Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1991 Jun;173(12):3855–3863. doi: 10.1128/jb.173.12.3855-3863.1991

Phylogenetic analysis and evolution of RNase P RNA in proteobacteria.

J W Brown 1, E S Haas 1, B D James 1, D A Hunt 1, J S Liu 1, N R Pace 1
PMCID: PMC208017  PMID: 1711030

Abstract

The secondary structures of the eubacterial RNase P RNAs are being elucidated by a phylogenetic comparative approach. Sequences of genes encoding RNase P RNA from each of the recognized subgroups (alpha, beta, gamma, and delta) of the proteobacteria have now been determined. These sequences allow the refinement, to nearly the base pair level, of the phylogenetic model for RNase P RNA secondary structure. Evolutionary change among the RNase P RNAs was found to occur primarily in four discrete structural domains that are peripheral to a highly conserved core structure. The new sequences were used to examine critically the proposed similarity (C. Guerrier-Takada, N. Lumelsky, and S. Altman, Science 246:1578-1584, 1989) between a portion of RNase P RNA and the "exit site" of the 23S rRNA of Escherichia coli. Phylogenetic comparisons indicate that these sequences are not homologous and that any similarity in the structures is, at best, tenuous.

Full text

PDF
3855

Images in this article

3860Image
on p.3860

Selected References

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

  1. Altman S. Ribonuclease P: an enzyme with a catalytic RNA subunit. Adv Enzymol Relat Areas Mol Biol. 1989;62:1–36. doi: 10.1002/9780470123089.ch1. [DOI] [PubMed] [Google Scholar]
  2. Boehm S. Similarities between a predicted secondary structure for the M1 RNA ribozyme and the tRNA binding center of 16 S rRNA from E. coli. FEBS Lett. 1987 Aug 17;220(2):283–287. doi: 10.1016/0014-5793(87)80830-x. [DOI] [PubMed] [Google Scholar]
  3. Brown J. W., Hunt D. A., Pace N. R. Nucleotide sequence of the 10Sa RNA gene of the beta-purple eubacterium Alcaligenes eutrophus. Nucleic Acids Res. 1990 May 11;18(9):2820–2820. doi: 10.1093/nar/18.9.2820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burgin A. B., Pace N. R. Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J. 1990 Dec;9(12):4111–4118. doi: 10.1002/j.1460-2075.1990.tb07633.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Gutell R. R., Schnare M. N., Gray M. W. A compilation of large subunit (23S-like) ribosomal RNA sequences presented in a secondary structure format. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2319–2330. doi: 10.1093/nar/18.suppl.2319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Jain S. K., Gurevitz M., Apirion D. A small RNA that complements mutants in the RNA processing enzyme ribonuclease P. J Mol Biol. 1982 Dec 15;162(3):515–533. doi: 10.1016/0022-2836(82)90386-2. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Khandjian E. W. UV crosslinking of RNA to nylon membrane enhances hybridization signals. Mol Biol Rep. 1986;11(2):107–115. doi: 10.1007/BF00364822. [DOI] [PubMed] [Google Scholar]
  12. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  14. Mead D. A., Szczesna-Skorupa E., Kemper B. Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. Protein Eng. 1986 Oct-Nov;1(1):67–74. doi: 10.1093/protein/1.1.67. [DOI] [PubMed] [Google Scholar]
  15. Ogden R. C., Adams D. A. Electrophoresis in agarose and acrylamide gels. Methods Enzymol. 1987;152:61–87. doi: 10.1016/0076-6879(87)52011-0. [DOI] [PubMed] [Google Scholar]
  16. Pace N. R., Smith D. K., Olsen G. J., James B. D. Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. Gene. 1989 Oct 15;82(1):65–75. doi: 10.1016/0378-1119(89)90031-0. [DOI] [PubMed] [Google Scholar]
  17. Pace N. R., Smith D. Ribonuclease P: function and variation. J Biol Chem. 1990 Mar 5;265(7):3587–3590. [PubMed] [Google Scholar]
  18. Papanicolaou C., Gouy M., Ninio J. An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):31–44. doi: 10.1093/nar/12.1part1.31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Reich C., Gardiner K. J., Olsen G. J., Pace B., Marsh T. L., Pace N. R. The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure. J Biol Chem. 1986 Jun 15;261(17):7888–7893. [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. Short J. M., Fernandez J. M., Sorge J. A., Huse W. D. Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res. 1988 Aug 11;16(15):7583–7600. doi: 10.1093/nar/16.15.7583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Takeshima T., Inoue C., Kitagawa Y., Kusano T. Nucleotide sequence of a Thiobacillus ferrooxidans chromosomal gene, which encodes putative RNA component of RNase P. Nucleic Acids Res. 1989 Nov 25;17(22):9482–9482. doi: 10.1093/nar/17.22.9482. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. Waugh D. S., Green C. J., Pace N. R. The design and catalytic properties of a simplified ribonuclease P RNA. Science. 1989 Jun 30;244(4912):1569–1571. doi: 10.1126/science.2472671. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES