Abstract
Gene A protein, a bacteriophage phi X174-encoded endonuclease involved in phi X replicative form (RF) DNA replication, nicks not only phi X RFI DNA but also RFI DNAs of several other spherical single-stranded DNA bacteriophages. The position of the phi X gene A protein nick and the nucleotide sequence surrounding this site in RF DNAs of the bacteriophages U3, G14, and alpha 3 were determined. Comparison of the nucleotide sequences which surround the nick site of the gene A protein in RF DNAs of phi X174, G4, St-1, U3, G14, and alpha 3 revealed that a strongly conserved 30-nucleotide stretch occurred in RF DNAs of all six phages. However, perfect DNA sequence homology around this site was only 10 nucleotides, the decamer sequence CAACTTGATA. The present results support the hypothesis that, for nicking of double-stranded supercoiled DNA by the phi X gene A protein, the presence of the recognition sequence CAACTTGATA and a specific gene A protein binding sequence upstream from the recognition sequence are required. The sequence data obtained so far from phages U3, G14, St-1, and alpha 3 have been compared with the nucleotide sequences and amino acid sequences of both phi X and G4. According to this comparison, the evolutionary relationship between phages G4, U3, and G14 is very close, which also holds for phages alpha 3 and St-1. However, the two groups are only distantly related, both to each other and to phi X.
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Selected References
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- Baas P. D., Jansz H. S. Bacteriophage phiX174 DNA synthesis in a replication-deficient host: determination of the origin of phiX DNA replication. J Mol Biol. 1976 Apr 15;102(3):633–656. doi: 10.1016/0022-2836(76)90339-9. [DOI] [PubMed] [Google Scholar]
- Baas P. D., Jansz H. S. PhiX174 replicative form DNA replication, origin and direction. J Mol Biol. 1972 Feb 14;63(3):569–576. doi: 10.1016/0022-2836(72)90448-2. [DOI] [PubMed] [Google Scholar]
- Baas P. D., Teertstra W. R., van Mansfeld A. D., Jansz H. S., van der Marel G. A., Veeneman G. H., van Boom J. H. Construction of viable and lethal mutations in the origin of bacteriophage 'phi' X174 using synthetic oligodeoxyribonucleotides. J Mol Biol. 1981 Nov 15;152(4):615–639. doi: 10.1016/0022-2836(81)90120-0. [DOI] [PubMed] [Google Scholar]
- Bradley D. E. A comparative study of some properties of the phi-X174 type bacteriophages. Can J Microbiol. 1970 Oct;16(10):965–971. doi: 10.1139/m70-165. [DOI] [PubMed] [Google Scholar]
- Eisenberg S., Griffith J., Kornberg A. phiX174 cistron A protein is a multifunctional enzyme in DNA replication. Proc Natl Acad Sci U S A. 1977 Aug;74(8):3198–3202. doi: 10.1073/pnas.74.8.3198. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eisenberg S., Kornberg A. Purification and characterization of phiX174 gene A protein. A multifunctional enzyme of duplex DNA replication. J Biol Chem. 1979 Jun 25;254(12):5328–5332. [PubMed] [Google Scholar]
- Fiddes J. C., Barrell B. G., Godson G. N. Nucleotide sequences of the separate origins of synthesis of bacteriophage G4 viral and complementary DNA strands. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1081–1085. doi: 10.1073/pnas.75.3.1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Francke B., Ray D. S. Formation of the parental replicative form DNA of bacteriophage phi-X174 and initial events in its replication. J Mol Biol. 1971 Nov 14;61(3):565–586. doi: 10.1016/0022-2836(71)90065-9. [DOI] [PubMed] [Google Scholar]
- Godson G. N., Barrell B. G., Staden R., Fiddes J. C. Nucleotide sequence of bacteriophage G4 DNA. Nature. 1978 Nov 16;276(5685):236–247. doi: 10.1038/276236a0. [DOI] [PubMed] [Google Scholar]
- Heidekamp F., Baas P. D., van Boom J. H., Veeneman G. H., Zipursky S. L., Jansz H. S. Construction and characterization of recombinant plasmid DNAs containing sequences of the origin of bacteriophage phi X174 DNA replication. Nucleic Acids Res. 1981 Jul 24;9(14):3335–3354. doi: 10.1093/nar/9.14.3335. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Heidekamp F., Langeveld S. A., Baas P. D., Jansz H. S. Studies of the recognition sequence of phi X174 gene A protein. Cleavage site of phi X gene A protein in St-1 RFI DNA. Nucleic Acids Res. 1980 May 10;8(9):2009–2021. doi: 10.1093/nar/8.9.2009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ikeda J. E., Yudelevich A., Hurwitz J. Isolation and characterization of the protein coded by gene A of bacteriophage phiX174 DNA. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2669–2673. doi: 10.1073/pnas.73.8.2669. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jansz H. S., Pouwels P. H., Schiphorst J. Preparation of double-stranded DNA (replicative form) of bacteriophage phi-X174: a simplified method. Biochim Biophys Acta. 1966 Sep;123(3):626–627. doi: 10.1016/0005-2787(66)90233-4. [DOI] [PubMed] [Google Scholar]
- Langeveld S. A., van Arkel G. A., Weisbeek P. J. Improved method for the isolation of the A and A* proteins of bacteriophage phi X174. FEBS Lett. 1980 Jun 2;114(2):269–272. doi: 10.1016/0014-5793(80)81131-8. [DOI] [PubMed] [Google Scholar]
- Langeveld S. A., van Mansfeld A. D., Baas P. D., Jansz H. S., van Arkel G. A., Weisbeek P. J. Nucleotide sequence of the origin of replication in bacteriophage phiX174 RF DNA. Nature. 1978 Feb 2;271(5644):417–420. doi: 10.1038/271417a0. [DOI] [PubMed] [Google Scholar]
- Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
- Radloff R., Bauer W., Vinograd J. A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc Natl Acad Sci U S A. 1967 May;57(5):1514–1521. doi: 10.1073/pnas.57.5.1514. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
- Sims J., Capon D., Dressler D. dnaG (primase)-dependent origins of DNA replication. Nucleotide sequences of the negative strand initiation sites of bacteriophages St-1, phi K, and alpha 3. J Biol Chem. 1979 Dec 25;254(24):12615–12628. [PubMed] [Google Scholar]
- Soeda E., Arrand J. R., Smolar N., Walsh J. E., Griffin B. E. Coding potential and regulatory signals of the polyoma virus genome. Nature. 1980 Jan 31;283(5746):445–453. doi: 10.1038/283445a0. [DOI] [PubMed] [Google Scholar]
- van Mansfeld A. D., Langeveld S. A., Baas P. D., Jansz H. S., van der Marel G. A., Veeneman G. H., van Boom J. H. Recognition sequence of bacteriophage phi X174 gene A protein--an initiator of DNA replication. Nature. 1980 Dec 11;288(5791):561–566. doi: 10.1038/288561a0. [DOI] [PubMed] [Google Scholar]
- van Mansfeld A. D., Langeveld S. A., Weisbeek P. J., Baas P. D., van Arkel G. A., Jansz H. S. Cleavage site of phiX174 gene-A protein in phiX and G4 RFI DNA. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):331–334. doi: 10.1101/sqb.1979.043.01.039. [DOI] [PubMed] [Google Scholar]