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. 1982 Oct 11;10(19):5949–5965. doi: 10.1093/nar/10.19.5949

Purification of ribonuclease H as a factor required for initiation of in vitro Co1E1 DNA replication.

T Itoh, J Tomizawa
PMCID: PMC320942  PMID: 6292861

Abstract

Escherichia coli ribonuclease H was purified to near-homogeneity and identified as the only additional factor required for initiation of in vitro Co1E1 DNA replication from the unique origin by RNA polymerase and DNA polymerase I. Both ribonuclease H activity and stimulating activity for Co1E1 DNA synthesis comigrate with the single protein band in gel electrophoresis. These two activities coincide throughout the process of purification. Some DNA synthesis takes place on covalently closed-circular DNA molecules other than Co1E1 DNA with the three purified enzymes. This DNA synthesis is suppressed by an Escherichia coli single-strand DNA binding protein and/or a high concentration of ribonuclease H. Negative superhelicity of template DNA is required for efficient primer formation. No evidence that supports involvement of ribonuclease III in initiation of Co1E1 DNA replication or its regulation was found.

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Selected References

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  1. Apirion D., Watson N. Mapping and characterization of a mutation in Escherichia coli that reduces the level of ribonuclease III specific for double-stranded ribonucleic acid. J Bacteriol. 1975 Oct;124(1):317–324. doi: 10.1128/jb.124.1.317-324.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arendes J., Carl P. L., Sugino A. A mutation in the rnh-locus of Escherichia coli affects the structural gene for RNase H. Examination of the mutant and wild type protein. J Biol Chem. 1982 May 10;257(9):4719–4722. [PubMed] [Google Scholar]
  3. Arndt-Jovin D. J., Jovin T. M., Bähr W., Frischauf A. M., Marquardt M. Covalent attachment of DNA to agarose. Improved synthesis and use in affinity chromatography. Eur J Biochem. 1975 Jun;54(2):411–418. doi: 10.1111/j.1432-1033.1975.tb04151.x. [DOI] [PubMed] [Google Scholar]
  4. Berkower I., Leis J., Hurwitz J. Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures. J Biol Chem. 1973 Sep 10;248(17):5914–5921. [PubMed] [Google Scholar]
  5. Blair D. G., Sherratt D. J., Clewell D. B., Helinski D. R. Isolation of supercoiled colicinogenic factor E 1 DNA sensitive to ribonuclease and alkali. Proc Natl Acad Sci U S A. 1972 Sep;69(9):2518–2522. doi: 10.1073/pnas.69.9.2518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bolivar F., Betlach M. C., Heyneker H. L., Shine J., Rodriguez R. L., Boyer H. W. Origin of replication of pBR345 plasmid DNA. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5265–5269. doi: 10.1073/pnas.74.12.5265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carl P. L., Bloom L., Crouch R. J. Isolation and mapping of a mutation in Escherichia coli with altered levels of ribonuclease H. J Bacteriol. 1980 Oct;144(1):28–35. doi: 10.1128/jb.144.1.28-35.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Conrad S. E., Campbell J. L. Role of plasmid-coded RNA and ribonuclease III in plasmid DNA replication. Cell. 1979 Sep;18(1):61–71. doi: 10.1016/0092-8674(79)90354-4. [DOI] [PubMed] [Google Scholar]
  9. Darlix J. L. Stimultaneous purification of Escherichia coli termination factor rho, RNAase III and RNAase H. Eur J Biochem. 1975 Feb 21;51(2):369–376. doi: 10.1111/j.1432-1033.1975.tb03937.x. [DOI] [PubMed] [Google Scholar]
  10. Dunn J. J. RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage. J Biol Chem. 1976 Jun 25;251(12):3807–3814. [PubMed] [Google Scholar]
  11. Dunn J. J., Studier F. W. Effect of RNAase III, cleavage on translation of bacteriophage T7 messenger RNAs. J Mol Biol. 1975 Dec 15;99(3):487–499. doi: 10.1016/s0022-2836(75)80140-9. [DOI] [PubMed] [Google Scholar]
  12. Ely S., Staudenbauer W. L. Regulation of plasmid DNA synthesis: isolation and characterization of copy number mutants of miniR6-5 and miniF plasmids. Mol Gen Genet. 1981;181(1):29–35. doi: 10.1007/BF00339001. [DOI] [PubMed] [Google Scholar]
  13. Gellert M., O'Dea M. H., Itoh T., Tomizawa J. Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. Proc Natl Acad Sci U S A. 1976 Dec;73(12):4474–4478. doi: 10.1073/pnas.73.12.4474. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Germond J. E., Hirt B., Oudet P., Gross-Bellark M., Chambon P. Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975 May;72(5):1843–1847. doi: 10.1073/pnas.72.5.1843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hillenbrand G., Staudenbauer W. L. Discriminatory function of ribonuclease H in the selective initiation of plasmid DNA replication. Nucleic Acids Res. 1982 Feb 11;10(3):833–853. doi: 10.1093/nar/10.3.833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Itoh T., Tomizawa J. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc Natl Acad Sci U S A. 1980 May;77(5):2450–2454. doi: 10.1073/pnas.77.5.2450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Itoh T., Tomizawa J. Initiation of replication of plasmid ColE1 DNA by RNA polymerase, ribonuclease H, and DNA polymerase I. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):409–417. doi: 10.1101/sqb.1979.043.01.047. [DOI] [PubMed] [Google Scholar]
  18. Kahn M. L., Figurski D., Ito L., Helinski D. R. Essential regions for replication of a stringent and a relaxed plasmid in Escherichia coli. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):99–103. doi: 10.1101/sqb.1979.043.01.015. [DOI] [PubMed] [Google Scholar]
  19. Kindler P., Keil T. U., Hofschneider P. H. Isolation and characterization of a ribonuclease 3 deficient mutant of Escherichia coli. Mol Gen Genet. 1973 Oct 16;126(1):53–59. doi: 10.1007/BF00333481. [DOI] [PubMed] [Google Scholar]
  20. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  21. McKnight G. S. A colorimetric method for the determination of submicrogram quantities of protein. Anal Biochem. 1977 Mar;78(1):86–92. doi: 10.1016/0003-2697(77)90011-2. [DOI] [PubMed] [Google Scholar]
  22. Miller H. I., Riggs A. D., Gill G. N. Ribonuclease H (hybrid) in Escherichia coli. Identification and characterization. J Biol Chem. 1973 Apr 10;248(7):2621–2624. [PubMed] [Google Scholar]
  23. Molineux I. J., Friedman S., Gefter M. L. Purification and properties of the Escherichia coli deoxyribonucleic acid-unwinding protein. Effects on deoxyribonucleic acid synthesis in vitro. J Biol Chem. 1974 Oct 10;249(19):6090–6098. [PubMed] [Google Scholar]
  24. Ohmori H., Tomizawa J. Nucleotide sequence of the region required for maintenance of colicin E1 plasmid. Mol Gen Genet. 1979 Oct 3;176(2):161–170. doi: 10.1007/BF00273210. [DOI] [PubMed] [Google Scholar]
  25. Sakakibara Y., Tomizawa J. I. Replication of colicin E1 plasmid DNA in cell extracts. Proc Natl Acad Sci U S A. 1974 Mar;71(3):802–806. doi: 10.1073/pnas.71.3.802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sugino Y., Tomizawa J., Kakefuda T. Location of non-DNA components of closed circular colicin E1 plasmid DNA. Nature. 1975 Feb 20;253(5493):652–654. doi: 10.1038/253652a0. [DOI] [PubMed] [Google Scholar]
  27. Sumida-Yasumoto C., Ikeda J. E., Benz E., Marians K. J., Vicuna R., Sugrue S., Zipursky S. L., Hurwitz J. Replication of phiX174 DNA: in vitro synthesis of phiX RFI DNA and circular, single-stranded DNA. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):311–329. doi: 10.1101/sqb.1979.043.01.038. [DOI] [PubMed] [Google Scholar]
  28. Tomizawa J. I., Ohmori H., Bird R. E. Origin of replication of colicin E1 plasmid DNA. Proc Natl Acad Sci U S A. 1977 May;74(5):1865–1869. doi: 10.1073/pnas.74.5.1865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tomizawa J. I., Sakakibara Y., Kakefuda T. Replication of colicin E1 plasmid DNA added to cell extracts. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1050–1054. doi: 10.1073/pnas.72.3.1050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tomizawa J., Itoh T. Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6096–6100. doi: 10.1073/pnas.78.10.6096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tomizawa J., Itoh T., Selzer G., Som T. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1421–1425. doi: 10.1073/pnas.78.3.1421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Vicuna R., Hurwitz J., Wallace S., Girard M. Selective inhibition of in vitro DNA synthesis dependent on phiX174 compared with fd DNA. I. Protein requirements for selective inhibition. J Biol Chem. 1977 Apr 25;252(8):2524–2533. [PubMed] [Google Scholar]

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