Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Oct 25;21(21):4900–4903. doi: 10.1093/nar/21.21.4900

A base-paired hairpin structure essential for the functional priming signal for DNA replication of the broad host range plasmid RSF1010.

D M Miao 1, Y Honda 1, K Tanaka 1, A Higashi 1, T Nakamura 1, Y Taguchi 1, H Sakai 1, T Komano 1, M Bagdasarian 1
PMCID: PMC311403  PMID: 8177737

Abstract

The two single-strand DNA initiation signals, ssiA(RSF1010) and ssiB(RSF1010) of the broad host-range plasmid RSF1010 contain proposed stem-loop structures. Nine single base-change mutations in the stem of the ssiA structure, each of which destroyed a relevant base pairing, damaged the ssiA activity. A second single-base change was introduced into each of the nine ssiA mutants in such a way that the base pairing was restored. Only three out of nine second base changes that restored the base pairing restored the ssiA activity up to the wild-type level. Thus, the three are intramolecular suppressors. The results strongly suggested that, in the area of the stem of ssiA where the suppressor mutations fell, base pairing was the most important structural parameter for the ssiA activity. By contrast, it is most probable that, in the other part of the stem of ssiA, both base-pairing and the intrinsic base sequence were the major determinants of the ssiA activity.

Full text

PDF
4900

Selected References

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

  1. Abarzúa P., Soeller W., Marians K. J. Mutational analysis of primosome assembly sites. I. Distinct classes of mutants in the pBR322 Escherichia coli factor Y DNA effector sequences. J Biol Chem. 1984 Nov 25;259(22):14286–14292. [PubMed] [Google Scholar]
  2. Bahk J. D., Kioka N., Sakai H., Komano T. A runaway-replication plasmid pSY343 contains two ssi signals. Plasmid. 1988 Nov;20(3):266–270. doi: 10.1016/0147-619x(88)90033-9. [DOI] [PubMed] [Google Scholar]
  3. Davey S. K., Faust E. A. Murine DNA polymerase.alpha-primase initiates RNA-primed DNA synthesis preferentially upstream of a 3'-CC(C/A)-5' motif. J Biol Chem. 1990 Mar 5;265(7):3611–3614. [PubMed] [Google Scholar]
  4. Gormley E. P., Davies J. Transfer of plasmid RSF1010 by conjugation from Escherichia coli to Streptomyces lividans and Mycobacterium smegmatis. J Bacteriol. 1991 Nov;173(21):6705–6708. doi: 10.1128/jb.173.21.6705-6708.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Grinter N. J., Barth P. T. Characterization of SmSu plasmids by restriction endonuclease cleavage and compatibility testing. J Bacteriol. 1976 Oct;128(1):394–400. doi: 10.1128/jb.128.1.394-400.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hiasa H., Tanaka K., Sakai H., Yoshida K., Honda Y., Komano T., Godson G. N. Distinct functional contributions of three potential secondary structures in the phage G4 origin of complementary DNA strand synthesis. Gene. 1989 Dec 7;84(1):17–22. doi: 10.1016/0378-1119(89)90134-0. [DOI] [PubMed] [Google Scholar]
  7. Honda Y., Akioka T., Takebe S., Tanaka K., Miao D., Higashi A., Nakamura T., Taguchi Y., Sakai H., Komano T. Mutational analysis of the specific priming signal essential for DNA replication of the broad host-range plasmid RSF1010. FEBS Lett. 1993 Jun 7;324(1):67–70. doi: 10.1016/0014-5793(93)81534-7. [DOI] [PubMed] [Google Scholar]
  8. Honda Y., Nakamura T., Tanaka K., Higashi A., Sakai H., Komano T., Bagdasarian M. DnaG-dependent priming signals can substitute for the two essential DNA initiation signals in oriV of the broad host-range plasmid RSF1010. Nucleic Acids Res. 1992 Apr 11;20(7):1733–1737. doi: 10.1093/nar/20.7.1733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Honda Y., Sakai H., Hiasa H., Tanaka K., Komano T., Bagdasarian M. Functional division and reconstruction of a plasmid replication origin: molecular dissection of the oriV of the broad-host-range plasmid RSF1010. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):179–183. doi: 10.1073/pnas.88.1.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Honda Y., Sakai H., Komano T., Bagdasarian M. RepB' is required in trans for the two single-strand DNA initiation signals in oriV of plasmid RSF1010. Gene. 1989 Aug 1;80(1):155–159. doi: 10.1016/0378-1119(89)90261-8. [DOI] [PubMed] [Google Scholar]
  11. Honda Y., Sakai H., Komano T. Two single-strand DNA initiation signals located in the oriV region of plasmid RSF1010. Gene. 1988 Sep 7;68(2):221–228. doi: 10.1016/0378-1119(88)90024-8. [DOI] [PubMed] [Google Scholar]
  12. Lin L. S., Meyer R. J. DNA synthesis is initiated at two positions within the origin of replication of plasmid R1162. Nucleic Acids Res. 1987 Oct 26;15(20):8319–8331. doi: 10.1093/nar/15.20.8319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Masai H., Nomura N., Arai K. The ABC-primosome. A novel priming system employing dnaA, dnaB, dnaC, and primase on a hairpin containing a dnaA box sequence. J Biol Chem. 1990 Sep 5;265(25):15134–15144. [PubMed] [Google Scholar]
  14. Masai H., Nomura N., Kubota Y., Arai K. Roles of phi X174 type primosome- and G4 type primase-dependent primings in initiation of lagging and leading strand syntheses of DNA replication. J Biol Chem. 1990 Sep 5;265(25):15124–15133. [PubMed] [Google Scholar]
  15. Nomura N., Low R. L., Ray D. S. Identification of ColE1 DNA sequences that direct single strand-to-double strand conversion by a phi X174 type mechanism. Proc Natl Acad Sci U S A. 1982 May;79(10):3153–3157. doi: 10.1073/pnas.79.10.3153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nomura N., Low R. L., Ray D. S. Identification of ColE1 DNA sequences that direct single strand-to-double strand conversion by a phi X174 type mechanism. Proc Natl Acad Sci U S A. 1982 May;79(10):3153–3157. doi: 10.1073/pnas.79.10.3153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Nomura N., Masai H., Inuzuka M., Miyazaki C., Ohtsubo E., Itoh T., Sasamoto S., Matsui M., Ishizaki R., Arai K. Identification of eleven single-strand initiation sequences (ssi) for priming of DNA replication in the F, R6K, R100 and ColE2 plasmids. Gene. 1991 Dec 1;108(1):15–22. doi: 10.1016/0378-1119(91)90482-q. [DOI] [PubMed] [Google Scholar]
  18. Ray D. S., Hines J. C., Kim M. H., Imber R., Nomura N. M13 vectors for selective cloning of sequences specifying initiation of DNA synthesis on single-stranded templates. Gene. 1982 Jun;18(3):231–238. doi: 10.1016/0378-1119(82)90160-3. [DOI] [PubMed] [Google Scholar]
  19. Roth Y. F. Eucaryotic primase. Eur J Biochem. 1987 Jun 15;165(3):473–481. doi: 10.1111/j.1432-1033.1987.tb11463.x. [DOI] [PubMed] [Google Scholar]
  20. Sakai H., Godson G. N. Isolation and construction of mutants of the G4 minus strand origin: analysis of their in vivo activity. Biochim Biophys Acta. 1985 Oct 3;826(1):30–37. doi: 10.1016/s0167-4781(85)80005-1. [DOI] [PubMed] [Google Scholar]
  21. Sakai H., Komano T., Godson G. N. Replication origin (oric) on the complementary DNA strand of Escherichia coli phage G4: biological properties of mutants. Gene. 1987;53(2-3):265–273. doi: 10.1016/0378-1119(87)90015-1. [DOI] [PubMed] [Google Scholar]
  22. Scherzinger E., Bagdasarian M. M., Scholz P., Lurz R., Rückert B., Bagdasarian M. Replication of the broad host range plasmid RSF1010: requirement for three plasmid-encoded proteins. Proc Natl Acad Sci U S A. 1984 Feb;81(3):654–658. doi: 10.1073/pnas.81.3.654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Scherzinger E., Haring V., Lurz R., Otto S. Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins. Nucleic Acids Res. 1991 Mar 25;19(6):1203–1211. doi: 10.1093/nar/19.6.1203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Scholz P., Haring V., Wittmann-Liebold B., Ashman K., Bagdasarian M., Scherzinger E. Complete nucleotide sequence and gene organization of the broad-host-range plasmid RSF1010. Gene. 1989 Feb 20;75(2):271–288. doi: 10.1016/0378-1119(89)90273-4. [DOI] [PubMed] [Google Scholar]
  25. Seery L., Devine K. M. Analysis of features contributing to activity of the single-stranded origin of Bacillus plasmid pBAA1. J Bacteriol. 1993 Apr;175(7):1988–1994. doi: 10.1128/jb.175.7.1988-1994.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sheaff R. J., Kuchta R. D. Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination. Biochemistry. 1993 Mar 30;32(12):3027–3037. doi: 10.1021/bi00063a014. [DOI] [PubMed] [Google Scholar]
  27. Tanaka K., Sakai T., Honda Y., Hiasa H., Sakai H., Komano T. Plasmid Co1IB contains an ssi signal close to the replication origin. Plasmid. 1991 Mar;25(2):125–130. doi: 10.1016/0147-619x(91)90024-q. [DOI] [PubMed] [Google Scholar]
  28. Travaglini E. C., Mildvan A. S., Loeb L. A. Kinetic analysis of Escherichia coli deoxyribonucleic acid polymerase I. J Biol Chem. 1975 Nov 25;250(22):8647–8656. [PubMed] [Google Scholar]
  29. Ueda K., Kobayashi S., Sakai H., Komano T. Cleavage of stem-and-loop structure DNA by bleomycin. Reaction on the bacteriophage G4 origin of complementary strand synthesis. J Biol Chem. 1985 May 10;260(9):5804–5807. [PubMed] [Google Scholar]
  30. Zhou H. S., Meyer R. J. Deletion of sites for initiation of DNA synthesis in the origin of broad host-range plasmid R1162. J Mol Biol. 1990 Aug 5;214(3):685–697. doi: 10.1016/0022-2836(90)90286-u. [DOI] [PubMed] [Google Scholar]

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

RESOURCES