Replication and Transcription of Bacteriophage ϕ29 DNA

Margarita Salas; Fernando Rojo

doi:10.1128/9781555818388.ch58

Chapter 58 : Replication and Transcription of Bacteriophage ϕ29 DNA

Authors: Margarita Salas¹, Fernando Rojo¹

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Centro de Biologia Molecular (CSIC-UAM), Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain

Content Type: Monograph

Publication Year: 1993

Category: Bacterial Pathogenesis; Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555818388

Chapter DOI: 10.1128/9781555818388.ch58

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Replication and Transcription of Bacteriophage ϕ29 DNA, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap58-1.gif /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap58-2.gif

Abstract:

The genome of Bacillus subtilis phage ø29 consists of a linear, double-stranded DNA 19,285 bp long with a 6-bp-long inverted terminal repeat (AAAGTA; 32, 114) and a terminal protein (TP) covalently linked at the 5' ends. Viral genes 1, 2, 3, 5, 6, and 17 are required for ø29 DNA replication. ø29 DNA polymerase is inhibited by drugs that are known inhibitors of eukaryotic DNA polymerase α such as aphidicolin, phosphonoacetic acid, and the nucleotide analogs butyl-anilino dATP (BuAdATP) and butyl-phenyl dGTP (BuPdGTP). The amino acid sequence RGD, which is found in cell adhesion proteins, is present at positions 256 to 258 in the ø29 and M2 TPs. Activation of the initiation of ø29 DNA replication by p6 requires not only formation of the complex but also its correct positioning relative to the ø29 DNA ends, suggesting that other proteins involved in the initiation of ø29 DNA replication (TP and/or DNA polymerase) recognize p6 at a precise position. Transcription of the ø29 genome takes place in two stages. At the beginning of the infection only the genes involved in DNA replication and transcription regulation are expressed. Genes coding for structural components of the phage particle and for proteins involved in morphogenesis and cell lysis are expressed later on in infection.

Citation: Salas M, Rojo F. 1993. Replication and Transcription of Bacteriophage ϕ29 DNA, p 843-857. In Sonenshein A, Hoch J, Losick R (ed), Bacillus subtilis and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch58

Key Concept Ranking

DNA Polymerase I: 0.5125
Transcription Start Site: 0.46845672
Linear Double-Stranded DNA: 0.4452721

0.5125

Highlighted Text: Show | Hide

Full text loading...

Figures

Replication and Transcription of Bacteriophage ϕ29 DNA

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818388.chap58-1,webId=/content/author/10.1128/9781555818388.chap58-1,properties={foaf_givenname=Margarita, foaf_name=Margarita Salas, foaf_surname=Salas, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818388.chap58-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818388.chap58-2,webId=/content/author/10.1128/9781555818388.chap58-2,properties={foaf_givenname=Fernando, foaf_name=Fernando Rojo, foaf_surname=Rojo, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818388.chap58-aff1]]}]]

/content/10.1128/9781555818388.chap58.fig58-1

Figure 1

Genetic and transcriptional maps of phage ϕ29 genome. (A) Genetic map (adapted from reference 69 ). Arrows indicate directions of transcription. The TP is shown attached to the 5' ends of the genome. (B) Transcription map. Arrowheads indicate directions of transcription from the different promoters (see text). The region containing the main early and late promoters is magnified to show the relative position of each promoter. Transcription terminators (TA1, TB1, TB2, and TD1) are represented by thick, filled arrowheads. The position and approximate length of each gene is indicated. SSB, single-stranded-DNA-binding protein.

10.1128/9781555818388/fig58-1_thmb.gif

10.1128/9781555818388/fig58-1.gif

Figure 1

/content/10.1128/9781555818388.chap58.fig58-2

Figure 2

Different stages and viral gene products involved in ϕ29 DNA replication. Based on structural and functional studies (see text for details), a two-domain structure analogous to that of the Klenow fragment of polymerase I is extrapolated for ϕ29 DNA polymerase. ϕ29 primer TP is indicated by black, and parental TP is shaded. DBP, DNA-binding protein; SSB, single-stranded-DNA-binding protein.

