Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Apr 1;24(7):1252–1259. doi: 10.1093/nar/24.7.1252

Comparative analysis of ribonuclease P RNA structure in Archaea.

E S Haas 1, D W Armbruster 1, B M Vucson 1, C J Daniels 1, J W Brown 1
PMCID: PMC145784  PMID: 8614627

Abstract

Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms, such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacteriurn trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis. The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro.

Full Text

The Full Text of this article is available as a PDF (122.7 KB).

Selected References

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

  1. Altman S., Kirsebom L., Talbot S. Recent studies of ribonuclease P. FASEB J. 1993 Jan;7(1):7–14. doi: 10.1096/fasebj.7.1.7916700. [DOI] [PubMed] [Google Scholar]
  2. Brown J. W., Haas E. S., James B. D., Hunt D. A., Liu J. S., Pace N. R. Phylogenetic analysis and evolution of RNase P RNA in proteobacteria. J Bacteriol. 1991 Jun;173(12):3855–3863. doi: 10.1128/jb.173.12.3855-3863.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brown J. W., Haas E. S., Pace N. R. Characterization of ribonuclease P RNAs from thermophilic bacteria. Nucleic Acids Res. 1993 Feb 11;21(3):671–679. doi: 10.1093/nar/21.3.671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Brown J. W. Phylogenetic comparative analysis of RNA structure on Macintosh computers. Comput Appl Biosci. 1991 Jul;7(3):391–393. doi: 10.1093/bioinformatics/7.3.391. [DOI] [PubMed] [Google Scholar]
  6. Darr S. C., Brown J. W., Pace N. R. The varieties of ribonuclease P. Trends Biochem Sci. 1992 May;17(5):178–182. doi: 10.1016/0968-0004(92)90262-8. [DOI] [PubMed] [Google Scholar]
  7. Darr S. C., Pace B., Pace N. R. Characterization of ribonuclease P from the archaebacterium Sulfolobus solfataricus. J Biol Chem. 1990 Aug 5;265(22):12927–12932. [PubMed] [Google Scholar]
  8. 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]
  9. Haas E. S., Brown J. W., Pitulle C., Pace N. R. Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2527–2531. doi: 10.1073/pnas.91.7.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Haas E. S., Brown J. W., Pitulle C., Pace N. R. Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2527–2531. doi: 10.1073/pnas.91.7.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hardt W. D., Schlegl J., Erdmann V. A., Hartmann R. K. Kinetics and thermodynamics of the RNase P RNA cleavage reaction: analysis of tRNA 3'-end variants. J Mol Biol. 1995 Mar 24;247(2):161–172. doi: 10.1006/jmbi.1994.0130. [DOI] [PubMed] [Google Scholar]
  12. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  13. James B. D., Olsen G. J., Liu J. S., Pace N. R. The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell. 1988 Jan 15;52(1):19–26. doi: 10.1016/0092-8674(88)90527-2. [DOI] [PubMed] [Google Scholar]
  14. LaGrandeur T. E., Darr S. C., Haas E. S., Pace N. R. Characterization of the RNase P RNA of Sulfolobus acidocaldarius. J Bacteriol. 1993 Aug;175(16):5043–5048. doi: 10.1128/jb.175.16.5043-5048.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lawrence N. P., Richman A., Amini R., Altman S. Heterologous enzyme function in Escherichia coli and the selection of genes encoding the catalytic RNA subunit of RNase P. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6825–6829. doi: 10.1073/pnas.84.19.6825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lawrence N., Wesolowski D., Gold H., Bartkiewicz M., Guerrier-Takada C., McClain W. H., Altman S. Characteristics of ribonuclease P from various organisms. Cold Spring Harb Symp Quant Biol. 1987;52:233–238. doi: 10.1101/sqb.1987.052.01.028. [DOI] [PubMed] [Google Scholar]
  17. Nieuwlandt D. T., Haas E. S., Daniels C. J. The RNA component of RNase P from the archaebacterium Haloferax volcanii. J Biol Chem. 1991 Mar 25;266(9):5689–5695. [PubMed] [Google Scholar]
  18. Oh B. K., Pace N. R. Interaction of the 3'-end of tRNA with ribonuclease P RNA. Nucleic Acids Res. 1994 Oct 11;22(20):4087–4094. doi: 10.1093/nar/22.20.4087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pace N. R., Brown J. W. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol. 1995 Apr;177(8):1919–1928. doi: 10.1128/jb.177.8.1919-1928.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. 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]
  22. Vogelstein B., Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci U S A. 1979 Feb;76(2):615–619. doi: 10.1073/pnas.76.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zuker M., Jaeger J. A., Turner D. H. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res. 1991 May 25;19(10):2707–2714. doi: 10.1093/nar/19.10.2707. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES