Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Oct 25;16(20):9611–9630. doi: 10.1093/nar/16.20.9611

The role of template superhelicity in the initiation of bacteriophage lambda DNA replication.

C Alfano 1, R McMacken 1
PMCID: PMC338767  PMID: 2847118

Abstract

The prepriming steps in the initiation of bacteriophage lambda DNA replication depend on the action of the lambda O and P proteins and on the DnaB helicase, single-stranded DNA binding protein (SSB), and DnaJ and DnaK heat shock proteins of the E. coli host. The binding of multiple copies of the lambda O protein to the phage replication origin (ori lambda) initiates the ordered assembly of a series of nucleoprotein structures that form at ori lambda prior to DNA unwinding, priming and DNA synthesis steps. Since the initiation of lambda DNA replication is known to occur only on supercoiled templates in vivo and in vitro, we examined how the early steps in lambda DNA replication are influenced by superhelical tension. All initiation complexes formed prior to helicase-mediated DNA-unwinding form with high efficiency on relaxed ori lambda DNA. Nonetheless, the DNA templates in these structures must be negatively supertwisted before they can be replicated. Once DNA helicase unwinding is initiated at ori lambda, however, later steps in lambda DNA replication proceed efficiently in the absence of superhelical tension. We conclude that supercoiling is required during the initiation of lambda DNA replication to facilitate entry of a DNA helicase, presumably the DnaB protein, between the DNA strands.

