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. 1985 Mar;53(3):871–878. doi: 10.1128/jvi.53.3.871-878.1985

Mutational mechanisms by which an inactive replication origin of bacteriophage M13 is turned on are similar to mechanisms of activation of ras proto-oncogenes.

M H Kim, D S Ray
PMCID: PMC254721  PMID: 3973968

Abstract

M13 viral strand synthesis is initiated by nicking of the viral strand of the duplex replicative form by the M13 gene II initiator protein at a specific site within a sequence of about 40 base pairs having dyad symmetry. Efficient replication of the M13 viral strand also requires the presence of an adjacent sequence of ca. 100 base pairs. Together these sequences constitute the minimal origin for M13 viral strand synthesis. A pBR322 derivative having a 182-base-pair insert of M13 DNA contains a functional M13 viral strand origin and, when provided with M13 gene functions in trans, replicates under conditions nonpermissive for the parent plasmid. Chimeric plasmids containing deletions within the sequence flanking the viral strand origin are unable to replicate under these conditions. We isolated spontaneous mutants of M13 based on their ability to activate replication of such plasmids. The mutations found in these strains, as well as several produced by oligonucleotide-directed mutagenesis, all result in the substitution of any of at least four different amino acids for a specific glycine residue near the amino-terminal end of the initiator protein. Other studies have shown that overproduction of the wild-type initiator protein also restores replication. These alternate mechanisms are discussed in terms of their striking similarity to the mechanisms of activation of the ras proto-oncogenes which can be activated either by increased expression of the wild-type protein or by substitution of any of several amino acids for a glycine residue near the amino terminus.

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Selected References

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

  1. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Capon D. J., Seeburg P. H., McGrath J. P., Hayflick J. S., Edman U., Levinson A. D., Goeddel D. V. Activation of Ki-ras2 gene in human colon and lung carcinomas by two different point mutations. Nature. 1983 Aug 11;304(5926):507–513. doi: 10.1038/304507a0. [DOI] [PubMed] [Google Scholar]
  3. Chang E. H., Furth M. E., Scolnick E. M., Lowy D. R. Tumorigenic transformation of mammalian cells induced by a normal human gene homologous to the oncogene of Harvey murine sarcoma virus. Nature. 1982 Jun 10;297(5866):479–483. doi: 10.1038/297479a0. [DOI] [PubMed] [Google Scholar]
  4. Cleary J. M., Ray D. S. Deletion analysis of the cloned replication origin region from bacteriophage M13. J Virol. 1981 Oct;40(1):197–203. doi: 10.1128/jvi.40.1.197-203.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cleary J. M., Ray D. S. Replication of the plasmid pBR322 under the control of a cloned replication origin from the single-stranded DNA phage M13. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4638–4642. doi: 10.1073/pnas.77.8.4638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. DeFeo D., Gonda M. A., Young H. A., Chang E. H., Lowy D. R., Scolnick E. M., Ellis R. W. Analysis of two divergent rat genomic clones homologous to the transforming gene of Harvey murine sarcoma virus. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3328–3332. doi: 10.1073/pnas.78.6.3328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dhar R., Ellis R. W., Shih T. Y., Oroszlan S., Shapiro B., Maizel J., Lowy D., Scolnick E. Nucleotide sequence of the p21 transforming protein of Harvey murine sarcoma virus. Science. 1982 Sep 3;217(4563):934–936. doi: 10.1126/science.6287572. [DOI] [PubMed] [Google Scholar]
  8. Dotto G. P., Enea V., Zinder N. D. Functional analysis of bacteriophage f1 intergenic region. Virology. 1981 Oct 30;114(2):463–473. doi: 10.1016/0042-6822(81)90226-9. [DOI] [PubMed] [Google Scholar]
  9. Dotto G. P., Horiuchi K., Jakes K. S., Zinder N. D. Replication origin of bacteriophage f1. Two signals required for its function. J Mol Biol. 1982 Dec 5;162(2):335–343. doi: 10.1016/0022-2836(82)90530-7. [DOI] [PubMed] [Google Scholar]
  10. Dotto G. P., Horiuchi K., Zinder N. D. Initiation and termination of phage f1 plus-strand synthesis. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7122–7126. doi: 10.1073/pnas.79.23.7122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dotto G. P., Horiuchi K., Zinder N. D. The functional origin of bacteriophage f1 DNA replication. Its signals and domains. J Mol Biol. 1984 Feb 5;172(4):507–521. doi: 10.1016/s0022-2836(84)80020-0. [DOI] [PubMed] [Google Scholar]
  12. Dotto G. P., Zinder N. D. Increased intracellular concentration of an initiator protein markedly reduces the minimal sequence required for initiation of DNA synthesis. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1336–1340. doi: 10.1073/pnas.81.5.1336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Duguet M., Yarranton G., Gefter M. The rep protein of Escherichia coli: interaction with DNA and other proteins. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):335–343. doi: 10.1101/sqb.1979.043.01.040. [DOI] [PubMed] [Google Scholar]
  14. Fidanián H. M., Ray D. S. Replication of bacteriophage M13. VII. Requirement of the gene 2 protein for the accumulation of a specific RFII species. J Mol Biol. 1972 Dec 14;72(1):51–63. doi: 10.1016/0022-2836(72)90067-8. [DOI] [PubMed] [Google Scholar]
  15. Geider K., Bäumel I., Meyer T. F. Intermediate stages in enzymatic replication of bacteriophage fd duplex DNA. J Biol Chem. 1982 Jun 10;257(11):6488–6493. [PubMed] [Google Scholar]
  16. Geider K., Kornberg A. Conversion of the M13 viral single strand to the double-stranded replicative forms by purified proteins. J Biol Chem. 1974 Jul 10;249(13):3999–4005. [PubMed] [Google Scholar]
  17. Geider K., Meyer T. F. Gene-II protein of bacteriophage fd in enzymatic replication of viral duplex DNA. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):59–62. doi: 10.1101/sqb.1979.043.01.010. [DOI] [PubMed] [Google Scholar]
  18. Gillam S., Jahnke P., Astell C., Phillips S., Hutchison C. A., 3rd, Smith M. Defined transversion mutations at a specific position in DNA using synthetic oligodeoxyribonucleotides as mutagens. Nucleic Acids Res. 1979 Jul 11;6(9):2973–2985. doi: 10.1093/nar/6.9.2973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Grant R. A., Lin T. C., Konigsberg W., Webster R. E. Structure of the filamentous bacteriophage fl. Location of the A, C, and D minor coat proteins. J Biol Chem. 1981 Jan 10;256(1):539–546. [PubMed] [Google Scholar]
  20. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  21. Hines J. C., Ray D. S. Construction and characterization of new coliphage M13 cloning vectors. Gene. 1980 Nov;11(3-4):207–218. doi: 10.1016/0378-1119(80)90061-x. [DOI] [PubMed] [Google Scholar]
  22. Hutchison C. A., 3rd, Edgell M. H. Genetic assay for small fragments of bacteriophage phi X174 deoxyribonucleic acid. J Virol. 1971 Aug;8(2):181–189. doi: 10.1128/jvi.8.2.181-189.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hutchison C. A., 3rd, Phillips S., Edgell M. H., Gillam S., Jahnke P., Smith M. Mutagenesis at a specific position in a DNA sequence. J Biol Chem. 1978 Sep 25;253(18):6551–6560. [PubMed] [Google Scholar]
  24. Ito H., Ike Y., Ikuta S., Itakura K. Solid phase synthesis of polynucleotides. VI. Further studies on polystyrene copolymers for the solid support. Nucleic Acids Res. 1982 Mar 11;10(5):1755–1769. doi: 10.1093/nar/10.5.1755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Johnston S., Ray D. S. Interference between M13 and oriM13 plasmids is mediated by a replication enhancer sequence near the viral strand origin. J Mol Biol. 1984 Aug 25;177(4):685–700. doi: 10.1016/0022-2836(84)90044-5. [DOI] [PubMed] [Google Scholar]
