Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1983 Apr;154(1):429–436. doi: 10.1128/jb.154.1.429-436.1983

Replication control mutations of plasmid R6-5 and their effects on interactions of the RNA-I control element with its target.

G Brady, J Frey, H Danbara, K N Timmis
PMCID: PMC217476  PMID: 6187730

Abstract

Nine high copy number mutations of plasmid R6-5, representing five phenotypically distinct groups, have been identified by DNA sequencing. In each mutant plasmid examined, a single nucleotide change was found. The effects of the mutations on possible gene products, and DNA-RNA secondary structure, were analyzed and compared with the observed phenotypes. The results of this study exclude the possibility that the primary plasmid replication control element, the product of the copA gene, is a polypeptide, and they are consistent with a model of plasmid replication control by the copA product which has the following features: (i) RNA-I, a short untranslated RNA molecule, is the product of the copA gene and regulates the frequency of initiation of plasmid replication, (ii) the hexanucleotide single-strand loop of the major hairpin of RNA-I is its active site, (iii) this active site functions by base pair interactions with its "target," its DNA template strand, or its complementary sequence on RNA-II, a transcript of opposite polarity that is the message of the repA gene, and (iv) the sequence and size of the loop, and the stability of the stem of the hairpin, are all critical factors that govern the functioning of RNA-I.

Full text

PDF
429

Selected References

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

  1. Andrés I., Slocombe P. M., Cabello F., Timmis J. K., Lurz R., Burkardt H. J., Timmis K. N. Plasmid replication functions. II. Cloning analysis of the repA replication region of antibiotic resistance plasmid R6-5. Mol Gen Genet. 1979 Jan 5;168(1):1–25. doi: 10.1007/BF00267929. [DOI] [PubMed] [Google Scholar]
  2. Danbara H., Brady G., Timmis J. K., Timmis K. N. Regulation of DNA replication: "target" determinant of the replication control elements of plasmid R6-5 lies within a control element gene. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4699–4703. doi: 10.1073/pnas.78.8.4699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Danbara H., Timmis J. K., Lurz R., Timmis K. N. Plasmid replication functions: two distinct segments of plasmid R1, RepA and RepD, express incompatibility and are capable of autonomous replication. J Bacteriol. 1980 Dec;144(3):1126–1138. doi: 10.1128/jb.144.3.1126-1138.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hashimoto-Gotoh T., Timmis K. N. Incompatibility properties of Col E1 and pMB1 derivative plasmids: random replication of multicopy replicons. Cell. 1981 Jan;23(1):229–238. doi: 10.1016/0092-8674(81)90287-7. [DOI] [PubMed] [Google Scholar]
  5. Hsiang M. W., Cole R. D., Takeda Y., Echols H. Amino acid sequence of Cro regulatory protein of bacteriophage lambda. Nature. 1977 Nov 17;270(5634):275–277. doi: 10.1038/270275a0. [DOI] [PubMed] [Google Scholar]
  6. Ishii K., Hashimoto-Gotoh T., Matsubara K. Random replication and random assortment model for plasmid incompatibility in bacteria. Plasmid. 1978 Sep;1(4):435–445. doi: 10.1016/0147-619x(78)90002-1. [DOI] [PubMed] [Google Scholar]
  7. Kollek R., Oertel W., Goebel W. Isolation and characterization of the minimal fragment required for autonomous replication ("basic replicon") of a copy mutant (pKN102) of the antibiotic resistance factor R1. Mol Gen Genet. 1978 Jun 1;162(1):51–57. doi: 10.1007/BF00333850. [DOI] [PubMed] [Google Scholar]
  8. Lacatena R. M., Cesareni G. Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication. Nature. 1981 Dec 17;294(5842):623–626. doi: 10.1038/294623a0. [DOI] [PubMed] [Google Scholar]
  9. Lurz R., Danbara H., Rückert B., Timmis K. N. Plasmid replication functions. VII. Electron microscopic localization of RNA polymerase binding sites in the replication control region of plasmid R6-5. Mol Gen Genet. 1981;183(3):490–496. doi: 10.1007/BF00268770. [DOI] [PubMed] [Google Scholar]
  10. Matsubara K. Genetic structure and regulation of a replicon of plasmid lambdadv. J Mol Biol. 1976 Apr 15;102(3):427–439. doi: 10.1016/0022-2836(76)90325-9. [DOI] [PubMed] [Google Scholar]
  11. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Miki T., Easton A. M., Rownd R. H. Cloning of replication, incompatibility, and stability functions of R plasmid NR1. J Bacteriol. 1980 Jan;141(1):87–99. doi: 10.1128/jb.141.1.87-99.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Molin S., Diaz R., Uhlin B. E., Nordström K. Runaway replication of plasmid R1 is not caused by loss of replication inhibitor activity of gene cop. J Bacteriol. 1980 Aug;143(2):1046–1048. doi: 10.1128/jb.143.2.1046-1048.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Molin S., Stougaard P., Light J., Nordström M., Nordström K. Isolation and characterization of new copy mutants of plasmid R1, and identification of a polypeptide involved in copy number control. Mol Gen Genet. 1981;181(1):123–130. doi: 10.1007/BF00339015. [DOI] [PubMed] [Google Scholar]
  15. Novick R. P., Hoppensteadt F. C. On plasmid incompatibility. Plasmid. 1978 Sep;1(4):421–434. doi: 10.1016/0147-619x(78)90001-x. [DOI] [PubMed] [Google Scholar]
  16. Ohtsubo E., Feingold J., Ohtsubo H., Mickel S., Bauer W. Unidirectional replication in Escherichia coli of three small plasmids derived from R factor R12. Plasmid. 1977 Nov;1(1):8–18. doi: 10.1016/0147-619x(77)90004-x. [DOI] [PubMed] [Google Scholar]
  17. Rosen J., Ryder T., Inokuchi H., Ohtsubo H., Ohtsubo E. Genes and sites involved in replication and incompatibility of an R100 plasmid derivative based on nucleotide sequence analysis. Mol Gen Genet. 1980;179(3):527–537. doi: 10.1007/BF00271742. [DOI] [PubMed] [Google Scholar]
  18. Rosen J., Ryder T., Ohtsubo H., Ohtsubo E. Role of RNA transcripts in replication incompatibility and copy number control in antibiotic resistance plasmid derivatives. Nature. 1981 Apr 30;290(5809):794–797. doi: 10.1038/290794a0. [DOI] [PubMed] [Google Scholar]
  19. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  20. Silver L., Chandler M., de la Tour E. B., Caro L. Origin and direction of replication of the drug resistance plasmid R100.1 and of a resistance transfer factor derivative in synchronized cultures. J Bacteriol. 1977 Sep;131(3):929–942. doi: 10.1128/jb.131.3.929-942.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Stougaard P., Light J., Molin S. Convergent transcription interferes with expression of the copy number control gene, copA, from plasmid R1. EMBO J. 1982;1(3):323–328. doi: 10.1002/j.1460-2075.1982.tb01168.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stougaard P., Molin S., Nordström K., Hansen F. G. The nucleotide sequence of the replication control region of the resistance plasmid R1drd-19. Mol Gen Genet. 1981;181(1):116–122. doi: 10.1007/BF00339014. [DOI] [PubMed] [Google Scholar]
  23. Stougaard P., Molin S., Nordström K. RNAs involved in copy-number control and incompatibility of plasmid R1. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6008–6012. doi: 10.1073/pnas.78.10.6008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Stuitje A. R., Spelt C. E., Veltkamp E., Nijkamp H. J. Identification of mutations affecting replication control of plasmid Clo DF13. Nature. 1981 Mar 19;290(5803):264–267. doi: 10.1038/290264a0. [DOI] [PubMed] [Google Scholar]
  25. Synenki R. M., Nordheim A., Timmis K. N. Plasmid replication functions. III. Origin and direction of replication of a "mini" plasmid derived from R6-5. Mol Gen Genet. 1979 Jan 5;168(1):27–36. doi: 10.1007/BF00267930. [DOI] [PubMed] [Google Scholar]
  26. Taylor D. P., Cohen S. N. Structural and functional analysis of cloned DNA segments containing the replication and incompatibility regions of a miniplasmid derived from a copy number mutant of NR1. J Bacteriol. 1979 Jan;137(1):92–104. doi: 10.1128/jb.137.1.92-104.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Timmis K. N., Cabello F., Cohen S. N. Cloning and characterization of EcoRI and HindIII restriction endonuclease-generated fragments of antibiotic resistance plasmids R6-5 and R6. Mol Gen Genet. 1978 Jun 14;162(2):121–137. doi: 10.1007/BF00267869. [DOI] [PubMed] [Google Scholar]
  28. Timmis K. N., Danbara H., Brady G., Lurz R. Inheritance functions of group IncFII transmissible antibiotic resistance plasmids. Plasmid. 1981 Jan;5(1):53–75. doi: 10.1016/0147-619x(81)90077-9. [DOI] [PubMed] [Google Scholar]
  29. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [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. Uhlin B. E., Nordström K. Plasmid incompatibility and control of replication: copy mutants of the R-factor R1 in Escherichia coli K-12. J Bacteriol. 1975 Nov;124(2):641–649. doi: 10.1128/jb.124.2.641-649.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wong E. M., Muesing M. A., Polisky B. Temperature-sensitive copy number mutants of CoIE1 are located in an untranslated region of the plasmid genome. Proc Natl Acad Sci U S A. 1982 Jun;79(11):3570–3574. doi: 10.1073/pnas.79.11.3570. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES