RNA-DNA hybrid formation at a bacteriophage T4 replication origin

Journal of Molecular Biology

Volumn 266, Issue 5, 1997, Pages 915-926

  Carles Kinch, Kelly ^a   Kreuzer, Kenneth N ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Bacteriophage T4; DNA unwinding element; Initiation of replication; Potassium permanganate; RNA DNA hybrid

Indexed keywords

BACTERIOPHAGE DNA; PRIMER RNA;

ARTICLE; BACTERIOPHAGE T4; DNA DENATURATION; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA RNA HYBRIDIZATION; HYBRID; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION;

EID: 0031567150     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0844     Document Type: Article

References (50)

1. Asai, T. & Kogoma, T. (1994). D-loops and R-loops: alternative mechanisms for the initiation of chromosome replication in Escherichia coli. J. Bacteriol, 176, 1807-1812.
2. Belanger, K. G., Mirzayan, C., Kreuzer, H. E., Alberts, B. M. & Kreuzer, K. N. (1996). Two-dimensional gel analysis of rolling circle replication in the presence and absence of bacteriophage T4 primase. Nucl. Acids Res. 24, 2166-2175.
3. Benson, K. H. & Kreuzer, K. N. (1992a). Plasmid models for bacteriophage T4 DNA replication: requirements for fork proteins. J. Virol. 66, 6960-6968.
4. Benson, K. H. & Kreuzer, K. N. (1992b). Role of MotA transcription factor in bacteriophage T4 DNA replication. J. Mol. Biol. 228, 88-100.
5. Brody, E., Rabussay, D. & Hall, D. H. (1983). Regulation of transcription of prereplicative genes. In Bacteriophage T4 (Mathews, C. K., Kutter, E. M., Mosig, G. & Berget, P. B., eds), pp. 174-183, American Society for Microbiology, Washington DC.
6. Brody, E. N., Kassavetis, G. A., Ouhammouch, M., Sanders, G. M., Tinker, R. L. & Geiduschek, E. P. (1995). Old phage, new insights: two recently recognized mechanisms of transcriptional regulation in bacteriophage T4 development. FEMS Microbiol. Letters, 128, 1-8.
7. Cha, T.-A. & Alberts, B. M. (1986). Studies of the DNA helicase-RNA primase unit from bacteriophage T4. A trinucleotide sequence on the DNA template starts RNA primer synthesis. J. Biol. Chem. 261, 7001-7010.
8. Dasgupta, S., Masukata, H. & Tomizawa, J. (1987). Multiple mechanisms for initiation of ColE1 DNA replication: DNA synthesis in the presence and absence of ribonuclease H. Cell, 51, 1113-1122.
9. Daube, S. S. & von Hippel, P. H. (1994). RNA displacement pathways during transcription from synthetic RNA-DNA bubble duplexes. Biochemistry, 33, 340-347.
10. Derbyshire, K. M., Salvo, J. J. & Grindley, N. D. F. (1986). A simple and efficient procedure for saturation mutagenesis using mixed oligodeoxynucleotides. Gene, 46, 145-152.
11. Derr, L. K. & Kreuzer, K. N. (1990). Expression and function of the uvsW gene of bacteriophage T4. J. Mol. Biol. 214, 643-656.
12. Guild, N., Gayle, M., Sweeney, R., Hollingsworth, T., Modeer, T. & Gold, L. (1988). Transcriptional activation of bacteriophage T4 middle promoters by the motA protein. J. Mol. Biol. 199, 241-258.
13. Holmes, D. S. & Quigley, M. (1981). A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114, 193-197.
14. Huang, R.-Y. & Kowalski, D. (1993). A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 12, 4521-4531.
15. Keppel, F., Fayet, O. & Georgopoulos, C. (1988). Strategies of bacteriophage DNA replication. In The Bacteriophages (Calendar, R., ed.), vol. 2, pp. 145-262, Plenum Press, New York.
16. Kogoma, T. (1986). RNase H-deficient mutants of Escherichia coli. J. Bacteriol. 166, 361-363.
17. Kogoma, T., Barnard, K. G. & Hong, X. (1994). RecA, Tus protein and constitutive stable DNA replication in Escherichia coli rnhA mutants. Mol. Gen. Genet. 244, 557-562.
18. Kowalski, D. & Eddy, M. J. (1989). The DNA unwinding element: A novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 8, 4335-4344.
19. Kowalski, D. & Sanford, J. P. (1982). Action of mung bean nuclease on supercoiled PM2 DNA. J. Biol. Chem. 257, 7820-7825.
20. Kowalski, D., Natale, D. & Eddy, M. J. (1988). Stable DNA unwinding, not "breathing", accounts for single-strand-specific nuclease hypersensitivity of specific A + T-rich sequences. Proc. Natl Acad. Sci. USA, 85, 9464-9468.
21. Kreuzer, K. N. & Alberts, B. M. (1985). A defective phage system reveals bacteriophage T4 replication origins that coincide with recombination hot spots. Proc. Natl Acad. Sci. USA, 82, 3345-3349.
22. Kreuzer, K. N. & Alberts, B. M. (1986). Characterization of a defective phage system for the analysis of bacteriophage T4 DNA replication origins. J. Mol. Biol. 188, 185-198.
