.
13. Dodson M., Echols H., Wickner S., Alfano C., Mensa-Wilmot K., Gomes B., LeBowitz J., Roberts J.D., McMacken R. Specialized nucleoprotein structures at the origin of replication of bacteriophage l: localized unwinding of duplex DNA by a six-protein reaction. Proc. Natl. Acad. Sci. USA. 83:1986;7638-7642.
14. Echols H. Multiple DNA-protein interactions governing high-precision DNA transactions. Science. 233:1986;1050-1056.
15. Eustanace R.J., Bustos S.A., Schleif R.F. Reaching out (locating and lengthening the interdomain linker in AraC protein). J. Mol. Biol. 242:1994;330-338.
16. Eustanace R.J., Schleif R.F. In vivo association of protein fragments giving active AraC. Proteins. 25:1996;501-505.
17. Filutowicz M., Appelt K. The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K γ origin and is essential for replication. Nucleic Acids Res. 16:1988;3829-3841.
18. Filutowicz M., Davis G., Greener A., Helinski D. Autorepressor properties of the π-initiation protein encoded by plasmid R6K. Nucleic Acids Res. 13:1985;103-114.
19. Filutowicz, M., McEachern, M.J., Greener, A., Mukhopadhyay, P., Uhlenhopp, E., Durland, R., Helinski, D.R., 1985b. Role of the π initiation protein and direct nucleotide sequence repeats in the regulation of plasmid R6K replication. In: Helinski, D.R., Cohen, S.N., Clewell, D.B., Jackson, D.A., Hollaender, A. (Eds.), Plasmids in Bacteria. Plenum Publishing, New York, pp. 125-140.
20. Filutowicz M., Uhlenhopp E., Helinski D.R. Binding of purified wild-type and mutant π initiation proteins to a replication origin region of plasmid R6K. J. Mol. Biol. 187:1985;225-239.
21. Filutowicz M., McEachern M.J., Helinski D.R. Positive and negative roles of an initiator protein at an origin of replication. Proc. Natl. Acad. Sci. USA. 83:1986;9645-9649.
22. Filutowicz, M., Dellis, S., Levchenko, I., Urh, M., Wu, F., York, D., 1994a. Regulation of replication of an iteron-containing DNA molecule. In: Cohn, W., Moldave, K. (Eds.), Progress in Nucleic Acid Research and Molecular Biology. Academic Press, San Diego, CA, pp. 239-273.
23. Filutowicz M., York D., Levchenko I. Cooperative binding of initiator protein to replication origin conferred by single amino acid substitution. Nucleic Acids Res. 22:1994;4211-4215.
24. Funnell B.E., Baker T.A., Kornberg A. Complete enzymatic replication of plasmids containing the origin of the Escherichia coli chromosome. J. Biol. Chem. 261:1986;5616-5624.
25. Germino J., Bastia D. Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA. Cell. 34:1983;125-134.
26. Greener A., Filutowicz M., McEachern M.J., Helinski D.R. N-Terminal truncated forms of the bifunctional π initiation protein express negative activity on plasmid R6K replication. Mol. Gen. Genet. 224:1990;24-32.
27. Gubler M., Bickle T.A. Increased protein flexibility leads to promiscuous protein-DNA interactions in type IC restriction-modification system. EMBO J. 10:1991;951-957.
28. Inuzuka M. Plasmid-encoded initiation protein is required for activity at all three origins of plasmid R6K DNA replication in vitro. FEBS Lett. 181:1985;236-240.
29. Irani M.H., Laszlo O., Adhaya S. A control element within a structural gene: the gal operon of Escherichia coli. Cell. 32:1983;783-788.
30. Ishiai M., Wada C., Kawasaki Y., Yura T. Replication initiatior protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor). Proc. Natl. Acad. Sci. USA. 91:1994;3839-3843.
31. Kaguni J.M., Fuller R.S., Kornberg A. Enzymatic replication of E. coli chromosomal origin is bidirectional. Nature. 296:1982;623-627.
32. Kawasaki Y., Wada C., Yura T. Roles of Escherichia coli heat shock proteins DnaK, DnaJ and GrpE in mini-F plasmid replication. Mol. Gen. Genet. 220:1990;227-282.
33. Kawasaki Y., Wada C., Yura T. Binding of RepE initiator protein to mini-F DNA origin (ori2). J. Biol. Chem. 267:1992;11520-11524.
34. Kelley W.L., Bastia D. Replication initiator protein of plasmid R6K autoregulates its own synthesis at the transcriptional step. Proc. Natl. Acad. Sci. USA. 82:1985;2574-2578.
35. Kelley W.L., Patel I., Bastia D. Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin γ of plasmid R6K. Proc. Natl. Acad. Sci. USA. 89:1992;5078-5082.
36. Kim Y.-J., Meyer R.J. An essential iteron-binding protein required for plasmid R1162 replication induces localized melting within the origin at a specific site in AT-rich DNA. J. Bacteriol. 173:1991;5539-5545.
37. Kobori J.A., Kornberg A. The Escherichia coli dnaC gene product, III. Properties of the DnaB-DnaC protein complex. J. Biol. Chem. 257:1982;13770-13775.
