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Nucleic Acids Res. Sep 1, 1996; 24(17): 3381–3391.
PMCID: PMC146102

A quantitative map of nucleotide substitution rates in bacterial rRNA.

Abstract

A recently developed method for estimating the variability of nucleotide sites in a sequence alignment [Van de Peer, Y., Van der Auwera, G. and De Wachter, R. (1996) J. Mol. Evol. 42, 201-210] was applied to bacterial 16S, 5S and 23S rRNAs. In this method, the variability of each nucleotide site is defined as its evolutionary rate relative to the average evolutionary rate of all the nucleotide sites of the molecule. Spectra of evolutionary rates were calculated for each rRNA and show the fastest evolving sites substituting at rates more than 1000 times that of the slowest ones. Variability maps are presented for each rRNA, consisting of secondary structure models where the variability of each nucleotide site is indicated by means of a colored dot. The maps can be interpreted in terms of higher order structure, function and evolution of the molecules and facilitate the selection of areas suitable for the design of PCR primers and hybridization probes. Variability measurement is also important for the precise estimation of evolutionary distances and the inference of phylogenetic trees.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Olsen GJ. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb Symp Quant Biol. 1987;52:825–837. [PubMed]
  • Jin L, Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol. 1990 Jan;7(1):82–102. [PubMed]
  • Van de Peer Y, Neefs JM, De Rijk P, De Wachter R. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol. 1993 Aug;37(2):221–232. [PubMed]
  • Van de Peer Y, Van der Auwera G, De Wachter R. The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J Mol Evol. 1996 Feb;42(2):201–210. [PubMed]
  • Manske CL, Chapman DJ. Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences. J Mol Evol. 1987;26(3):226–251. [PubMed]
  • Uzzell T, Corbin KW. Fitting discrete probability distributions to evolutionary events. Science. 1971 Jun 11;172(3988):1089–1096. [PubMed]
  • Holmquist R, Goodman M, Conroy T, Czelusniak J. The spatial distribution of fixed mutations within genes coding for proteins. J Mol Evol. 1983;19(6):437–448. [PubMed]
  • Wakeley J. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J Mol Evol. 1993 Dec;37(6):613–623. [PubMed]
  • Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 1995 Jul;12(4):546–557. [PubMed]
  • Van de Peer Y, Nicolaï S, De Rijk P, De Wachter R. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 1996 Jan 1;24(1):86–91. [PMC free article] [PubMed]
  • De Rijk P, Van de Peer Y, De Wachter R. Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 1996 Jan 1;24(1):92–97. [PMC free article] [PubMed]
  • Erdmann VA, Wolters J, Huysmans E, De Wachter R. Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences. Nucleic Acids Res. 1985;13 (Suppl):r105–r153. [PMC free article] [PubMed]
  • Neefs JM, Van de Peer Y, De Rijk P, Goris A, De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):1987–2015. [PMC free article] [PubMed]
  • Nelles L, Fang BL, Volckaert G, Vandenberghe A, De Wachter R. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucleic Acids Res. 1984 Dec 11;12(23):8749–8768. [PMC free article] [PubMed]
  • De Rijk P, Neefs JM, Van de Peer Y, De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1992 May 11;20 (Suppl):2075–2089. [PMC free article] [PubMed]
  • Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 1993 Jul 1;21(13):3025–3049. [PMC free article] [PubMed]
  • Gutell RR, Larsen N, Woese CR. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. [PMC free article] [PubMed]
  • Gutell RR. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 1994 Sep;22(17):3502–3507. [PMC free article] [PubMed]
  • Ninio J. Properties of nucleic acid representations. I. Topology. Biochimie. 1971;53(4):485–494. [PubMed]
  • Hunter WN, Brown T, Anand NN, Kennard O. Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair. Nature. 1986 Apr 10;320(6062):552–555. [PubMed]
