Protein-primed DNA replication: A transition between two modes of priming by a unique DNA polymerase

EMBO Journal

Volumn 16, Issue 9, 1997, Pages 2519-2527

  Méndez, Juan ^a,b   Blanco, Luis ^a   Salas, Margarita ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b Simons Center for Quantitative Biology   (United States)

Author keywords

Linear DNA replication; Protein priming; Sliding back; Terminal protein

Indexed keywords

DNA POLYMERASE; PRIMER DNA; RNA POLYMERASE; VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACILLUS SUBTILIS; DNA REPLICATION; DNA STRUCTURE; DNA SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

BACILLUS PHAGES; CATALYSIS; DIMERIZATION; DNA MUTATIONAL ANALYSIS; DNA PRIMERS; DNA REPLICATION; DNA, VIRAL; DNA-DIRECTED DNA POLYMERASE; MODELS, GENETIC; TEMPLATES, GENETIC; VIRAL PROTEINS;

BACILLUS SUBTILIS; DNA VIRUSES;

EID: 0040528887     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.9.2519     Document Type: Article

References (39)

1. Barthelemy, I., Salas, M. and Mellado, R.P. (1986) In vivo transcription of bacteriophage φ29 DNA: transcription initiation sites. J. Virol., 60, 874-879.
2. Basu, S. and Maitra, U. (1986) Specific binding of monomeric bacteriophage T3 and T7 RNA polymerases to their respective cognate promoters requires the initiating ribonucleoside triphosphate (GTP). J. Mol. Biol., 190, 425-437.
3. Bernad, a., Blanco, L., Lázaro, J.M., Martín, G. and Salas, M. (1989) A covserved 3′-5′ exoonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell, 59, 219-228.
4. Blanco, L. and Salas, M. (1996) Relating structure to function in φ29 DNA polymerase. J. Biol. Chem., 271, 8509-8512.
5. Blanco, L., Gutiérrez, J., Lázaro, J.M., Bernad, A. and Salas, M. (1986) Replication of phage φ29 DNA in vitro: Role of the viral protein p6 in initiation and elongation. Nucleic Acids Res., 14, 4923-4937.
6. + ions on φ29 DNA-protein p3 replication: formation of a complex between the terminal protein and the DNA polymerase. J. Virol., 61, 3983-3991.
7. Blanco, L., Bernad, A. and Salas, M. (1988) Transition from initiation to elongation in the protein-primed φ29 DNA replication. Salt-dependent stimulation by the viral protein p6. J. Virol., 62, 4167-4172.
8. Blanco, L., Bernad, A., Lázaro, J.M., Martín, G., Garmendia, C. and Salas, M. (1989) Highly efficient DNA synthesis by the phage φ29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem., 264, 8935-8940.
9. Blanco, L., Bernard, A., Esteban, J.A. and Salas, M. (1992) DNA-independent deoxynucleotidylation of the φ29 terminal protein by the φ29 DNA polymerase. J. Biol. Chem., 267, 1223-1230.
10. 3NSxYG' is involved in template-primer binding and dNTP selection. J. Biol. Chem., 268, 16763-16770.
11. Blasco, M.A., Méndez, J., Lázaro, J.M., Blanco, L. and Salas, M. (1995) Primer-terminus stabilization at the φ29 DNA polymerase active site: mutational analysis of conserved motif KxY. J. Biol. Chem., 270, 2735-2740.
12. Borner, G., Patra, D., Lafer, E.M. and Sousa, R. (1992) Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J., 11, 3765-3775.
13. Caldentey, J., Blanco, L., Savilahti, H., Bamford, D.H. and Salas, M. (1992) In vitro replication of bacteriophage PRD1 DNA. Metal activation of protein-primed initiation and DNA elongation. Nucleic Acids Res., 20, 3971-3976.
14. Caldentey, J., Blanco, L., Bambord, D.H. and Salas, M. (1993) In vitro replication of bacteriophage PRD1 DNA. Characterization of the protein-primed initiation site. Nucleic Acids Res., 21, 3725-3730.
15. Chen, C.W. (1996)Complications and implications of linear bacterial chromosomes. Trends Genet., 12, 192-196.
16. de Vega, M., Lázaro, J.M., Salas, M. and Blanco, L. (1996) Primer-terminus stabilization at the 3′-5′ exonuclease active site of φ29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. EMBO J., 15, 1182-1192.