10.1128/9781555818388/fig58-2_thmb.gif

10.1128/9781555818388/fig58-2.gif

Figure 2

/content/10.1128/9781555818388.chap58.fig58-3

Figure 3

Sliding-back model for transition from protein-primed initiation to DNA elongation. Darkly shaded areas correspond to polymerization domains of ϕ29 DNA polymerase that define a cleft proposed to be used both as DNA- and TP-binding sites. ϕ29 TP, serving as primer for the nascent strand, is indicated by black, whereas parental ϕ29 TP, which is covalently bound to the displaced strand, is indicated by light shading. The sequence indicated corresponds to the 6-bp inverted terminal repeat present at each ϕ29 DNA end. See text for details.

10.1128/9781555818388/fig58-3_thmb.gif

10.1128/9781555818388/fig58-3.gif

Figure 3

/content/10.1128/9781555818388.chap58.fig58-4

Figure 4

p4-binding site. The DNA region represented spans the area from the early A2b promoter (bottom left) to the divergent late A3 promoter (right), with a p4-binding site between them. RNA polymerase (RNP) is bound to the late A3 promoter. Positions protected from the attack of hydroxyl radicals by p4 or by the RNA polymerase bound at the late A3 promoter are shown by open and filled dots, respectively. p4-binding sequences are represented by thickened lines in the DNA sequence. Guanine residues whose methylation interferes with p4 binding to DNA are also shown (©)· Arrows indicate positions that become hypersensitive to DNase I cleavage upon p4 binding, most likely as a consequence of the protein-induced DNA curvature. Positions -56 and -102 do not appear when both p4 and RNA polymerase are bound to the late A3 promoter and are shown in parentheses. Note that the p4-binding site partially overlaps the early A2b promoter, thus displacing the RNA polymerase from it and directing the polymerase to the late A3 promoter.

10.1128/9781555818388/fig58-4_thmb.gif

10.1128/9781555818388/fig58-4.gif

Figure 4

References

/content/book/10.1128/9781555818388.chap58

1. A1onso, J. C,, F. Rojo,, and M. Salas. Unpublished data.

1a.. Barthelemy, I.,, J. M. Lázaro,, E. Mindez,, R. P. Mellado,, and M. Salas. 1987. Purification in an active form of the phage φ29 protein p4 that controls the viral late transcription. Nucleic Acids Res. 15: 7781– 7793.

2. Barthelemy, I.,, R. P. Mellado,, and M. Salas. 1988. Symmetrical transcription in bacteriophage φ29 DNA. Biochimie 70: 605– 609.

3. Barthelemy, I.,, R. P. Mellado,, and M. Salas. 1989. In vitro transcription of bacteriophage φ29 DNA: inhibition of early promoters by the viral replication protein p6. J. Virol. 63: 460– 462.

4. Barthelemy, I.,, and M. Salas. 1989. Characterization of a new prokaryotic transcriptional activator and its DNA recognition site. J. Mol. Biol. 208: 225– 232.

5. Barthelemy, I.,, M. Salas,, and R. P. Mellado. 1986. In vivo transcription of bacteriophage φ29 DNA: transcription initiation sites. J. Virol. 60: 874– 879.

6. Barthelemy, I.,, M. Salas,, and R. P. Mellado. 1987. In vivo transcription of bacteriophage φ29: transcription termination. J. Virol. 61: 1751– 1755.

7. Benes, V.,, L. Arnold,, J. Smrt,, and V. Paces. 1989. Nucleotide sequence of the right early region of Bacillus phage φ15 and comparison with related phages: reorganization of gene 17 during evolution. Gene 75: 341– 347.

8.Bernad, A., L. Blanco, J. M. Lázaro, G. Martín, and M. Salas. 1989. A conserved 3′ → 5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59: 219– 228.

9.Bernad, A., J. M. Lázaro, M. Salas, and L. Blanco. 1990. The highly conserved amino acid sequence motif Tyr-Asp-Thr-Asp-Ser in α-like DNA polymerases is required by phage φ29 DNA polymerase for protein-primed initiation and polymerization. Proc. Natl. Acad. Sci. USA 87: 4610– 4614.

10.Bernad, A., A. Zaballos, M. Salas, and L. Blanco. 1987. Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases. EMBO J. 6: 4221– 4225.

11. Blanco, L.,, A. Bernad,, M. A. Blasco,, and M. Salas. 1991. A general structure for DNA-dependent DNA polymerases. Gene 100: 27– 38.

12. Blanco, L.,, A. Bernad,, J. A. Esteban,, and M. Salas. 1992. DNA-independent deoxynucleotidylation of the φ29 terminal protein by the φ29 DNA polymerase. J. Biol. Chem. 267: 1225– 1230.

13. Blanco, L.,, A. Bernad,, J. M. Lázaro,, G. Martín,, C. Garmendia,, and M. Salas. 1989. Highly efficient DNA synthesis by the phage φ29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264: 8935– 8940.

14. Blanco, L.,, A. Bernad,, and M. Salas. 1988. Transition from initiation to elongation in protein-primed φ29 DNA replication: salt-dependent stimulation by the viral protein p6. J. Virol. 62: 4167– 4172.

15. Blanco, L.,, A. Bernad,, and M. Salas. 1992. Evidence favouring the hypothesis of a conserved 3′ → 5′ exonuclease active site in DNA-dependent DNA polymerases. Gene 112: 139– 144.

16. Blanco, L.,, J. A. García,, M. A. Peñalva,, and M. Salas. 1983. Factors involved in the initiation of phage φ29 DNA replication in vitro: requirement of the gene 2 product for the formation of the protein p3-dAMP complex. Nucleic Acids Res. 11: 1309– 1323.

17. Blanco, L.,, J. A. García,, and M. Salas. 1984. C1oning and expression of gene 2, required for the protein-primed initiation of the Bacillus subtilis phage φ29 DNA replication. Gene 29: 33– 40.

18. Blanco, L.,, J. Gutiercez,, J. M. Lázaro,, A. Bernad,, and M. Salas. 1986. Replication of phage φ29 DNA in vitro: role of the viral protein p6 in initiation and elongation. Nucleic Acids Res. 14: 4923– 4937.

19. Blanco, L.,, I. Prieto,, J. Gutiérrez,, A. Bernad,, J. M. Lázaro,, J. M. Hermoso,, and M. Salas. 1987. Effect of NH4+ ions on φ29 DNA-protein p3 replication: formation of a complex between the terminal protein and the DNA polymerase. J. Virol. 61: 3983– 3991.

20. Blanco, L.,, and M. Salas. 1984. Characterization and purification of a phage φ29-encoded DNA polymerase required for the initiation of replication. Proc. Natl. Acad. Sci. USA 81: 5325– 5329.

21. Blanco, L.,, and M. Salas. 1985. Characterization of a 3′ → 5′ exonuclease activity in the phage φ29-encoded DNA polymerase. Nucleic Acids Res. 13: 1239– 1249.

22. Blanco, L.,, and M. Salas. 1985. Replication of phage φ29 DNA with purified terminal protein and DNA polymerase: synthesis of full-length φ29 DNA. Proc. Natl. Acad. Sci. USA 82: 6404– 6408.

23. Blanco, L.,, and M. Salas. 1986. Effect of aphidicolin and nucleotide analogs on the phage φ29 DNA polymerase. Virology 153: 179– 187.

24. Blasco, M. A.,, A. Bernad,, L. Blanco,, and M. Salas. 1991. Characterization and mapping of the pyrophosphorolytic activity of the phage φ29 DNA polymerase. J. Biol. Chem. 266: 7904– 7909.

25. Blasco, M. A.,, L. Blanco,, E. Parés,, M. Salas,, and A. Bernad. 1990. Structural and functional analysis of temperature sensitive mutants of the phage φ29 DNA polymerase. Nucleic Acids Res. 18: 4763– 4770.

25a.. Blasco, M. A.,, J. A. Esteban,, J. Méndez,, L. Blanco,, and M. Salas. 1993. Structural and functional studies on φ29 DNA polymerase. Chromosoma 102: 32– 38.

25b.. Blasco, M. A.,, J. M. Lázaro,, A. Bernad,, L. Blanco,, and M. Salas. 1992. φ29 DNA polymerase active site: mutants in conserved residues Tyr254 and Tyr390 are affected in dNTP binding. J. Biol. Chem. 267: 19427– 19434.

25c.. Blasco, M. A.,, J. M. Lázaro,, L. Blanco,, and M. Salas. Unpublished data.

26. Bracco, L.,, D. Kotlarz,, A. Kolb,, S. Diekmann,, and H. Buc. 1989. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 8: 4289– 4296.

26a.. Bravo, A. Unpublished data.

27. Brennan, R. G.,, and B. W. Mathews. 1989. The helix-turn-helix DNA binding motif. J. Biol. Chem. 264: 1903– 1906.

28. Carrascosa, J. L.,, A. Camacho,, F. Moreno,, F. Jiménez,, R. P. Mellado,, E. Viñuela,, and M. Salas. 1976. Bacillus subtilis phage φ29: characterization of gene products and functions. Eur. J. Biochem. 66: 229– 241.

29. Derbyshire, V.,, P. S. Freemont,, M. R. Sanderson,, L. Beese,, J. M. Friedman,, C. M. Joyce,, and t. A. Steitz. 1988. Genetic and crystallographic studies of the 3′ → 5′ exonucleolytic site of DNA polymerase I. Science 240: 199– 201.

30. Dodd, I. B.,, and J. B. Egan. 1990. Improved detection of helix-turn-helix DNA binding motives in protein sequences. Nucleic Acids Res. 18: 5019– 5026.

31. Escarmis, C,, D. Guirao,, and M. Salas. 1989. Replication of recombinant φ29 DNA molecules in Bacillus subtilis protoplasts. Virology 169: 150– 160.

32. Escarmis, C,, and M. Salas. 1981. Nucleotide sequence at the termini of the DNA of Bacillus subtilis phage φ29. Proc. Natl. Acad. Sci. USA 78: 1446– 1450.

33. Escarmis, C,, and M. Salas. 1982. Nucleotide sequence of the early genes 3 and 4 of bacteriophage φ29. Nucleic Acids Res. 10: 5785– 5798.

34. Esteban, J. A.,, A. Bernad,, M. Salas,, and L. Blanco. 1992. Metal activation of synthetic and degradative activities of φ29 DNA polymerase, a model enzyme for protein-primed replication. Biochemistry 31: 350– 359.

34a.. Esteban, J. A.,, M. Salas,, and L. Blanco. 1993. Fidelity of φ29 DNA polymerase: comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem. 268, in press.

35. Freemont, P. S.,, J. M. Friedman,, L. S. Beese,, M. R. Sanderson,, and t. A. Steitz. 1988. Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl. Acad. Sci. USA 85: 8924– 8928.

35a.. Freire, R.,, M. Serrano,, M. Salas,, and J. M. Hermoso. Unpublished data.

36. García, J. A.,, M. A. Peñalva,, L. Blanco,, and M. Salas. 1984. Template requirements for the initiation of phage φ29 DNA replication in vitro. Proc. Natl. Acad. Sci. USA 81: 80– 84.

37. Garmendia, C,, A. Bernad,, J. A. Esteban,, L. Blanco,, and M. Salas. 1992. The bacteriophage φ29 DNA polymerase, a proofreading enzyme. J. Biol. Chem. 267: 2594– 2599.

38. Garmendia, C.,, J. M. Hermoso,, and M. Salas. 1990. Functional domain for priming activity in the phage φ29 terminal protein. Gene 88: 73– 79.

39. Garmendia, C,, M. Salas,, and J. M. Hermoso. 1988. Site-directed mutagenesis in the DNA linking site of bacteriophage φ29 terminal protein: isolation and characterization of Ser232 → Thr mutant. Nucleic Acids Res. 16: 5727– 5740.

40. Garvey, K. J.,, H. Yoshikawa,, and J. Ito. 1985. The complete sequence of the Bacillus phage φ29 right early region. Gene 40: 301– 309.

41. Gibbs, J. S.,, H. C. Chiou,, J. D. Hall,, D. W. Mount,, M. J. Retondo,, S. K. Weller,, and D. M. Coen. 1985. Sequence and mapping analysis of the herpes simplex virus DNA polymerase gene predict a C-terminal substrate binding domain. Proc. Natl. Acad. Sci. USA 82: 7969– 7973.

42. Guo, P.,, S. Erlckson,, and D. Anderson. 1987. A small viral RNA is required for in vitro packaging of bacteriophage φ29 DNA. Science 236: 690– 694.

43. Gutiérrez, J.,, J. A. García,, L. Blanco,, and M. Salas. 1986. C1oning and template activity of the origins of replication of phage φ29 DNA. Gene 43: 1– 11.

44. Gutiérrez, J.,, C. Garmendia,, and M. Salas. 1988. Characterization of the origins of replication of bacteriophage φ29 DNA. Nucleic Acids Res. 16: 5895– 5914.

45. Gutiérrez, C,, G. Martín,, J. M. Sogo,, and M. Salas. 1991. Mechanism of stimulation of DNA replication by bacteriophage φ29 single-stranded DNA-binding protein p5. J. Biol. Chem. 266: 2104– 2111.

