Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Feb 11;21(3):427–434. doi: 10.1093/nar/21.3.427

Determinants of Escherichia coli RNase P cleavage site selection: a detailed in vitro and in vivo analysis.

S G Svärd 1, L A Kirsebom 1
PMCID: PMC309135  PMID: 7680119

Abstract

The location of the Escherichia coli RNase P cleavage site was studied both in vitro and in vivo. We show that selection of the cleavage site is dependent on the nucleotide at the cleavage site and the length of the acceptor-stem. Within the acceptor-stem the number of nucleotides on the 5'-half of the acceptor-stem appears to be the important determinant, rather than the number of base pairs in the acceptor-stem. We also demonstrate that the length of the T-stem and a G to C substitution at position 57 in the tRNA(Tyr)Su3 precursor influence the location of the cleavage site under certain conditions. With respect to the function of the subunits of RNase P our data suggest that the nucleotide at position 333 in M1 RNA, and the C5 protein, are important for the identification of the cleavage site.

Full text

PDF
427

Images in this article

429Image
on p.429
429Image
on p.429
430Image
on p.430
432Image
on p.432

Selected References

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

  1. Baer M. F., Reilly R. M., McCorkle G. M., Hai T. Y., Altman S., RajBhandary U. L. The recognition by RNase P of precursor tRNAs. J Biol Chem. 1988 Feb 15;263(5):2344–2351. [PubMed] [Google Scholar]
  2. Brown J. W., Pace N. R. Ribonuclease P RNA and protein subunits from bacteria. Nucleic Acids Res. 1992 Apr 11;20(7):1451–1456. doi: 10.1093/nar/20.7.1451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burkard U., Willis I., Söll D. Processing of histidine transfer RNA precursors. Abnormal cleavage site for RNase P. J Biol Chem. 1988 Feb 15;263(5):2447–2451. [PubMed] [Google Scholar]
  4. Carrara G., Calandra P., Fruscoloni P., Doria M., Tocchini-Valentini G. P. Site selection by Xenopus laevis RNAase P. Cell. 1989 Jul 14;58(1):37–45. doi: 10.1016/0092-8674(89)90400-5. [DOI] [PubMed] [Google Scholar]
  5. Forster A. C., Altman S. External guide sequences for an RNA enzyme. Science. 1990 Aug 17;249(4970):783–786. doi: 10.1126/science.1697102. [DOI] [PubMed] [Google Scholar]
  6. Green C. J., Vold B. S. Structural requirements for processing of synthetic tRNAHis precursors by the catalytic RNA component of RNase P. J Biol Chem. 1988 Jan 15;263(2):652–657. [PubMed] [Google Scholar]
  7. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983 Dec;35(3 Pt 2):849–857. doi: 10.1016/0092-8674(83)90117-4. [DOI] [PubMed] [Google Scholar]
  8. Guerrier-Takada C., Lumelsky N., Altman S. Specific interactions in RNA enzyme-substrate complexes. Science. 1989 Dec 22;246(4937):1578–1584. doi: 10.1126/science.2480641. [DOI] [PubMed] [Google Scholar]
  9. Guerrier-Takada C., van Belkum A., Pleij C. W., Altman S. Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA. Cell. 1988 Apr 22;53(2):267–272. doi: 10.1016/0092-8674(88)90388-1. [DOI] [PubMed] [Google Scholar]
  10. Hegg L. A., Thurlow D. L. Residual tRNA secondary structure in 'denaturing' 8M urea/TBE polyacrylamide gels: effects on electrophoretic mobility and dependency on prior chemical modification of the tRNA. Nucleic Acids Res. 1990 May 25;18(10):2993–3000. doi: 10.1093/nar/18.10.2993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Holm P. S., Krupp G. The acceptor stem in pre-tRNAs determines the cleavage specificity of RNase P. Nucleic Acids Res. 1992 Feb 11;20(3):421–423. doi: 10.1093/nar/20.3.421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kahle D., Wehmeyer U., Krupp G. Substrate recognition by RNase P and by the catalytic M1 RNA: identification of possible contact points in pre-tRNAs. EMBO J. 1990 Jun;9(6):1929–1937. doi: 10.1002/j.1460-2075.1990.tb08320.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kim S. H., Quigley G. J., Suddath F. L., McPherson A., Sneden D., Kim J. J., Weinzierl J., Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science. 1973 Jan 19;179(4070):285–288. doi: 10.1126/science.179.4070.285. [DOI] [PubMed] [Google Scholar]
  14. Kirsebom L. A., Altman S. Reaction in vitro of some mutants of RNase P with wild-type and temperature-sensitive substrates. J Mol Biol. 1989 Jun 20;207(4):837–840. doi: 10.1016/0022-2836(89)90250-7. [DOI] [PubMed] [Google Scholar]
  15. Kirsebom L. A., Baer M. F., Altman S. Differential effects of mutations in the protein and RNA moieties of RNase P on the efficiency of suppression by various tRNA suppressors. J Mol Biol. 1988 Dec 20;204(4):879–888. doi: 10.1016/0022-2836(88)90048-4. [DOI] [PubMed] [Google Scholar]
  16. Kirsebom L. A., Svärd S. G. The kinetics and specificity of cleavage by RNase P is mainly dependent on the structure of the amino acid acceptor stem. Nucleic Acids Res. 1992 Feb 11;20(3):425–432. doi: 10.1093/nar/20.3.425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Miller J. H., Coulondre C., Farabaugh P. J. Correlation of nonsense sites in the lacI gene with specific codons in the nucleotide sequence. Nature. 1978 Aug 24;274(5673):770–775. doi: 10.1038/274770a0. [DOI] [PubMed] [Google Scholar]
  18. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Perreault J. P., Altman S. Important 2'-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J Mol Biol. 1992 Jul 20;226(2):399–409. doi: 10.1016/0022-2836(92)90955-j. [DOI] [PubMed] [Google Scholar]
  20. Reed R. E., Baer M. F., Guerrier-Takada C., Donis-Keller H., Altman S. Nucleotide sequence of the gene encoding the RNA subunit (M1 RNA) of ribonuclease P from Escherichia coli. Cell. 1982 Sep;30(2):627–636. doi: 10.1016/0092-8674(82)90259-8. [DOI] [PubMed] [Google Scholar]
  21. Reich C., Olsen G. J., Pace B., Pace N. R. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science. 1988 Jan 8;239(4836):178–181. doi: 10.1126/science.3122322. [DOI] [PubMed] [Google Scholar]
  22. Reilly R. M., RajBhandary U. L. A single mutation in loop IV of Escherichia coli SuIII tRNA blocks processing at both 5'- and 3'-ends of the precursor tRNA. J Biol Chem. 1986 Feb 25;261(6):2928–2935. [PubMed] [Google Scholar]
  23. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  24. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sprinzl M., Dank N., Nock S., Schön A. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2127–2171. doi: 10.1093/nar/19.suppl.2127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Svärd S. G., Kirsebom L. A. Several regions of a tRNA precursor determine the Escherichia coli RNase P cleavage site. J Mol Biol. 1992 Oct 20;227(4):1019–1031. doi: 10.1016/0022-2836(92)90518-o. [DOI] [PubMed] [Google Scholar]
  27. Thurlow D. L., Shilowski D., Marsh T. L. Nucleotides in precursor tRNAs that are required intact for catalysis by RNase P RNAs. Nucleic Acids Res. 1991 Feb 25;19(4):885–891. doi: 10.1093/nar/19.4.885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Vioque A., Arnez J., Altman S. Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J Mol Biol. 1988 Aug 20;202(4):835–848. doi: 10.1016/0022-2836(88)90562-1. [DOI] [PubMed] [Google Scholar]

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

RESOURCES