Plasmid rolling circle replication: Identification of the RNA polymerase-directed primer RNA and requirement for DNA polymerase I for lagging strand synthesis

EMBO Journal

Volumn 16, Issue 18, 1997, Pages 5784-5795

  Kramer, M Gabriela ^b   Khan, Saleem A ^a   Espinosa, Manuel ^b  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

DNA polymerase I; Lagging strand synthesis; Primer RNA; RNA polymerase; Rolling circle replication

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; DOUBLE STRANDED DNA; PLASMID DNA; PRIMER RNA; RNA POLYMERASE; SINGLE STRANDED DNA;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DNA REPLICATION; DNA STRAND; DNA SYNTHESIS; ENZYME DEFICIENCY; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA SYNTHESIS; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE;

BASE SEQUENCE; BINDING SITES; DNA POLYMERASE I; DNA REPLICATION; DNA, SINGLE-STRANDED; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, STRUCTURAL; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID CONFORMATION; PLASMIDS; PROMOTER REGIONS (GENETICS); RNA; RNA, BACTERIAL; STREPTOCOCCUS PNEUMONIAE;

STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE;

EID: 0030766851     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.18.5784     Document Type: Article

References (47)

1. Baas, P.D. and Jansz, H.S. (1988) Single-stranded DNA phage origins. Curr. Top. Microbiol. Immunol., 136, 31-70.
2. Birch, P. and Khan, S.A. (1992) Replication of single-stranded plasmid pT181 DNA in vitro. Proc. Natl Acad. Sci. USA, 89, 290-294.
3. Boe, L., Gros, M.F., te Riele, H., Ehrlich, S.D. and Gruss, A.D. (1989) Replication origins of single-stranded DNA plasmid pUB110. J. Bacteriol., 171, 3366-3372.
4. Boe, L., Nielsen, T.T., Madsen, S.M., Andrup, L. and Bolander, G. (1991) Cloning and characterization of two plasmids from Bacillus thuringiensis in Bacillus subtilis. Plasmid, 25, 190-197.
5. Bron, S., Bosma, P., van Belkum, M.J. and Luxen, E. (1987) Stability function in the Bacillus subtilis plasmid pTA1060. Plasmid, 18, 8-15.
6. Buckle, M., Fritsch, A., Roux, P., Geiselmann, J. and Buc, H. (1991) Kinetic studies on promoter-RNA polymerase complexes. Methods Enzymol., 208, 236-258.
7. Ceska, T.A., Sayers, J.R., Stier, G. and Suck, D. (1996) A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease. Nature, 382, 90-93.
8. del Solar, G., Puyet, A. and Espinosa, M. (1987a) Initiation signals for the conversion of single stranded to double stranded DNA forms in the streptococcal plasmid pLS1. Nucleic Acids Res., 15, 5561-5580.
9. del Solar, G., Díaz, R. and Espinosa, M. (1987b) Replication of the streptococcal plasmid pMV158 and derivatives in cell-free extracts of Escherichia coli. Mol. Gen. Genet., 206, 428-435.
10. del Solar, G., Moscoso, M. and Espinosa, M. (1993a) Rolling circle-replicating plasmids from Gram-positive and Gram-negative bacteria: a wall falls. Mol. Microbiol., 8, 789-796.
11. del Solar, G., Kramer, M.G., Ballester, S. and Espinosa, M. (1993b) Replication of the promiscuous plasmid pLS1: a region encompassing the minus origin of replication is associated with stable plasmid inheritance. Mol. Gen. Genet., 241, 97-105.
12. del Solar, G., Alonso, J.C., Espinosa, M. and Díaz-Orejas, R. (1996) Broad-host-range plasmid replication: an open question. Mol. Microbiol., 21, 661-666.
13. Dempsey, L.A., Zhao, A.C. and Khan, S.A. (1995) Localization of the start sites of lagging-strand replication of rolling circle plasmids from Gram-positive bacteria. Mol. Microbiol., 15, 679-687.
14. Díaz, A., Lacks, S.A. and López, P. (1992) The 5′ to 3′ exonuclease activity of DNA polymerase I is essential for Streptococcus pneumoniae. Mol. Microbiol., 6, 3009-3019.
15. Díaz, A., Lacks, S.A. and López, P. (1994) Multiple roles for DNA polymerase I in establishment and replication of the promiscuous plasmid pLS1. Mol. Microbiol., 14, 773-783.
16. Geider, K. and Kornberg, A. (1974) Conversion of the M13 viral single strand to the double-stranded replicative forms by purified proteins. J. Biol. Chem., 249, 3999-4005.
17. Glucksmann-Kuis, M.A., Dai, X., Markiewicz, P. and Rothman-Denes, L.B. (1996) E.coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition. Cell, 84, 147-154.
18. Gruss, A.D. and Ehrlich, S.D. (1989) The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol. Rev., 53, 231-241.
19. Gruss, A.D., Ross, H.F. and Novick, R.P. (1987) Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc. Natl Acad. Sci. USA, 84, 2165-2169.
20. Guzmán, L. and Espinosa, M. (1997) The mobilization protein, MobM, of the streptococcal plasmid pMV158 specifically cleaves supercoiled DNA at the plasmid oriT. J. Mol. Biol., 266, 688-702.
21. Higashitani, N., Higashitani, A. and Horiuchi, K. (1993) Nucleotide sequence of the primer RNA for DNA replication of filamentous bacteriophages. J. Virol., 67, 2175-2181.