Full text

PDF
9611

Images in this article

Selected References

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

  1. Anderl A., Klein A. Replication of lambda dv DNA in vitro. Nucleic Acids Res. 1982 Mar 11;10(5):1733–1740. doi: 10.1093/nar/10.5.1733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arai K., Kornberg A. Mechanism of dnaB protein action. II. ATP hydrolysis by dnaB protein dependent on single- or double-stranded DNA. J Biol Chem. 1981 May 25;256(10):5253–5259. [PubMed] [Google Scholar]
  3. 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. 1986 Apr 11;45(1):53–64. doi: 10.1016/0092-8674(86)90537-4. [DOI] [PubMed] [Google Scholar]
  4. Bergsma D. J., Olive D. M., Hartzell S. W., Subramanian K. N. Territorial limits and functional anatomy of the simian virus 40 replication origin. Proc Natl Acad Sci U S A. 1982 Jan;79(2):381–385. doi: 10.1073/pnas.79.2.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bochner B. R., Zylicz M., Georgopoulos C. Escherichia coli DnaK protein possesses a 5'-nucleotidase activity that is inhibited by AppppA. J Bacteriol. 1986 Nov;168(2):931–935. doi: 10.1128/jb.168.2.931-935.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bramhill D., Kornberg A. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell. 1988 Mar 11;52(5):743–755. doi: 10.1016/0092-8674(88)90412-6. [DOI] [PubMed] [Google Scholar]
  7. Broach J. R., Li Y. Y., Feldman J., Jayaram M., Abraham J., Nasmyth K. A., Hicks J. B. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. doi: 10.1101/sqb.1983.047.01.132. [DOI] [PubMed] [Google Scholar]
  8. Challberg M. D., Rawlins D. R. Template requirements for the initiation of adenovirus DNA replication. Proc Natl Acad Sci U S A. 1984 Jan;81(1):100–104. doi: 10.1073/pnas.81.1.100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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 lambda: localized unwinding of duplex DNA by a six-protein reaction. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7638–7642. doi: 10.1073/pnas.83.20.7638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dodson M., Roberts J., McMacken R., Echols H. Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4678–4682. doi: 10.1073/pnas.82.14.4678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fuller C. W., Beauchamp B. B., Engler M. J., Lechner R. L., Matson S. W., Tabor S., White J. H., Richardson C. C. Mechanisms for the initiation of bacteriophage T7 DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):669–679. doi: 10.1101/sqb.1983.047.01.078. [DOI] [PubMed] [Google Scholar]
  12. Kearsey S. Structural requirements for the function of a yeast chromosomal replicator. Cell. 1984 May;37(1):299–307. doi: 10.1016/0092-8674(84)90326-x. [DOI] [PubMed] [Google Scholar]
  13. LeBowitz J. H., Zylicz M., Georgopoulos C., McMacken R. Initiation of DNA replication on single-stranded DNA templates catalyzed by purified replication proteins of bacteriophage lambda and Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jun;82(12):3988–3992. doi: 10.1073/pnas.82.12.3988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. McMacken R., Kornberg A. A multienzyme system for priming the replication of phiX174 viral DNA. J Biol Chem. 1978 May 10;253(9):3313–3319. [PubMed] [Google Scholar]
  16. Mizuuchi K., Mizuuchi M., O'Dea M. H., Gellert M. Cloning and simplified purification of Escherichia coli DNA gyrase A and B proteins. J Biol Chem. 1984 Jul 25;259(14):9199–9201. [PubMed] [Google Scholar]
  17. Moriya S., Ogasawara N., Yoshikawa H. Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region. Nucleic Acids Res. 1985 Apr 11;13(7):2251–2265. doi: 10.1093/nar/13.7.2251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nelson H. C., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19;330(6145):221–226. doi: 10.1038/330221a0. [DOI] [PubMed] [Google Scholar]
  19. Oka A., Sugimoto K., Takanami M., Hirota Y. Replication origin of the Escherichia coli K-12 chromosome: the size and structure of the minimum DNA segment carrying the information for autonomous replication. Mol Gen Genet. 1980 Apr;178(1):9–20. doi: 10.1007/BF00267207. [DOI] [PubMed] [Google Scholar]
  20. Schnos M., Zahn K., Inman R. B., Blattner F. R. Initiation protein induced helix destabilization at the lambda origin: a prepriming step in DNA replication. Cell. 1988 Feb 12;52(3):385–395. doi: 10.1016/s0092-8674(88)80031-x. [DOI] [PubMed] [Google Scholar]
  21. Stenzel T. T., Patel P., Bastia D. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell. 1987 Jun 5;49(5):709–717. doi: 10.1016/0092-8674(87)90547-2. [DOI] [PubMed] [Google Scholar]
  22. Tamanoi F., Stillman B. W. Initiation of adenovirus DNA replication in vitro requires a specific DNA sequence. Proc Natl Acad Sci U S A. 1983 Nov;80(21):6446–6450. doi: 10.1073/pnas.80.21.6446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Tomizawa J., Ogawa T. Replication of phage lambda DNA. Cold Spring Harb Symp Quant Biol. 1968;33:533–551. doi: 10.1101/sqb.1968.033.01.061. [DOI] [PubMed] [Google Scholar]
  24. Tsurimoto T., Matsubara K. Replication of lambda dv plasmid in vitro promoted by purified lambda O and P proteins. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7639–7643. doi: 10.1073/pnas.79.24.7639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ueda K., McMacken R., Kornberg A. dnaB protein of Escherichia coli. Purification and role in the replication of phiX174 DNA. J Biol Chem. 1978 Jan 10;253(1):261–269. [PubMed] [Google Scholar]
  26. Umek R. M., Kowalski D. The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell. 1988 Feb 26;52(4):559–567. doi: 10.1016/0092-8674(88)90469-2. [DOI] [PubMed] [Google Scholar]
  27. Umek R. M., Kowalski D. Yeast regulatory sequences preferentially adopt a non-B conformation in supercoiled DNA. Nucleic Acids Res. 1987 Jun 11;15(11):4467–4480. doi: 10.1093/nar/15.11.4467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Weiner J. H., Bertsch L. L., Kornberg A. The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication. J Biol Chem. 1975 Mar 25;250(6):1972–1980. [PubMed] [Google Scholar]
  29. Wickner S. H. DNA replication proteins of Escherichia coli and phage lambda. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):303–310. doi: 10.1101/sqb.1979.043.01.037. [DOI] [PubMed] [Google Scholar]
  30. Wickner S. H., Zahn K. Characterization of the DNA binding domain of bacteriophage lambda O protein. J Biol Chem. 1986 Jun 5;261(16):7537–7543. [PubMed] [Google Scholar]
  31. Wickner S., McKenney K. Deletion analysis of the DNA sequence required for the in vitro initiation of replication of bacteriophage lambda. J Biol Chem. 1987 Sep 25;262(27):13163–13167. [PubMed] [Google Scholar]
  32. Wickner S., Wright M., Hurwitz J. Association of DNA-dependent and -independent ribonucleoside triphosphatase activities with dnaB gene product of Escherichia coli. Proc Natl Acad Sci U S A. 1974 Mar;71(3):783–787. doi: 10.1073/pnas.71.3.783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wold M. S., Mallory J. B., Roberts J. D., LeBowitz J. H., McMacken R. Initiation of bacteriophage lambda DNA replication in vitro with purified lambda replication proteins. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6176–6180. doi: 10.1073/pnas.79.20.6176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zahn K., Blattner F. R. Binding and bending of the lambda replication origin by the phage O protein. EMBO J. 1985 Dec 16;4(13A):3605–3616. doi: 10.1002/j.1460-2075.1985.tb04124.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zahn K., Blattner F. R. Direct evidence for DNA bending at the lambda replication origin. Science. 1987 Apr 24;236(4800):416–422. doi: 10.1126/science.2951850. [DOI] [PubMed] [Google Scholar]
  36. Zylicz M., Gorska I., Taylor K., Georgopoulos C. Bacteriophage lambda replication proteins: formation of a mixed oligomer and binding to the origin of lambda DNA. Mol Gen Genet. 1984;196(3):401–406. doi: 10.1007/BF00436186. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES