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PMID: 8206839 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Comparative analysis of functional and structural features in the primase-dependent priming signals, G sites, from phages and plasmids.

Journal of bacteriology ·Vol. 176 ·No. 12 ·1994-06-00 ·Pages 3606-13

Tanaka K, Rogi T, Hiasa H, Miao DM, Honda Y, Nomura N, Sakai H, Komano T

Abstract

The primase-dependent priming signals, G sites, are directly recognized by the Escherichia coli primase (dnaG gene product) and conduct the synthesis of primer RNAs. In nucleotide sequence and secondary structure, there is no striking resemblance between the phage- and plasmid-derived G sites, except for the limited sequence homology near the start position of primer RNA synthesis. In this study, we analyzed the structure and function of a G site of plasmid R100, G site (R100), and discovered the necessity of the coexistence of two domains (domains I and III), which contains blocks A, B, and C, which are nucleotide sequences highly conserved among the plasmid-derived G sites. However, neither the internal region, domain II, between domains I and III nor the potential secondary structure proposed by Bahk et al. (J. D. Bahk, N. Kioka, H. Sakai, and T. Komano, Plasmid 20:266-270, 1988) is essential for single-stranded DNA initiation activity. Furthermore, chimeric G sites constructed between a G site of phage G4, G site(G4), and G site(R100) maintained significant single-stranded DNA initiation activities. These results strongly suggest that phage- and plasmid-derived G sites have functionally equivalent domains. The primase-dependent priming mechanisms of phage- and plasmid-derived G sites are discussed.

Related Genes
dnaG
MeSH Terms
Base Sequence Coliphages/genetics DNA Mutational Analysis DNA Primase DNA Replication DNA, Recombinant Escherichia coli/genetics Models, Genetic Molecular Sequence Data Nucleic Acid Conformation Protein Binding R Factors/genetics RNA Nucleotidyltransferases/metabolism Regulatory Sequences, Nucleic Acid/genetics Sequence Homology, Nucleic Acid Structure-Activity Relationship
Chemicals
DNA, Recombinant DNA Primase RNA Nucleotidyltransferases
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Tanaka K
Department of Agricultural Chemistry, Kyoto University, Japan.
Rogi T
Hiasa H
Miao D M
Honda Y
Nomura N
Sakai H
Komano T
References (39)
39 references, click to expand
  1. The RNA primer synthesized by primase to initiate phage G4 DNA replication.
    J Biol Chem. 1978 Feb 10;253(3):765-9 PMID: 340458
  2. Primase from Escherichia coli primes single-stranded templates in the absence of single-stranded DNA-binding protein or other auxiliary proteins. Template sequence requirements based on the bacteriophage G4 complementary strand origin and Okazaki fragment initiation sites.
    J Biol Chem. 1993 Jun 15;268(17):12970-6 PMID: 8509429
  3. Movement and site selection for priming by the primosome in phage phi X174 DNA replication.
    Proc Natl Acad Sci U S A. 1981 Feb;78(2):707-11 PMID: 6262762
  4. Escherichia coli factor Y sites of plasmid pBR322 can function as origins of DNA replication.
    Proc Natl Acad Sci U S A. 1981 Oct;78(10):6111-5 PMID: 6273849
  5. 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):3153-7 PMID: 6212928
  6. M13 vectors for selective cloning of sequences specifying initiation of DNA synthesis on single-stranded templates.
    Gene. 1982 Jun;18(3):231-8 PMID: 6290326
  7. Identification of a primosome assembly site in the region of the ori 2 replication origin of the Escherichia coli mini-F plasmid.
    Proc Natl Acad Sci U S A. 1983 Dec;80(23):7132-6 PMID: 6316346
  8. Mutational analysis of primosome assembly sites. II. Role of secondary structure in the formation of active sites.
    J Biol Chem. 1984 Nov 25;259(22):14293-300 PMID: 6150042
  9. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors.
    Gene. 1985;33(1):103-19 PMID: 2985470
  10. Replication of pBR322 DNA in vitro with purified proteins. Requirement for topoisomerase I in the maintenance of template specificity.
    J Biol Chem. 1985 Aug 5;260(16):9316-25 PMID: 2991240
  11. 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):30-7 PMID: 2994737
  12. Mutational analysis of primosome assembly sites. Evidence for alternative DNA structures.
    J Biol Chem. 1985 Oct 5;260(22):12266-72 PMID: 2931433
  13. The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA.
    Nucleic Acids Res. 1985 Dec 20;13(24):8749-64 PMID: 3001649
  14. The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA.
    Nucleic Acids Res. 1985 Dec 20;13(24):8765-85 PMID: 3001650
  15. DNA requirements at the bacteriophage G4 origin of complementary-strand DNA synthesis.
    J Virol. 1986 May;58(2):450-8 PMID: 3754589
  16. Replication origin (oric) on the complementary DNA strand of Escherichia coli phage G4: biological properties of mutants.
    Gene. 1987;53(2-3):265-73 PMID: 3609749
  17. Plasmid pACYC184 contains an ssi signal for initiation of single-strand phage DNA replication.
    Gene. 1988 May 15;65(1):93-9 PMID: 2840359
  18. Initiation of lagging-strand synthesis for pBR322 plasmid DNA replication in vitro is dependent on primosomal protein i encoded by dnaT.
    J Biol Chem. 1988 Oct 15;263(29):15016-23 PMID: 2844795
  19. Two single-strand DNA initiation signals located in the oriV region of plasmid RSF1010.
    Gene. 1988 Sep 7;68(2):221-8 PMID: 3065143
  20. Role of the potential secondary structures in phage G4 origin of complementary DNA strand synthesis.
    Gene. 1988 Nov 30;71(2):323-30 PMID: 3224827
  21. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution.
    Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172-5 PMID: 2648393
  22. A runaway-replication plasmid pSY343 contains two ssi signals.
    Plasmid. 1988 Nov;20(3):266-70 PMID: 3072580
  23. Leading strand synthesis of R1 plasmid replication in vitro is primed by primase alone at a specific site downstream of oriR.
    J Biol Chem. 1989 May 15;264(14):8082-90 PMID: 2542261
  24. The Escherichia coli primosome can translocate actively in either direction along a DNA strand.
    J Biol Chem. 1989 Aug 25;264(24):14531-42 PMID: 2547799
  25. 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 PMID: 2691335
  26. Mutational analysis of the primer RNA template region in the replication origin (oric) of bacteriophage G4: priming signal recognition by Escherichia coli primase.
    Gene. 1989 Dec 7;84(1):9-16 PMID: 2558060
  27. 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):15124-33 PMID: 2144283
  28. 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):15134-44 PMID: 2168401
  29. High efficiency transformation of Escherichia coli with plasmids.
    Gene. 1990 Nov 30;96(1):23-8 PMID: 2265755
  30. Plasmid Co1IB contains an ssi signal close to the replication origin.
    Plasmid. 1991 Mar;25(2):125-30 PMID: 1857752
  31. 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 PMID: 1761225
  32. Structural and functional features of cis-acting sequences in the basic replicon of plasmid ColIb-P9.
    Nucleic Acids Res. 1992 Jun 11;20(11):2705-10 PMID: 1614857
  33. Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition.
    Cell. 1992 Aug 7;70(3):491-500 PMID: 1643660
  34. Mapping of the in vivo start site for leading strand DNA synthesis in plasmid R1.
    EMBO J. 1992 Dec;11(12):4481-7 PMID: 1425582
  35. Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination.
    Biochemistry. 1993 Mar 30;32(12):3027-37 PMID: 7681326
  36. 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. 1993 Apr 15;268(11):8026-39 PMID: 8463320
  37. Roles of the G site and phi X174-type primosome assembly site in priming of leading-strand synthesis: initiation by a mobile primosome and replication-fork arrest by RepA protein bound to oriR.
    Gene. 1993 Apr 15;126(1):9-16 PMID: 8386129
  38. 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 PMID: 8504862
  39. An RNA transcribed from DNA at the origin of phage fd single strand to replicative form conversion.
    Proc Natl Acad Sci U S A. 1978 Feb;75(2):645-9 PMID: 204927
Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/jb.176.12.3606-3613.1994
Published
1994-06-00
Pages
3606-13
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC205550
Subset
IM
External Links
PubMed source DOI: 10.1128/jb.176.12.3606-3613.1994 PMC Full Text View journal details
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