46.Gutiérrez, C,, J. M. Sogo,, and M. Salas. 1991. Analysis of replication intermediates produced during bacteriophage φ29 DNA replication in vitro. J. Mol. Biol. 222: 983– 994.

47. Hagen, E. W.,, B. E. Reilly,, M. E. Tosi,, and D. L. Anderson. 1976. Analysis of gene function of bacteriophage φ29 of Bacillus subtilis: identification of cistrons essential for viral assembly. J. Virol. 19: 501– 517.

48. Hermoso, J. M.,, E. Méndez,, F. Soriano,, and M. Salas. 1985. Location of the serine residue involved in the linkage between the terminal protein and the DNA of φ29. Nucleic Acids Res. 13: 7715– 7728.

49. Hermoso, J. M.,, and M. Salas. 1980. Protein p3 is linked to the DNA of phage φ29 DNA through a phosphoester bond between serine and 5′-dAMP. Proc. Natl. Acad. Sci. USA 77: 6425– 6428.

50. Heumann, H.,, M. Ricchetti,, and W. Werel. 1988. DNA-dependent RNA polymerase of Escherichia coli induces bending or an increased flexibility of DNA by specific complex formation. EMBO J. 7: 4379– 4381.

51. Hirokawa, H.,, K. Matsumoto,, and M. Ohashi,. 1982. Replication of Bacillus small phage DNA, p. 45– 46. In D. Schlessinger (ed.), Microbiology—1982. American Society for Microbiology, Washington, D.C.

52. Hogan, M. E.,, M. W. Roberson,, and R. Austin. 1989. DNA flexibility may dominate DNase I cleavage. Proc. Natl. Acad. Sci. USA 86: 9273– 9277.

53. Huberman, J. A. 1981. New views of the biochemistry of eukaryotic DNA replication revealed by aphidicolin, an unusual inhibitor of DNA polymerase. Cell 23: 647– 648.

54. Inciarte, M. R.,, M. Salas,, and J. M. Sogo. 1980. Structure of replicating DNA molecules of Bacillus subtilis bacteriophage φ29. J. Virol. 34: 187– 199.

55. Ito, J. 1978. Bacteriophage φ29 terminal protein: its association with the 5′ termini of the φ29 genome. J. Virol. 28: 895– 904.

56. Khan, N. W.,, G. E. Wright,, L. W. Dudycz,, and N. C. Brown. 1984. Butylphenyl dGTP: a selective and potent inhibitor of mammalian DNA polymerase alpha. Nucleic Acids Res. 12: 3695– 3706.

57. Knight, K. L.,, and R. T. Sauer. 1989. DNA binding specificity of the Arc and Mnt repressors is determined by a short region of N-terminal residues. Proc. Natl. Acad. Sci. USA 86: 797– 801.

58. Kobayashi, H.,, K. Kitabayaski,, K. Matsumoto,, and H. Hirokawa. 1991. Primer protein of bacteriophage M2 exposes the RGD receptor site upon linking the first deoxynucleotide. Mol. Gen. Genet. 226: 65– 69.

59. Kobayashi, H.,, K. Kitabayaski,, K. Matsumoto,, and H. Hirokawa. 1991. Receptor sequence of the terminal protein of bacteriophage M2 that interacts with an RGD (Arg-Gly-Asp) sequence of the primer protein. Virology 185: 901– 903.

60. Kobayashi, H.,, K. Matsumoto,, S. Misawa,, K. Miura,, and H. Hirokawa. 1989. An inhibitory effect of RGD peptide on protein-priming reaction of bacteriophages φ29 and M2. Mol. Gen. Genet. 220: 8– 11.

61. Lavigne, M.,, M. Herbert,, A. Kolb,, and H. Buc. 1992. Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J. Mol. Biol. 224: 293– 306.

62. Leavitt, M. C,, and J. Ito. 1987. Nucleotide sequence of Bacillus phage Nf terminal protein gene. Nucleic Acids Res. 15: 5251– 5259.

63. Martín, G.,, J. M. Lázaro,, E. Méndez,, and M. Salas. 1989. Characterization of phage φ29 protein p5 as a single-stranded DNA binding protein. Function in φ29 DNA-protein p3 replication. Nucleic Acids Res. 17: 3663– 3672.

64. Martín, G.,, and M. Salas. 1988. Characterization and cloning of gene 5 of Bacillus subtilis phage φ29. Gene 67: 193– 201.

65. Matsumoto, K.,, T. Saito,, and H. Kirokawa. 1983. In vitro initiation of bacteriophage φ29 and M2 DNA replication: genes required for formation of a complex between the terminal protein and 5′ dAMP. Mol. Gen. Genet. 191: 26– 30.

66. McA1lister, C. F.,, and E. c. Achberger. 1989. Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J. Biol. Chem. 264: 10451– 10456.

67. Mellado, R. P.,, I. Barthelemy,, and M. Salas. 1986. In vivo transcription of bacteriophage φ29 DNA early and late promoter sequences. J. Mol. Biol. 191: 191– 197.

68. Mellado, R. P.,, I. Barthelemy,, and M. Salas. 1986. In vitro transcription of bacteriophage φ29 DNA. Correlation between in vitro and in vivo promoters. Nucleic Acids Res. 14: 4731– 4741.

69. Mellado, R. P.,, F. Moreno,, E. Viñuela,, M. Salas,, B. E. Reilly,, and D. L. Anderson. 1976. Genetic analysis of bacteriophage φ29 of Bacillus subtilis: integration and mapping of nonsense mutants of two collections. J. Virol. 19: 495– 500.

70. Mellado, R. P.,, M. A. Peñalva,, M. R. Inciarte,, and M. Salas. 1980. The protein covalently linked to the 5′ termini of the DNA of Bacillus subtilis phage φ29 is involved in the initiation of DNA replication. Virology 104: 84– 96.

70a.. Méndez, J.,, L. Blanco,, J. A. Esteban,, A. Bernad,, and M. Salas. 1992. Initiation of φ29 DNA replication occurs at the second 3′ nucleotide of the linear template: a sliding-back mechanism for protein-primed DNA replication. Proc. Natl. Acad. Sci. USA 89: 9579– 9583.

71. Mizukami, Y.,, T. Seklya,, and H. Hirokawa. 1986. Nucleotide sequence of gene F of Bacillus phage Nf. Gene 42: 231– 235.

72. Nuez, B.,, F. Rojo,, I. Barthelemy,, and M. Salas. 1991. Identification of the sequences recognized by phage φ29 transcriptional activator: possible interaction between the activator and the RNA polymerase. Nucleic Acids Res. 19: 2337– 2342.

72a.. Nuez, B.,, F. Rojo,, and M. Salas. 1992. Phage φ29 regulatory protein p4 stabilizes the binding of the RNA polymerase to the late promoter in a process involving direct protein-protein contacts. Proc. Natl. Acad. Sci. USA 89: 11401– 11405.

73. Ollis, D. L.,, R. Brick,, R. Hamlin,, N. G. Xuong,, and T. A. Steitz. 1985. Structure of the large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature (London) 313: 762– 766.

74. Ortin, J.,, E. Viñuela,, M. Salas,, and C. Vasquez. 1971. DNA-protein complex in circular DNA from phage φ29. Nature New Biol. 234: 275– 277.

75. Otero, M. J.,, J. M. Lázaro,, and M. Salas. 1990. Deletions at the N terminus of bacteriophage φ29 protein p6: DNA binding and activity in φ29 DNA replication. Gene 95: 25– 30.

76. Otero, M. J.,, and M. Salas. 1989. Regions at the carboxyl end of bacteriophage protein p6 required for DNA binding and activity in φ29 DNA replication. Nucleic Acids Res. 17: 4567– 4577.

77. Pandey, V. N.,, K. R. Williams,, K. L. Stone,, and M. J. Modak. 1987. Photoafhnity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking. Biochemistry 26: 7744– 7748.

78. Pastrana, R.,, J. M. Lázaro,, L. Blanco,, J. A. García,, E. Méndez,, and M. Salas. 1985. Overproduction and purification of protein p6 of Bacillus subtilis phage φ29: role in the initiation of DNA replication. Nucleic Acids Res. 13: 3083– 3100.

79. Peñalva, M. A.,, and M. Salas. 1982. Initiation of phage φ29 DNA replication in vitro: formation of a covalent complex between the terminal protein, p3, and 5′-dAMP. Proc. Natl. Acad. Sci. USA 79: 5522– 5526.

80. Prieto, I.,, J. M. Lázaro,, J. A. García,, J. M. Hermoso,, and M. Salas. 1984. Purification in a functional form of the terminal protein of Bacillus subtilis phage φ29. Proc. Natl. Acad. Sci. USA 81: 1639– 1643.

81. Prieto, I.,, E. Méndez,, and M. Salas. 1989. Characterization, overproduction and purification of the product of gene 1 of Bacillus subtilis phage φ29. Gene 77: 195– 204.

82. Prieto, I.,, M. Serrano,, J. M. Lázaro,, M. Salas,, and J. M. Hermoso. 1988. Interaction of the bacteriophage φ29 protein p6 with double-stranded DNA. Proc. Natl. Acad. Sci. USA 85: 314– 318.

83. Reha-Krantz, L. J. 1988. Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants. Relating structure to function. J. Mol. Biol. 202: 711– 724.

84. Rojo, F.,, and M. Salas. 1990. Short N-terminal deletions in the phage φ29 transcriptional activator protein p4 impair its DNA binding ability. Gene 96: 75– 81.

85. Rojo, F.,, and M. Salas. 1991. A DNA curvature can substitute phage φ29 regulatory protein p4 when acting as a transcriptional repressor. EMBO J. 10: 3429– 3438.

86. Rojo, F.,, A. Zaballos,, and M. Salas. 1990. Bend induced by phage φ29 transcriptional activator in the viral late promoter is required for activation. J. Mol. Biol. 211: 713– 725.

87. Rush, J.,, and W. H. Konigsberg. 1990. Photoaffinity labeling of the Klenow fragment with 8-azido-dATP. J. Biol. Chem. 265: 4821– 4827.

88. Salas, M., 1988>. Phages with protein attached to the DNA ends, p. 169– 191. In R. Calendar (ed.), The Bacteriophages, vol. 1. Plenum Press, New York.

89. Salas, M. 1991. Protein-priming of DNA replication. Annu. Rev. Biochem. 60: 39– 71.

90. Salas, M.,, R. P. Mellado,, E. Viñuela,, and J. M. Sogo. 1978. Characterization of a protein covalently linked to the 5′ termini of the DNA of Bacillus subtilis phage φ29. J. Mol. Biol. 119: 269– 291.

91. Schleif, R. 1988. DNA binding by proteins. Science 241: 1182– 1187.

92. Serrano, M.,, I. Barthelemy,, and M. Salas. 1991. Transcription activation at a distance by phage φ29 protein p4. Effect of bent and non-bent intervening DNA sequences. J. Mol. Biol. 219: 403– 414.

93. Serrano, M.,, J. Gutiérrez,, I. Prieto,, J. M. Hermoso,, and M. Salas. 1989. Signals at the bacteriophage φ29 DNA replication origins required for protein p6 binding and activity. EMBO J. 8: 1879– 1885.

93a.. Serrano, M.,, C. Gutiérrez,, M. Salas,, and J. M. Hermoso. The superhelical path of the DNA in the nucleoprotein complex that activates the initiation of phage φ29 DNA replication. J. Mol. Biol., in press.

93b.. Serrano, M.,, and M. Salas. Unpublished data.

94. Serrano, M.,, M. Salas,, and J. M. Hermoso. 1990. A novel nucleoprotein complex at a replication origin. Science 248: 1012– 1016.

95. Shih, M. F.,, K. Watabe,, and J. Ito. 1982. In vitro complex formation between bacteriophage φ29 terminal protein and deoxynucleotide. Biochem. Biophys. Res. Commun. 105: 1031– 1036.

96. Shih, M. F.,, K. Watabe,, H. Yoshikawa,, and J. Ito. 1984. Antibodies specific for the φ29 terminal protein inhibit the initiation of DNA replication in vitro. Virology 133: 56– 64.

96a.. Soengas, M. S.,, J. A. Esteban,, J. M. Lázaro,, A. Bernad,, M. A. Blasco,, M. Salas,, and L. Blanco. 1992. Site-directed mutagenesis at the EcoIII motif of φ29 DNA polymerase: overlapping structural domains for the 3′-5′ exonuclease and strand-displacement activities. EMBO J. 11: 4227– 4237.

97. Sogo, J. M.,, J. A. García,, M. A. Peñalva,, and M. Salas. 1982. Structure of protein-containing replicative intermediates of Bacillus subtilis phage φ29 DNA. Virology 116: 1– 18.

98. Sogo, J. M.,, M. R. Inciarte,, J. Corral,, E. Viñuela,, and M. Salas. 1979. RNA polymerase binding sites and transcription of the DNA of Bacillus subtilis phage φ29. J. Mol. Biol. 127: 411– 436.

99. Sogo, J. M.,, M. Lozano,, and M. Salas. 1984. In vitro transcription of the Bacillus subtilis phage φ29 DNA by Bacillus subtilis and Escherichia coli RNA polymerases. Nucleic Acids Res. 12: 1943– 1960.

100. Suck, D.,, A. Lahm,, and C. Oefner. 1988. Structure refinement to 2 Å of a nicked DNA oligonucleotide complex with DNase I. Nature (London) 332: 464– 468.

101. Talavera, A.,, F. Jiménez,, M. Salas,, and E. Viñuela. 1971. Temperature-sensitive mutants of bacteriophage φ29. Virology 46: 586– 595.

102. Talavera, A.,, M. Salas,, and E. Viñuela. 1972. Temperature-sensitive mutants affected in DNA synthesis in phage φ29 of Bacillus subtilis. Eur. J. Biochem. 31: 367– 371.

103. Tomalsky, M. D.,, J. Wu,, and L. K. Miller. 1988. The location, sequence, transcription and regulation of a baculovirus DNA polymerase gene. Virology 167: 591– 600.

104. Vlcek, C,, and V. Paces. 1986. Nucleotide sequence of the late region of Bacillus phage φ29 completes the 19285-bp sequence of φ29 genome. Comparison with the homologous sequence of phage PZA. Gene 46: 215– 225.

105. Watabe, K.,, M. Leusch,, and J. Ito. 1984. Replication of bacteriophage φ29 DNA in vitro: the roles of terminal protein and DNA polymerase. Proc. Natl. Acad. Sci. USA 81: 5374– 5378.

106. Watabe, K.,, M. Leusch,, and J. Ito. 1984. A 3′ to 5′ exonuclease activity is associated with phage φ29 DNA polymerase. Biochem. Biophys. Res. Commun. 123: 1019– 1026.

107. Watabe, K.,, M. F. Shih,, and J. Ito. 1983. Protein-primed initiation of phage φ29 DNA replication. Proc. Natl. Acad. Sci. USA 80: 4248– 4252.

108. Watabe, K.,, M. F. Shih,, A. Sugino,, and J. Ito. 1982. In vitro replication of bacteriophage φ29 DNA. Proc. Natl. Acad. Sci. USA 79: 5245– 5248.

109. Whlteley, H. R.,, W. D. Ramey,, G. B. Spiegelman,, and R. D. Holder. 1986. Modulation of in vivo and in vitro transcription of bacteriophage φ29 early genes. Virology 155: 392– 401.

110. Wichitwechkarn, J.,, D. Johnson,, and D. Anderson. 1992. Mutant prohead RNAs in the in vitro packaging of φ29 DNA-gp3. J. Mol. Biol. 223: 991– 998.

111. Wu, H.-W.,, and D. M. Crothers. 1984. The locus of sequence-directed and protein-induced DNA bending. Nature (London) 308: 509– 513.

112. Yanofsky, S.,, F. Kawamura,, and J. Ito. 1976. Thermolabile transfecting DNA from temperature-sensitive mutant of phage φ29. Nature (London) 259: 60– 63.

113. Yehle, C. O. 1978. Genome-linked protein associated with the 5′ termini of bacteriophage φ29 DNA. J. Virol. 27: 776– 783.

114. Yoshlkawa, H.,, T. Friedmann,, and J. Ito. 1981. Nucleotide sequences at the termini of φ29 DNA. Proc. Natl. Acad. Sci. USA 78: 1336– 1340.

115. Yoshlkawa, H.,, and J. Ito. 1982. Nucleotide sequence of the major early region of bacteriophage φ29. Gene 17: 323– 335.

116. Zaballos, A.,, and M. Salas. 1989. Functional domains in the bacteriophage φ29 terminal protein for interaction with the φ29 DNA polymerase and with DNA. Nucleic Acids Res. 17: 10353– 10366.

117. Zlnkel, S. S.,, and D. M. Crothers. 1991. Catabolite activator protein-induced DNA bending in transcription initiation. J. Mol. Biol. 219: 201– 205.

118. Zwieb, C.,, J. Kim,, and S. Adhya. 1989. DNA bending by negative regulatory proteins: gal and lac repressors. Genes Dev. 3: 602– 611.