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. 1989 Dec 25;17(24):10353–10366. doi: 10.1093/nar/17.24.10353

Functional domains in the bacteriophage phi 29 terminal protein for interaction with the phi 29 DNA polymerase and with DNA.

A Zaballos 1, M Salas 1
PMCID: PMC335305  PMID: 2602154

Abstract

Deletion mutants at the amino- and carboxyl-ends of the phi 29 terminal protein, as well as internal deletion and substitution mutants, whose ability to prime the initiation of phi 29 DNA replication was affected to different extent, have been assayed for their capacity to interact with DNA or with the phi 29 DNA polymerase. One DNA binding domain at the amino end of the terminal protein has been mapped. Two regions involved in the binding to the DNA polymerase, an internal region near the amino-terminus and a carboxyl-terminal one, have been also identified. Interaction with both DNA and phi 29 DNA polymerase are required to led to the formation of terminal protein-dAMP initiation complex to start 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. Barthelemy I., Salas M., Mellado R. P. In vivo transcription of bacteriophage phi 29 DNA: transcription initiation sites. J Virol. 1986 Dec;60(3):874–879. doi: 10.1128/jvi.60.3.874-879.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Blanco L., Bernad A., Lázaro J. M., Martín G., Garmendia C., Salas M. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem. 1989 May 25;264(15):8935–8940. [PubMed] [Google Scholar]
  3. 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]
  4. Blanco L., Prieto I., Gutiérrez J., Bernad A., Lázaro J. M., Hermoso J. M., Salas M. Effect of NH4+ ions on phi 29 DNA-protein p3 replication: formation of a complex between the terminal protein and the DNA polymerase. J Virol. 1987 Dec;61(12):3983–3991. doi: 10.1128/jvi.61.12.3983-3991.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Blanco L., Salas M. Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5325–5329. doi: 10.1073/pnas.81.17.5325. [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. Escarmís C., Salas M. Nucleotide sequence of the early genes 3 and 4 of bacteriophage phi 29. Nucleic Acids Res. 1982 Oct 11;10(19):5785–5798. doi: 10.1093/nar/10.19.5785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Garmendia C., Salas M., Hermoso J. M. Site-directed mutagenesis in the DNA linking site of bacteriophage phi 29 terminal protein: isolation and characterization of a Ser232----Thr mutant. Nucleic Acids Res. 1988 Jul 11;16(13):5727–5740. doi: 10.1093/nar/16.13.5727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gutiérrez J., García J. A., Blanco L., Salas M. Cloning and template activity of the origins of replication of phage phi 29 DNA. Gene. 1986;43(1-2):1–11. doi: 10.1016/0378-1119(86)90002-8. [DOI] [PubMed] [Google Scholar]
  11. Gutiérrez J., Vinós J., Prieto I., Méndez E., Hermoso J. M., Salas M. Signals in the phi 29 DNA-terminal protein template for the initiation of phage phi 29 DNA replication. Virology. 1986 Dec;155(2):474–483. doi: 10.1016/0042-6822(86)90209-6. [DOI] [PubMed] [Google Scholar]
  12. Harding N. E., Ito J. DNA replication of bacteriophage phi 29: characterization of the intermediates and location of the termini of replication. Virology. 1980 Jul 30;104(2):323–338. doi: 10.1016/0042-6822(80)90337-2. [DOI] [PubMed] [Google Scholar]
  13. Hermoso J. M., Méndez E., Soriano F., Salas M. Location of the serine residue involved in the linkage between the terminal protein and the DNA of phage phi 29. Nucleic Acids Res. 1985 Nov 11;13(21):7715–7728. doi: 10.1093/nar/13.21.7715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hermoso J. M., Salas M. Protein p3 is linked to the DNA of phage phi 29 through a phosphoester bond between serine and 5'-dAMP. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6425–6428. doi: 10.1073/pnas.77.11.6425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Inciarte M. R., Lázaro J. M., Salas M., Vińuela E. Physical map of bacteriophage phi29 DNA. Virology. 1976 Oct 15;74(2):314–323. [PubMed] [Google Scholar]
  16. Inciarte M. R., Salas M., Sogo J. M. Structure of replicating DNA molecules of Bacillus subtilis bacteriophage phi 29. J Virol. 1980 Apr;34(1):187–199. doi: 10.1128/jvi.34.1.187-199.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  18. Landschulz W. H., Johnson P. F., McKnight S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
  19. Matsumoto K., Saito T., Kim C. I., Ando T., Hirokawa H. Bacteriophage phi 29 DNA replication in vitro: participation of the terminal protein and the gene 2 product in elongation. Mol Gen Genet. 1984;196(3):381–386. doi: 10.1007/BF00436183. [DOI] [PubMed] [Google Scholar]
  20. McDonell M. W., Simon M. N., Studier F. W. Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline gels. J Mol Biol. 1977 Feb 15;110(1):119–146. doi: 10.1016/s0022-2836(77)80102-2. [DOI] [PubMed] [Google Scholar]
  21. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ortin J., Viñuela E., Salas M., Vasquez C. DNA-protein complex in circular DNA from phage phi-29. Nat New Biol. 1971 Dec 29;234(52):275–277. doi: 10.1038/newbio234275a0. [DOI] [PubMed] [Google Scholar]
  23. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  24. Pastrana R., Lázaro J. M., Blanco L., García J. A., Méndez E., Salas M. Overproduction and purification of protein P6 of Bacillus subtilis phage phi 29: role in the initiation of DNA replication. Nucleic Acids Res. 1985 May 10;13(9):3083–3100. doi: 10.1093/nar/13.9.3083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Prieto I., Lázaro J. M., García J. A., Hermoso J. M., Salas M. Purification in a functional form of the terminal protein of Bacillus subtilis phage phi 29. Proc Natl Acad Sci U S A. 1984 Mar;81(6):1639–1643. doi: 10.1073/pnas.81.6.1639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Prieto I., Serrano M., Lázaro J. M., Salas M., Hermoso J. M. Interaction of the bacteriophage phi 29 protein p6 with double-stranded DNA. Proc Natl Acad Sci U S A. 1988 Jan;85(2):314–318. doi: 10.1073/pnas.85.2.314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Reha-Krantz L. J. Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants. Relating structure to function. J Mol Biol. 1988 Aug 20;202(4):711–724. doi: 10.1016/0022-2836(88)90552-9. [DOI] [PubMed] [Google Scholar]
  28. Salas M., Mellado R. P., Viñuela E. Characterization of a protein covalently linked to the 5' termini of the DNA of Bacillus subtilis phage phi29. J Mol Biol. 1978 Feb 25;119(2):269–291. doi: 10.1016/0022-2836(78)90438-2. [DOI] [PubMed] [Google Scholar]
  29. Serrano M., Gutiérrez J., Prieto I., Hermoso J. M., Salas M. Signals at the bacteriophage phi 29 DNA replication origins required for protein p6 binding and activity. EMBO J. 1989 Jun;8(6):1879–1885. doi: 10.1002/j.1460-2075.1989.tb03584.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sogo J. M., García J. A., Peñalva M. A., Salas M. Structure of protein-containing replicative intermediates of Bacillus subtilis phage phi 29 DNA. Virology. 1982 Jan 15;116(1):1–18. doi: 10.1016/0042-6822(82)90398-1. [DOI] [PubMed] [Google Scholar]
  31. Tomalski M. D., Wu J. G., Miller L. K. The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene. Virology. 1988 Dec;167(2):591–600. [PubMed] [Google Scholar]
  32. Vlcek C., Paces V. Nucleotide sequence of the late region of Bacillus phage phi 29 completes the 19,285-bp sequence of phi 29 genome. Comparison with the homologous sequence of phage PZA. Gene. 1986;46(2-3):215–225. doi: 10.1016/0378-1119(86)90406-3. [DOI] [PubMed] [Google Scholar]
  33. Watabe K., Leusch M., Ito J. Replication of bacteriophage phi 29 DNA in vitro: the roles of terminal protein and DNA polymerase. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5374–5378. doi: 10.1073/pnas.81.17.5374. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Yoshikawa H., Ito J. Nucleotide sequence of the major early region of bacteriophage phi 29. Gene. 1982 Mar;17(3):323–335. doi: 10.1016/0378-1119(82)90149-4. [DOI] [PubMed] [Google Scholar]
  35. Zaballos A., Lázaro J. M., Méndez E., Mellado R. P., Salas M. Effects of internal deletions on the priming activity of the phage phi 29 terminal protein. Gene. 1989 Nov 30;83(2):187–195. doi: 10.1016/0378-1119(89)90104-2. [DOI] [PubMed] [Google Scholar]
  36. Zaballos A., Mellado R. P., Salas M. Initiation of phage phi 29 DNA replication by mutants with deletions at the amino end of the terminal protein. Gene. 1988;63(1):113–121. doi: 10.1016/0378-1119(88)90550-1. [DOI] [PubMed] [Google Scholar]
  37. Zaballos A., Salas M., Mellado R. P. Initiation of phage phi 29 DNA replication by mutants with deletions at the carboxyl end of the terminal protein. Gene. 1986;43(1-2):103–110. doi: 10.1016/0378-1119(86)90013-2. [DOI] [PubMed] [Google Scholar]

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