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. 1990 Nov 25;18(22):6553–6557. doi: 10.1093/nar/18.22.6553

Characterization of a DNA binding protein of bacteriophage PRD1 involved in DNA replication.

T M Pakula 1, J Caldentey 1, M Serrano 1, C Gutierrez 1, J M Hermoso 1, M Salas 1, D H Bamford 1
PMCID: PMC332609  PMID: 2251117

Abstract

Escherichia coli phage PRD1 protein P12, involved in PRD1 DNA replication in vivo, has been highly purified from E. coli cells harbouring a gene XII-containing plasmid. Protein P12 binds to single-stranded DNA as shown by gel retardation assays and nuclease protection experiments. Binding of protein P12 to single-stranded DNA increases about 14% the contour length of the DNA as revealed by electron microscopy. Binding to single-stranded DNA seems to be cooperative, and it is not sequence specific. Protein P12 also binds to double-stranded DNA although with an affinity 10 times lower than to single-stranded DNA. Using the in vitro phage phi 29 DNA replication system, it is shown that protein P12 stimulates the overall phi 29 DNA replication.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bamford D. H., Mindich L. Characterization of the DNA-protein complex at the termini of the bacteriophage PRD1 genome. J Virol. 1984 May;50(2):309–315. doi: 10.1128/jvi.50.2.309-315.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bamford D. H., Rouhiainen L., Takkinen K., Söderlund H. Comparison of the lipid-containing bacteriophages PRD1, PR3, PR4, PR5 and L17. J Gen Virol. 1981 Dec;57(Pt 2):365–373. doi: 10.1099/0022-1317-57-2-365. [DOI] [PubMed] [Google Scholar]
  3. Bamford D., McGraw T., MacKenzie G., Mindich L. Identification of a protein bound to the termini of bacteriophage PRD1 DNA. J Virol. 1983 Aug;47(2):311–316. doi: 10.1128/jvi.47.2.311-316.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bamford J. K., Bamford D. H. Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane. Virology. 1990 Aug;177(2):445–451. doi: 10.1016/0042-6822(90)90508-o. [DOI] [PubMed] [Google Scholar]
  5. Blanco L., Bernad A., Salas M. Transition from initiation to elongation in protein-primed phi 29 DNA replication: salt-dependent stimulation by the viral protein p6. J Virol. 1988 Nov;62(11):4167–4172. doi: 10.1128/jvi.62.11.4167-4172.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Blanco L., Salas M. Replication of phage phi 29 DNA with purified terminal protein and DNA polymerase: synthesis of full-length phi 29 DNA. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6404–6408. doi: 10.1073/pnas.82.19.6404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carthew R. W., Chodosh L. A., Sharp P. A. An RNA polymerase II transcription factor binds to an upstream element in the adenovirus major late promoter. Cell. 1985 Dec;43(2 Pt 1):439–448. doi: 10.1016/0092-8674(85)90174-6. [DOI] [PubMed] [Google Scholar]
  8. Chase J. W., Williams K. R. Single-stranded DNA binding proteins required for DNA replication. Annu Rev Biochem. 1986;55:103–136. doi: 10.1146/annurev.bi.55.070186.000535. [DOI] [PubMed] [Google Scholar]
  9. Cleat P. H., Hay R. T. Co-operative interactions between NFI and the adenovirus DNA binding protein at the adenovirus origin of replication. EMBO J. 1989 Jun;8(6):1841–1848. doi: 10.1002/j.1460-2075.1989.tb03579.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Delius H., Mantell N. J., Alberts B. Characterization by electron microscopy of the complex formed between T4 bacteriophage gene 32-protein and DNA. J Mol Biol. 1972 Jun 28;67(3):341–350. doi: 10.1016/0022-2836(72)90454-8. [DOI] [PubMed] [Google Scholar]
  11. Field J., Gronostajski R. M., Hurwitz J. Properties of the adenovirus DNA polymerase. J Biol Chem. 1984 Aug 10;259(15):9487–9495. [PubMed] [Google Scholar]
  12. Gerendasy D. D., Ito J. The genome of lipid-containing bacteriophage PRD1, which infects gram-negative bacteria, contains long, inverted terminal repeats. J Virol. 1987 Feb;61(2):594–596. doi: 10.1128/jvi.61.2.594-596.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gerendasy D., Ito J. Nucleotide sequence and transcription of the right early region of bacteriophage PRD1. J Bacteriol. 1990 Apr;172(4):1889–1898. doi: 10.1128/jb.172.4.1889-1898.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Griffith J. D., Harris L. D., Register J., 3rd Visualization of SSB-ssDNA complexes active in the assembly of stable RecA-DNA filaments. Cold Spring Harb Symp Quant Biol. 1984;49:553–559. doi: 10.1101/sqb.1984.049.01.062. [DOI] [PubMed] [Google Scholar]