22. Itoh, T. and Tomizawa, J. (1978) Initiation of replication of plasmid ColE1 DNA by RNA polymerase, ribonuclease H, and DNA polymerase I. Cold Spring Harbor Symp. Quant. Biol., 48, 409-417.
23. Khan, S.A. (1996) Mechanism of replication and copy number control of plasmids in Gram-positive bacteria. In Setlow, J.K. (ed.), Genetic Engineering. Plenum Press, New York, Vol. 18, pp. 183-201.
24. Kornberg, A. and Baker, T.A. (1992) DNA Replication. W.H. Freeman & Co., New York.
25. Kramer, M.G., del Solar, G. and Espinosa, M. (1995) Lagging-strand origins of the promiscuous plasmid pMV158: physical and functional characterization. Microbiology, 141, 655-662.
26. Lacks, S.A., López, P., Greenberg, B. and Espinosa, M. (1986) Identification and analysis of genes for tetracycline resistance and replication functions in the broad-host-range plasmid pLS1. J. Mol. Biol., 192, 753-765.
27. Leenhouts, K., Tolner, J.B., Bron, S., Kok, J., Venema, G. and Seegers, J.F.M.L. (1991) Nucleotide sequence and characterization of the broad-host-range lactococcal plasmid pWV01. Plasmid, 26, 55-66.
28. López, P., Martínez, S., Díaz, A., Espinosa, M. and Lacks, S.A. (1989) Characterization of the polA gene of Streptococcus pneumoniae and comparison of the DNA Poll it encodes to homologous enzymes from Escherichia coli and phage T7. J. Biol. Chem., 264, 4255-4263.
29. Meijer, W.J.J., van der Lelie, D., Venema, G. and Bron, S. (1995a) Effects of the generation of single-stranded DNA on the maintenance of plasmid pMV158 and derivatives in Lacotococcus lactis. Plasmid, 33, 91-99.
30. Meijer, W.J.J., van der Lelie, D., Venema, G. and Bron, S. (1995b) Effects of the generation of single-stranded DNA on the maintenance of plasmid pMV158 and derivatives in different Bacillus subtilis strains. Plasmid, 33, 79-89.
31. Mencía, M., Monsalve, M., Rojo, F. and Salas, M. (1996) Transcription activation by phage φ29 protein p4 is mediated by interaction with the α subunit of Bacillus subtilis RNA polymerase. Proc. Natl Acad. Sci. USA, 93, 6616-6620.
32. Murray, R.W., Koepsel, R.R. and Khan, S.A. (1989) Synthesis of single-stranded plasmid pT181 DNA in vitro: initiation and termination of DNA replication. J. Biol. Chem., 264, 1051-1057.
33. Novick, R.P. (1989) Staphylococcal plasmids and their replication. Annu. Rev. Microbiol., 43, 537-565.
34. Novick, R.P., Projan, S.J., Rosenblum, W. and Edelman, I. (1984) Staphylococcal plasmid cointegrates are formed by host-and phage-mediated general rec systems that act on short regions of homology. Mol. Gen. Genet., 195, 374-377.
35. Pons, M.E., Díaz, A., Lacks, S.A. and López, P. (1991) The polymerase domain of Streptococcus pneumoniae DNA polymerase I. High expression, purification and characterization. Eur. J. Biochem., 201, 147-155.
36. Priebe, S.D. and Lacks, S.A. (1989) Region of the streptococcal plasmid pMV158 required for conjugative mobilization. J. Bacteriol., 171, 4778-4784.
37. Ross, W., Khoosheh, K.G., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K. and Gourse, R.L. (1993) A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science, 262, 1407-1413.
38. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
39. Seegers, J.F.M.L., Zhao, A.C., Meijer, W.J.J., Khan, S.A., Venema, G. and Bron, S. (1995) Structural and functional analysis of the single-strand origin of replication from the lactococcal plasmid pWV01. Mol. Gen. Genet., 249, 43-50.
40. Sun, W. and Godson, G.N. (1993) Binding and phasing of Escherichia coli single-stranded DNA-binding protein by the secondary structure of phage G4 origin of complementary DNA strand synthesis (G4oric). J. Biol. Chem., 268, 8026-8039.
41. te Riele, H., Michel, B. and Ehrlich, S.D. (1986) Are single-stranded circles intermediates in plasmid DNA replication? EMBO J., 5, 631-637.
42. van der Lelie, D., Bron, S., Venema, G. and Oskam, L. (1989) Similarity of minus origins of replication and flanking open reading frames of plasmids pUB100, pTB913 and pMV158. Nucleic Acids Res., 17, 7283-7294.
43. Wahle, E. and Kornberg, A. (1988) The partition locus of plasmid pSC101 is a specific binding site for DNA gyrase. EMBO J., 7, 1889-1895.
44. Wilson, K.S. and von Hippel, P.H. (1995) Transcription termination at intrinsic terminators: the role of the RNA hairpin. Proc. Natl Acad. Sci. USA, 92, 8793-8797.
45. Zaman, S., Radnedge, L., Richards, H. and Ward, J.M. (1993) Analysis of the site for second-strand initiation during replication of the Streptomyces plasmid pIJ101. J. Gen. Microbiol., 139, 669-676.
46. Zhang, Y., Praszkier, J., Hodgson, A. and Pittard, A.J. (1994) Molecular analysis and characterization of a broad-host-range plasmid pEP2. J. Bacteriol., 176, 5718-5728.
47. Zinder, N. and Horiuchi, K. (1985) Multiregulatory element of filamentous bacteriophages. Microbiol. Rev., 49, 101-106.