38. Kogoma T. Stable DNA replication: interplay between DNA replication, homologous recombination and transcription. Microbiol. Mol. Biol. Rev. 61:1997;212-238.
39. Kolter R., Helinski D.R. Plasmid R6K DNA replication, II. Direct nucleotide sequence repeats are required for an active γ-origin. J. Mol. Biol. 161:1982;45-56.
40. Kolter R., Inuzuka M., Helinski D.R. Trans-complementation-dependent replication of a low molecular weight origin fragment from plasmid R6K. Cell. 15:1978;1199-1208.
41. Kornberg, A., Baker, T., 1991. DNA Replication, 2nd ed. W.H. Freeman, New York.
42. Krebs M.P., Reznikoff W.S. Transcriptional and translational initiation sites of IS50. Control of transposase and inhibitor expression. J. Mol. Biol. 192:1986;781-791.
43. LeBowitz J.H., McMacken R. The Escherichia coli DnaB replication protein is a DNA helicase. J. Biol. Chem. 261:1986;4738-4748.
44. Leung P.C., Teplow D.B., Harshey R.M. Interaction of distinct domains in Mu transposase with Mu DNA ends and an internal transpositional enhancer. Nature. 338:1989;656-658.
45. Levchenko I., Filutowicz M. Initiator protein π can bind independently to two domains of the g origin core of plasmid R6K: the direct repeats and the A+T-rich segment. Nucleic Acids Res. 24:1996;1936-1942.
46. Levchenko I., York D., Filutowicz M. The dimerization domain of R6K plasmid replication initiator protein π revealed by analysis of a truncated protein. Gene. 145:1994;65-68.
47. Levchenko I., Inman R.B., Filutowicz M. Replication of the R6K γ origin in vitro: dependence on wt π and hyperactive πS87N protein variant. Gene. 193:1997;97-103.
48. Linder P., Churchward G., Xia G.X., Yu Y.Y., Caro L. An essential replication gene, repA, of plasmid pSC101 is autoregulated. J. Mol. Biol. 181:1985;383-393.
49. Little J.W., Hill S.A. Deletions within a hinge region of a specific DNA-binding protein. Proc. Natl. Acad. Sci. USA. 82:1985;2301-2305.
50. MacAllister T.W., Kelley W.L., Miron A., Stenzel T.T., Bastia D. Replication of plasmid R6K origin γ in vitro. J. Biol. Chem. 266:1991;16056-16062.
51. Mallory J.B., Alfano C., McMacken R. Host virus interactions in the initiation of bacteriophage λ DNA replication. Recruitment of Escherichia coli DnaB helicase by λ π replication protein. J. Biol. Chem. 265:1990;13297-13307.
52. Manen D., Upegui-Gonzalez L.-C., Caro L. Monomers and dimers of the RepA protein in plasmid pSC101 replication: domains in RepA. Proc. Natl. Acad. Sci. USA. 89:1992;8923-8927.
53. Marmorstein R., Carey M., Ptashne M., Harrison S. Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae. Nature. 356:1992;408-414.
54. McEachern M.J., Filutowicz M., Helinski D.R. 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. 82:1985;1480-1484.
55. McEachern, M.J., Filutowicz, M., Yang, S., Greener, A., Mukhopadhyay, P., Helinski, D.R., 1986. Elements involved in the copy control regulation of the antibiotic resistance plasmid R6K. In: Levy, S.B., Novick, R.P. (Eds.), Banbury Report 24: Antibiotic Resistance Genes: Ecology, Transfer, and Expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 195-207.
56. McEachern M.J., Bott M.A., Tooker P.A., Helinski D.R. Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins. Proc. Natl. Acad. Sci. USA. 86:1989;7942-7946.
57. Mensa-Wilmot K., Seaby R., Alfano C., Wold M.S., Gomes B., McMacken R. Reconstitution of a nine-protein system initiates bacteriophage λ DNA replication. J. Biol. Chem. 264:1989;2853-2861.
58. Miron A., Mukherjee S., Bastia D. 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. 11:1992;1205-1216.
59. Moitoso de Vargas L., Pargellis C.A., Hasan N.M., Bushman E.W., Landy A. Autonomous DNA binding domains of λ integrase recognize two different sequence families. Cell. 54:1988;923-929.
60. Mosig G., Colowick N., Gruidl M.E., Chang A. Multiple initiation mechanisms adapt phage T4 DNA replication to physiological changes during T4's development. FEMS Microbiol. Rev. 17:1995;83-98.
61. Mukherjee S., Erickson H., Bastia D. 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. 85:1988;6287-6291.
62. Mukherjee S., Erickson H., Bastia D. Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell. 52:1988;375-383.
63. Oertel-Buchheit P., Schmidt-Dorr T., Granger-Schnarr M., Schnarr M. Spacing requirements between LexA operator half-sites can be relaxed by fusing the LexA binding domain with some alternative dimerization domains. J. Mol. Biol. 229:1993;1-7.
64. Pósfai G., Koob M., Hradečná Z., Hasan N., Filutowicz M., Szybalski W. In vivo excision and amplification of large fragments of the Escherichia coli genome. Nucleic Acids Res. 22:1994;2392-2398.