  15. Hay R. T., Russell W. C. Recognition mechanisms in the synthesis of animal virus DNA. Biochem J. 1989 Feb 15;258(1):3–16. doi: 10.1042/bj2580003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  17. Hsieh J. C., Jung G. H., Leavitt M. C., Ito J. Primary structure of the DNA terminal protein of bacteriophage PRD1. Nucleic Acids Res. 1987 Nov 11;15(21):8999–9009. doi: 10.1093/nar/15.21.8999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kelly T. J., Wold M. S., Li J. Initiation of viral DNA replication. Adv Virus Res. 1988;34:1–42. doi: 10.1016/s0065-3527(08)60514-x. [DOI] [PubMed] [Google Scholar]
  19. Liljeström P., Laamanen I., Palva E. T. Structure and expression of the ompB operon, the regulatory locus for the outer membrane porin regulon in Salmonella typhimurium LT-2. J Mol Biol. 1988 Jun 20;201(4):663–673. doi: 10.1016/0022-2836(88)90465-2. [DOI] [PubMed] [Google Scholar]
  20. Lindenbaum J. O., Field J., Hurwitz J. The adenovirus DNA binding protein and adenovirus DNA polymerase interact to catalyze elongation of primed DNA templates. J Biol Chem. 1986 Aug 5;261(22):10218–10227. [PubMed] [Google Scholar]
  21. Martín G., Lázaro J. M., Méndez E., Salas M. Characterization of the phage phi 29 protein p5 as a single-stranded DNA binding protein. Function in phi 29 DNA-protein p3 replication. Nucleic Acids Res. 1989 May 25;17(10):3663–3672. doi: 10.1093/nar/17.10.3663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. McGraw T., Yang H. L., Mindich L. Establishment of a physical and genetic map for bacteriophage PRD1. Mol Gen Genet. 1983;190(2):237–244. doi: 10.1007/BF00330646. [DOI] [PubMed] [Google Scholar]
  23. Mindich L., Bamford D., Goldthwaite C., Laverty M., Mackenzie G. Isolation of nonsense mutants of lipid-containing bacteriophage PRD1. J Virol. 1982 Dec;44(3):1013–1020. doi: 10.1128/jvi.44.3.1013-1020.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mindich L., Cohen J., Weisburd M. Isolation of nonsense suppressor mutants in Pseudomonas. J Bacteriol. 1976 Apr;126(1):177–182. doi: 10.1128/jb.126.1.177-182.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Olkkonen V. M., Bamford D. H. Quantitation of the adsorption and penetration stages of bacteriophage phi 6 infection. Virology. 1989 Jul;171(1):229–238. doi: 10.1016/0042-6822(89)90530-8. [DOI] [PubMed] [Google Scholar]
  26. Olsen R. H., Siak J. S., Gray R. H. Characteristics of PRD1, a plasmid-dependent broad host range DNA bacteriophage. J Virol. 1974 Sep;14(3):689–699. doi: 10.1128/jvi.14.3.689-699.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pakula T. M., Savilahti H., Bamford D. H. The organization of the right-end early region of bacteriophage PRD1 genome. Gene. 1989 Dec 21;85(1):53–58. doi: 10.1016/0378-1119(89)90463-0. [DOI] [PubMed] [Google Scholar]
  28. Prasad B. V., Chiu W. Sequence comparison of single-stranded DNA binding proteins and its structural implications. J Mol Biol. 1987 Feb 5;193(3):579–584. doi: 10.1016/0022-2836(87)90268-3. [DOI] [PubMed] [Google Scholar]
  29. Remaut E., Tsao H., Fiers W. Improved plasmid vectors with a thermoinducible expression and temperature-regulated runaway replication. Gene. 1983 Apr;22(1):103–113. doi: 10.1016/0378-1119(83)90069-0. [DOI] [PubMed] [Google Scholar]
  30. Savilahti H., Bamford D. H. Linear DNA replication: inverted terminal repeats of five closely related Escherichia coli bacteriophages. Gene. 1986;49(2):199–205. doi: 10.1016/0378-1119(86)90280-5. [DOI] [PubMed] [Google Scholar]
  31. Savilahti H., Bamford D. H. The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase. Gene. 1987;57(1):121–130. doi: 10.1016/0378-1119(87)90183-1. [DOI] [PubMed] [Google Scholar]
  32. Savilahti H., Caldentey J., Bamford D. H. Bacteriophage PRD1 terminal protein: expression of gene VIII in Escherichia coli and purification of the functional P8 product. Gene. 1989 Dec 21;85(1):45–51. doi: 10.1016/0378-1119(89)90462-9. [DOI] [PubMed] [Google Scholar]
  33. Serrano M., Salas M., Hermoso J. M. A novel nucleoprotein complex at a replication origin. Science. 1990 May 25;248(4958):1012–1016. doi: 10.1126/science.2111580. [DOI] [PubMed] [Google Scholar]
  34. Stuiver M. H., van der Vliet P. C. Adenovirus DNA-binding protein forms a multimeric protein complex with double-stranded DNA and enhances binding of nuclear factor I. J Virol. 1990 Jan;64(1):379–386. doi: 10.1128/jvi.64.1.379-386.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tabor S., Richardson C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767–4771. doi: 10.1073/pnas.84.14.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Wang Y. S., Hall J. D. Characterization of a major DNA-binding domain in the herpes simplex virus type 1 DNA-binding protein (ICP8). J Virol. 1990 May;64(5):2082–2089. doi: 10.1128/jvi.64.5.2082-2089.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]

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