  26. Kim M. H., Hines J. C., Ray D. S. Viable deletions of the M13 complementary strand origin. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6784–6788. doi: 10.1073/pnas.78.11.6784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Marvin D. A., Hohn B. Filamentous bacterial viruses. Bacteriol Rev. 1969 Jun;33(2):172–209. doi: 10.1128/br.33.2.172-209.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. McPherson A., Jurnak F., Wang A., Kolpak F., Molineux I., Rich A. Gene-V product of bacteriophage fd: structure of a DNA-unwinding protein and its complexes with DNA. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):21–28. doi: 10.1101/sqb.1979.043.01.005. [DOI] [PubMed] [Google Scholar]
  29. Meyer T. F., Geider K. Enzymatic synthesis of bacteriophage fd viral DNA. Nature. 1982 Apr 29;296(5860):828–832. doi: 10.1038/296828a0. [DOI] [PubMed] [Google Scholar]
  30. Meyer T. F., Geider K., Kurz C., Schaller H. Cleavage site of bacteriophage fd gene II-protein in the origin of viral strand replication. Nature. 1979 Mar 22;278(5702):365–367. doi: 10.1038/278365a0. [DOI] [PubMed] [Google Scholar]
  31. Miyoshi K., Huang T., Itakura K. Solid-phase synthesis of polynucleotides. III. Synthesis of polynucleotides with defined sequences by the block coupling phosphotriester method. Nucleic Acids Res. 1980 Nov 25;8(22):5491–5505. doi: 10.1093/nar/8.22.5491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Model P., McGill C., Mazur B., Fulford W. D. The replication of bacteriophage f1: gene V protein regulates the synthesis of gene II protein. Cell. 1982 Jun;29(2):329–335. doi: 10.1016/0092-8674(82)90149-0. [DOI] [PubMed] [Google Scholar]
  33. Neel B. G., Hayward W. S., Robinson H. L., Fang J., Astrin S. M. Avian leukosis virus-induced tumors have common proviral integration sites and synthesize discrete new RNAs: oncogenesis by promoter insertion. Cell. 1981 Feb;23(2):323–334. doi: 10.1016/0092-8674(81)90128-8. [DOI] [PubMed] [Google Scholar]
  34. Oey J. L., Knippers R. Properties of the isolated gene 5 protein of bacteriophage fd. J Mol Biol. 1972 Jul 14;68(1):125–138. doi: 10.1016/0022-2836(72)90268-9. [DOI] [PubMed] [Google Scholar]
  35. Payne G. S., Courtneidge S. A., Crittenden L. B., Fadly A. M., Bishop J. M., Varmus H. E. Analysis of avian leukosis virus DNA and RNA in bursal tumours: viral gene expression is not required for maintenance of the tumor state. Cell. 1981 Feb;23(2):311–322. doi: 10.1016/0092-8674(81)90127-6. [DOI] [PubMed] [Google Scholar]
  36. Pratt D., Erdahl W. S. Genetic control of bacteriophage M13 DNA synthesis. J Mol Biol. 1968 Oct 14;37(1):181–200. doi: 10.1016/0022-2836(68)90082-x. [DOI] [PubMed] [Google Scholar]
  37. Rawlins D. R., Rosenfeld P. J., Wides R. J., Challberg M. D., Kelly T. J., Jr Structure and function of the adenovirus origin of replication. Cell. 1984 May;37(1):309–319. doi: 10.1016/0092-8674(84)90327-1. [DOI] [PubMed] [Google Scholar]
  38. Ray D. S., Kook K. Insertion of the Tn3 transposon into the genome of the single-stranded DNA phage M13. Gene. 1978 Oct;4(2):109–119. doi: 10.1016/0378-1119(78)90024-0. [DOI] [PubMed] [Google Scholar]
  39. Reddy E. P., Reynolds R. K., Santos E., Barbacid M. A point mutation is responsible for the acquisition of transforming properties by the T24 human bladder carcinoma oncogene. Nature. 1982 Nov 11;300(5888):149–152. doi: 10.1038/300149a0. [DOI] [PubMed] [Google Scholar]
  40. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Scott J. F., Kornberg A. Purification of the rep protein of Escherichia coli. An ATPase which separates duplex DNA strands in advance of replication. J Biol Chem. 1978 May 10;253(9):3292–3297. [PubMed] [Google Scholar]
  42. Shortle D. R., Margolskee R. F., Nathans D. Mutational analysis of the simian virus 40 replicon: pseudorevertants of mutants with a defective replication origin. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6128–6131. doi: 10.1073/pnas.76.12.6128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Sugden B., De Troy B., Roberts R. J., Sambrook J. Agarose slab-gel electrophoresis equipment. Anal Biochem. 1975 Sep;68(1):36–46. doi: 10.1016/0003-2697(75)90676-4. [DOI] [PubMed] [Google Scholar]
  44. Tabin C. J., Bradley S. M., Bargmann C. I., Weinberg R. A., Papageorge A. G., Scolnick E. M., Dhar R., Lowy D. R., Chang E. H. Mechanism of activation of a human oncogene. Nature. 1982 Nov 11;300(5888):143–149. doi: 10.1038/300143a0. [DOI] [PubMed] [Google Scholar]
  45. Tsuchida N., Ryder T., Ohtsubo E. Nucleotide sequence of the oncogene encoding the p21 transforming protein of Kirsten murine sarcoma virus. Science. 1982 Sep 3;217(4563):937–939. doi: 10.1126/science.6287573. [DOI] [PubMed] [Google Scholar]
  46. Wallace R. B., Schold M., Johnson M. J., Dembek P., Itakura K. Oligonucleotide directed mutagenesis of the human beta-globin gene: a general method for producing specific point mutations in cloned DNA. Nucleic Acids Res. 1981 Aug 11;9(15):3647–3656. doi: 10.1093/nar/9.15.3647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Winberg G., Hammarskjöld M. L. Isolation of DNA from agarose gels using DEAE-paper. Application to restriction site mapping of adenovirus type 16 DNA. Nucleic Acids Res. 1980 Jan 25;8(2):253–264. doi: 10.1093/nar/8.2.253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zagursky R. J., Berman M. L. Cloning vectors that yield high levels of single-stranded DNA for rapid DNA sequencing. Gene. 1984 Feb;27(2):183–191. doi: 10.1016/0378-1119(84)90139-2. [DOI] [PubMed] [Google Scholar]
  49. van Wezenbeek P. M., Hulsebos T. J., Schoenmakers J. G. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd. Gene. 1980 Oct;11(1-2):129–148. doi: 10.1016/0378-1119(80)90093-1. [DOI] [PubMed] [Google Scholar]

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