65. Ratnakar P.V., Mohanty B.K., Lobert M., Bastia D. The replication initiator protein π of the plasmid R6K specifically interacts with the host-encoded helicase DnaB. Proc. Natl. Acad. Sci. USA. 93:1996;5522-5526.
66. Reeder T., Schleif R. AraC protein can activate transcription from only one position and when pointed in only one direction. J. Mol. Biol. 231:1993;205-218.
67. Reznikoff W.S. The Tn5 transposon. Annu. Rev. Microbiol. 47:1993;945-963.
68. Sauer R.T., Smith D.L., Johnson A.D. Flexibility of the yeast alpha 2 repressor enables it to occupy the ends of its operator, leaving the center free. Genes Dev. 2:1988;807-816.
69. Schleif R. DNA looping. Annu. Rev. Biochem. 61:1992;199-224.
70. Shafferman A., Kolter R., Stalker D.M., Helinski D.R. Plasmid R6K replication, III. Regulatory properties of the π initiation protein. J. Mol. Biol. 161:1982;57-76.
71. Stalker D.M., Filutowicz M., Helinski D.R. Release of initiation control by a mutational alteration in the R6K π protein required for plasmid DNA replication. Proc. Natl. Acad. Sci. USA. 80:1983;5500-5504.
72. Stalker D.M., Kolter R., Helinski D.R. Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K. Proc. Natl. Acad. Sci. USA. 76:1979;1150-1154.
73. Stalker D.M., Kolter R., Helinski D.R. Plasmid R6K DNA replication, I. complete nucleotide sequence of an autonomously replicating segment. J. Mol. Biol. 161:1982;33-43.
74. Sugiura S., Tanaka M., Masamune Y., Yamaguchi K. DNA binding properties of purified initiator protein (Rep) encoded by plasmid pSC101. J. Biochem. 107:1990;369-376.
75. Tilly K., Yarmolinsky M. Participation of Escherichia coli heat shock proteins DnaJ, DnaK, and GrpE in P1 plasmid replication. J. Bacteriol. 171:1989;6025-6029.
76. Urh, M., 1996. Studies of the mechanisms controlling replication of plasmid R6K. Ph.D. Thesis. University of Wisconsin-Madison.
77. Urh M., Flashner Y., Shafferman A., Filutowicz M. Altered (copy-up) forms of initiaior protein π supress the point mutations inactivating the γ origin of plasmid R6K. J. Bacteriol. 177:1995;6732-6739.
78. Urh M., York D., Filutowicz M. Buffer composition mediates a switch between cooperative and independent binding of an initiator protein to DNA. Gene. 164:1995;1-7.
79. Urh, M., Wu, J., Wu, J., Forest, K., Inman, R.B., Filutowicz, M., 1998. Assemblies of replication initiator protein on symmetric and asymmetric DNA sequences depend on multiple protein oligomerization surfaces. J. Mol. Biol., in press.
80. Wickner S., Hurvitz J. Interaction of Escherichia coli dnaB and dnaC(D) gene products in vitro. Proc. Natl. Acad. Sci. USA. 72:1975;921-925.
81. Wickner S., Skowyra D., Hoskins J., McKenney K. DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. USA. 89:1992;10345-10349.
82. Wu F., Goldberg I., Filutowicz M. Roles of a 106-bp origin enhancer and Escherichia coli DnaA protein in replication of plasmid R6K. Nucleic Acids Res. 20:1992;811-817.
83. Wu F., Levchenko I., Filutowicz M. 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. 176:1994;6795-6801.
84. Wu F., Levchenko I., Filutowicz M. A DNA segment conferring stable maintenance on R6K γ-origin core replicons. J. Bacteriol. 177:1995;6338-6345.
85. Wu F., Wu J., Ehley J., Filutowicz M. Preponderance of Fis-binding sites in the R6K γ origin and the curious effect of the penicillin resistance marker on replication of this origin in the absence of Fis. J. Bacteriol. 178:1996;4965-4974.
86. Wu J., Sektas M., Chen D., Filutowicz M. Two forms of replication initiator protein: positive and negative controls. Proc. Natl. Acad. Sci. USA. 94:1997;13967-13972.
87. York D., Filutowicz M. Autoregulation-deficient mutant of plasmid R6K-encoded π protein distinguishes between palindromic and nonpalindromic binding sites. J. Biol. Chem. 268:1993;21854-21861.
88. York D., Ivanov V., Gan J., Filutowicz M. Translational options for the pir gene of plasmid R6K: multiple forms of the replication initiator protein π Gene. 116:1992;7-12.
89. Yung B.Y.-M., Kornberg A. The DnaA initiator protein binds separate domains in the replication origin of Escherichia coli. J. Biol. Chem. 264:1989;6146-6150.
90. Żylicz M., Ang D., Liberek K., Georgopoulus C. Initiation of λ DNA replication with purified host- and bacteriophage-encoded proteins: the role of the DnaK, DnaJ, and GrpE heat shock proteins. EMBO J. 8:1989;1601-1608.