17. Eick, D., Wedel, A. and Heumann, H. (1994) From initiation to elongation: comparison of transcription by prokaryotic and eukaryotic RNA polymerases. Trends Genet., 10, 292-296.
18. Esteban, J.A., Bernad, A., Salas, M. and Blanco, L. (1992) Metal activation of synthetic and degradative activities of φ29 DNA polymerase, a model enzyme for protein-primed DNA replication. Biochemistry, 31, 350-359.
19. Esteban, J.A. Salas, M. and Blanco, L. (1993) Fidelity of φ29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem., 268, 2719-2726.
20. Esteban, J.A., Soengas, M.S., Salas, M. and Blanco, L. (1994) 3′→5′ exonuclease active site of φ29 DNA polymerase. Evidence favoring a metal-ion-assisted reaction mechanism. J. Biol. Chem., 269, 31946-31954.
21. Griep, M.A. (1995) Primase structure and function. Indian J. Biochem., 32, 171-178.
22. Illana, B., Blanco, L. and Salas, M. (1996) Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J. Mol. Biol., 264, 453-464.
23. Joyce, C.M. and Steitz, T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem., 63, 777-822.
24. King, A. and Van der Vliet, P.C. (1994) A precursor terminal protein-trinucleotide intermediate during initiation of adenovirus DNA replication: regeneration of molecular ends in vitro by a jumping back mechanism EMBO J., 13, 5786-5792.
25. Lázaro, J.M., Blanco, L. and Salas, M. (1995) Purification of bacteriophage φ29 DNA polymerase. Methods Enzymol., 262, 42-49.
26. Martín, A.C., Blanco, L., García, P. Salas, M. and Méndez, J. (1996) Protein-primed initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3′ nucleotide of the linear template: a stepwise sliding-back mechanism. J. Mol. Biol., 260, 369-377.
27. Matsumoto, K., Saito, T., Kim, C.I., Ando, T. and Hirokawa, H. (1984) Bacteriophage phi 29 DNA replication in vitro: participation of the terminal protein and the gene 2 product in elongation. Mol. Gen. Genet., 196, 381-386.
28. Méndez, J., Blanco, L., Esteban, J.A., Bernard, A. and Salas, M. (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.
29. Salas, M. (1991) Protein-priming of DNA replication. Annu. Rev. Biochem., 60, 39-71.
30. Salas, M., Miller, J.T., Leis, J. and DePamphilis, M.L. (1996) Mechanisms for priming DNA synthesis. In DePamphilis, M.L. (ed.), DNA Replication Eukaryotic Cells. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 131-176.
31. Serrano, M. Salas, M. and Hermoso, J.M. (1990) A novel nucleoprotein complex at a replication origin. Science, 248, 1012-1016.
32. Shi, Y., Gamper, H. and Hearst, J.E. (1988) Interaction of T7 RNA polymerase with DNA in an elongation complex arrested at a specific psoralen adduct site. J. Biol. Chem., 263, 527-534.
33. Soengas, M.S. Esteban, J.A., Lázaro, J.M., Bernad, A., Blasco, M.A., Salas, M. and Blanco, L. (1992) Site-directed mutagenesis at the Exo III motif of φ29 DNA polymerase. Overlapping structural domains for the 3′→5′ exonuclease and strand-displacement activities. EMBO J . 11, 4227-4237.
34. Sousa, R. (1996) Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sci., 21, 186-190.
35. Sousa, R., Patra, D. and Lafer, E.M. (1992) Model for the mechanism of bacteriophage T7 RNAP transcription initiation and termination. J. Mol. Biol., 224, 319-334.
36. Truniger, V., Lázaro, J.M., Salas, M. and Blanco, L. (1996) A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases. EMBO J., 15, 3430-3441.
37. Watabe, K., Shih, M.F. and Ito, J. (1983) In vitro replication of bacteriophage phi29 DNA. Proc. Natl. Acad. Sci. USA, 80, 4248-4252.
38. Yoshikawa, H. and Ito, J. (1982) Terminal proteins and short inverted terminal repeats of the small Bacillus bacteriophage genomes. Proc. Natl Acad. Sci. USA, 78, 1336-1340.
39. Zaballos, A., Lázaro, J.M., Méndez, E., Mellado, R.P. and Salas, M. (1989) Effects of internal deletions on the priming activity ot the phage φ29 terminal protein. Gene, 83, 187-195.