23. Kreuzer, K. N. & Morrical, S. W. (1994). Initiation of DNA replication. In Molecular Biology of Bacteriophage T4 (Karam, J. D., ed.), pp. 28-42, ASM Press, Washington DC.
24. Kreuzer, K. N., Engman, H. W. & Yap, W. Y. (1988a). Tertiary initiation of replication in bacteriophage T4. Deletion of the overlapping uvsY promoter/ replication origin from the phage genome. J. Biol. Chem. 263, 11348-11357.
25. Kreuzer, K. N., Yap, W. Y., Menkens, A. E. & Engman, H. W. (1988b). Recombination-dependent replication of plasmids during bacteriophage T4 infection. J. Biol. Chem. 263, 11366-11373.
26. Kutter, E., Stidham, T., Guttman, B., Batts, D., Peterson, S., Djavakhishvili, T., Arisaka, F., Mesyanzhinov, V., Rüger, W. & Mosig, G. (1994). Genomic map of bacteriophage T4. In Molecular Biology of Bacteriophage T4 (Karam, J. D., ed.), pp. 28-42, ASM Press, Washington DC.
27. Landgraf, R., Chen, C. B. & Sigman, D. S. (1995). Double stranded scission of DNA directed through sequence-specific R-loop formation. Nucl. Acids Res. 23, 3524-3530.
28. Lee, D. N. & Landick, R. (1992). Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase. J. Mol. Biol. 228, 759-777.
29. Lin, S. & Kowalski, D. (1994). DNA helical instability facilitates initiation at the SV40 replication origin. J. Mol. Biol. 235, 496-507.
30. Luder, A. & Mosig, G. (1982). Two alternative mechanisms for initiation of DNA replication forks in bacteriophage T4: priming by RNA polymerase and by recombination. Proc. Natl. Acad. Sci. USA, 79, 1101-1105.
31. Macdonald, P. M., Seaby, R. M., Brown, W. & Mosig, G. (1983). Initiator DNA from a primary origin and induction of a secondary origin of bacteriophage T4 DNA replication. In Microbiology -1983 (Schlessinger, D., ed.), pp. 111-116, American Society for Microbiology, Washington DC.
32. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982). Molecular cloning. A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Marians, K. J. (1992). Prokaryotic DNA replication. Annu. Rev. Biochem. 61, 673-719.
34. Masukata, H. & Tomizawa, J. (1984). Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication. Cell, 36, 513-522.
35. Masukata, H. & Tomizawa, J. (1986). Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript. Cell, 44, 125-136.
36. Masukata, H. & Tomizawa, J. (1990). A mechanism of formation of a persistent hybrid between elongating RNA and template DNA. Cell, 62, 331-338.
37. Masukata, H., Dasgupta, S. & Tomizawa, J.-I. (1987). Transcriptional activation of ColE1 DNA synthesis by displacement of the nontranscribed strand. Cell, 51, 1123-1130.
38. Menkens, A. E. & Kreuzer, K. N. (1988). Deletion analysis of bacteriophage T4 tertiary origins. A promoter sequence is required for a rifampicin-resistant replication origin. J. Biol. Chem. 263, 11358-11365.
39. Miller, C. A. & Kowalski, D. (1993). cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 5360-5369.
40. Mosig, G. (1994). Homologous recombination. In Molecular Biology of Bacteriophage T4 (Karam, J. D., ed.), pp. 54-82, ASM Press, Washington DC.
41. Mosig, G. & Eiserling, F. (1988). Phage T4 structure and metabolism. In The Bacteriophages (Calendar, R., ed.), vol. 2, pp. 521-606, Plenum Press, New York.
42. Nelson, M. A., Ericson, M., Gold, L. & Pulitzer, J. F. (1982). The isolation and characterization of TabR bacteria: hosts that restrict bacteriophage T4 rII mutants. Mol. Gen. Genet. 188, 60-68.
43. 4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 8074-8081.
44. Sasse-Dwight, S. & Gralla, J. D. (1991). Footprinting protein-DNA complexes in vivo. Methods Enzymol. 208, 146-168.
45. Stitt, B. & Hinton, D. (1994). Regulation of middle gene transcription. In Molecular Biology of Bacteriophage T4 (Karam, J., ed.), pp. 142-160, ASM Press, Washington DC.
46. Umek, R. M. & Kowalski, D. (1987). Yeast regulatory sequences preferentially adopt a non-B conformation in supercoiled DNA. Nucl. Acids Res. 15, 4467-4480.
47. Umek, R. M. & Kowalski, D. (1988). The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell, 52, 559-567.
48. von Meyenburg, K., Boye, E., Skarstad, K., Koppes, L. & Kogoma, T. (1987). Mode of initiation of constitutive stable DNA replication in RNase H-defective mutants of Escherichia coli K-12. J. Bacteriol. 169, 2650-2658.
49. Williams, D. L. & Kowalski, D. (1993). Easily unwound DNA sequences and hairpin structures in the Epstein-Barr virus origin of plasmid replication. J. Virol. 67, 2707-2715.
50. Xu, B. & Clayton, D. A. (1995). A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence. Mol. Cell. Biol. 15, 580-589.