  • Raué HA, Klootwijk J, Musters W. Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog Biophys Mol Biol. 1988;51(2):77–129. [PubMed]
  • Powers T, Noller HF. Dominant lethal mutations in a conserved loop in 16S rRNA. Proc Natl Acad Sci U S A. 1990 Feb;87(3):1042–1046. [PMC free article] [PubMed]
  • Brimacombe R. The structure of ribosomal RNA: a three-dimensional jigsaw puzzle. Eur J Biochem. 1995 Jun 1;230(2):365–383. [PubMed]
  • Tapprich WE, Hill WE. Involvement of bases 787-795 of Escherichia coli 16S ribosomal RNA in ribosomal subunit association. Proc Natl Acad Sci U S A. 1986 Feb;83(3):556–560. [PMC free article] [PubMed]
  • Tapprich WE, Goss DJ, Dahlberg AE. Mutation at position 791 in Escherichia coli 16S ribosomal RNA affects processes involved in the initiation of protein synthesis. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4927–4931. [PMC free article] [PubMed]
  • Woese CR, Gutell RR. Evidence for several higher order structural elements in ribosomal RNA. Proc Natl Acad Sci U S A. 1989 May;86(9):3119–3122. [PMC free article] [PubMed]
  • Powers T, Noller HF. A functional pseudoknot in 16S ribosomal RNA. EMBO J. 1991 Aug;10(8):2203–2214. [PMC free article] [PubMed]
  • De Rijk P, Van de Peer Y, Chapelle S, De Wachter R. Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 1994 Sep;22(17):3495–3501. [PMC free article] [PubMed]
  • Noller HF, Kop J, Wheaton V, Brosius J, Gutell RR, Kopylov AM, Dohme F, Herr W, Stahl DA, Gupta R, et al. Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res. 1981 Nov 25;9(22):6167–6189. [PMC free article] [PubMed]
  • Brimacombe R, Stiege W. Structure and function of ribosomal RNA. Biochem J. 1985 Jul 1;229(1):1–17. [PMC free article] [PubMed]
  • Wolters J, Erdmann VA. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res. 1988;16 (Suppl):r1–70. [PMC free article] [PubMed]
  • Van den Eynde H, De Wachter R. Variable base pairing in a helix of eubacterial 5 S ribosomal RNA points to the existence of a conformational switch. FEBS Lett. 1987 Jun 15;217(2):191–196. [PubMed]
  • Egebjerg J, Christiansen J, Brown RS, Larsen N, Garrett RA. Protein L18 binds primarily at the junctions of helix II and internal loops A and B in Escherichia coli 5 S RNA. Implications for 5 S RNA structure. J Mol Biol. 1989 Apr 20;206(4):651–668. [PubMed]
  • Höpfl P, Ludwig W, Schleifer KH, Larsen N. The 23S ribosomal RNA higher-order structure of Pseudomonas cepacia and other prokaryotes. Eur J Biochem. 1989 Nov 6;185(2):355–364. [PubMed]
  • Hassouna N, Michot B, Bachellerie JP. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res. 1984 Apr 25;12(8):3563–3583. [PMC free article] [PubMed]
  • Pace NR. Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. Bacteriol Rev. 1973 Dec;37(4):562–603. [PMC free article] [PubMed]
  • Burgin AB, Parodos K, Lane DJ, Pace NR. The excision of intervening sequences from Salmonella 23S ribosomal RNA. Cell. 1990 Feb 9;60(3):405–414. [PubMed]
  • Ware VC, Renkawitz R, Gerbi SA. rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 28S beta rRNAs in Sciara coprophila. Nucleic Acids Res. 1985 May 24;13(10):3581–3597. [PMC free article] [PubMed]
  • Clark CG. On the evolution of ribosomal RNA. J Mol Evol. 1987;25(4):343–350. [PubMed]
  • Spencer DF, Collings JC, Schnare MN, Gray MW. Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata. EMBO J. 1987 Apr;6(4):1063–1071. [PMC free article] [PubMed]
  • Boer PH, Gray MW. Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. Cell. 1988 Nov 4;55(3):399–411. [PubMed]
  • Van de Peer Y, Rensing SA, Maier UG, De Wachter R. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7732–7736. [PMC free article] [PubMed]
  • Woese CR, Stackebrandt E, Ludwig W. What are mycoplasmas: the relationship of tempo and mode in bacterial evolution. J Mol Evol. 1984;21(4):305–316. [PubMed]
  • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. [PubMed]
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [PMC free article] [PubMed]
  • Olsen GJ, Woese CR, Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol. 1994 Jan;176(1):1–6. [PMC free article] [PubMed]

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