• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. May 24, 1980; 8(10): 2275–2293.
PMCID: PMC324077

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.


We have derived a secondary structure model for 16S ribosomal RNA on the basis of comparative sequence analysis, chemical modification studies and nuclease susceptibility data. Nucleotide sequences of the E. coli and B. brevis 16S rRNA chains, and of RNAse T1 oligomer catalogs from 16S rRNAs of over 100 species of eubacteria were used for phylogenetic comparison. Chemical modification of G by glyoxal, A by m-chloroperbenzoic acid and C by bisulfite in naked 16S rRNA, and G by kethoxal in active and inactive 30S ribosomal subunits was taken as an indication of single stranded structure. Further support for the structure was obtained from susceptibility to RNases A and T1. These three approaches are in excellent agreement. The structure contains fifty helical elements organized into four major domains, in which 46 percent of the nucleotides of 16S rRNA are involved in base pairing. Phylogenetic comparison shows that highly conserved sequences are found principally in unpaired regions of the molecule. No knots are created by the structure.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.4M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Pace NR. Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. Bacteriol Rev. 1973 Dec;37(4):562–603. [PMC free article] [PubMed]
  • Shine J, Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. [PMC free article] [PubMed]
  • Steitz JA, Jakes K. How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4734–4738. [PMC free article] [PubMed]
  • Dunn JJ, Buzash-Pollert E, Studier FW. Mutations of bacteriophage T7 that affect initiation of synthesis of the gene 0.3 protein. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2741–2745. [PMC free article] [PubMed]
  • Noller HF, Chaires JB. Functional modification of 16S ribosomal RNA by kethoxal. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3115–3118. [PMC free article] [PubMed]
  • Ofengand J, Liou R, Kohut J, 3rd, Schwartz I, Zimmermann RA. Covalent cross-linking of transfer ribonucleic acid to the ribosomal P site. Mechanism and site of reaction in transfer ribonucleic acid. Biochemistry. 1979 Oct 2;18(20):4322–4332. [PubMed]
  • Prince JB, Hixson SS, Zimmermann RA. Photochemical cross-linking of tRNALys and tRNA2Glu to 16 S RNA at the P site of Escherichia coli ribosomes. J Biol Chem. 1979 Jun 10;254(11):4745–4749. [PubMed]
  • Santer M, Shane S. Area of 16S ribonucleic acid at or near the interface between 30S and 50S ribosomes of Escherichia coli. J Bacteriol. 1977 May;130(2):900–910. [PMC free article] [PubMed]
  • Chapman NM, Noller HF. Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes. J Mol Biol. 1977 Jan 5;109(1):131–149. [PubMed]
  • Herr W, Chapman NM, Noller HF. Mechanism of ribosomal subunit association: discrimination of specific sites in 16 S RNA essential for association activity. J Mol Biol. 1979 Jun 5;130(4):433–449. [PubMed]
  • Helser TL, Davies JE, Dahlberg JE. Mechanism of kasugamycin resistance in Escherichia coli. Nat New Biol. 1972 Jan 5;235(53):6–9. [PubMed]
  • Carbon P, Ehresmann C, Ehresmann B, Ebel JP. The complete nucleotide sequence of the ribosomal 16-S RNA from Excherichia coli. Experimental details and cistron heterogeneities. Eur J Biochem. 1979 Oct 15;100(2):399–410. [PubMed]
  • Brosius J, Dull TJ, Noller HF. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):201–204. [PMC free article] [PubMed]
  • Fox GE, Woese CR. 5S RNA secondary structure. Nature. 1975 Aug 7;256(5517):505–507. [PubMed]
  • Noller HF. Topography of 16S RNA in 30S ribosomal subunits. Nucleotide sequences and location of sites of reaction with kethoxal. Biochemistry. 1974 Nov 5;13(23):4694–4703. [PubMed]
  • Hogan JJ, Noller HF. Altered topography of 16S RNA in the inactive form of Escherichia coli 30S ribosomal subunits. Biochemistry. 1978 Feb 21;17(4):587–593. [PubMed]
  • Ehresmann C, Stiegler P, Carbon P, Ungewickell E, Garrett RA. The topography of the 5' end of 16-S RNA in the presence and absence of ribosomal proteins S4 and S20. Eur J Biochem. 1980 Feb;103(3):439–446. [PubMed]
  • Ehresmann C, Stiegler P, Fellner P, Ebel JP. The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. III. Further studies. Biochimie. 1975;57(6-7):711–748. [PubMed]
  • Müller R, Garrett RA, Noller HF. The structure of the RNA binding site of ribosomal proteins S8 and S15. J Biol Chem. 1979 May 25;254(10):3873–3878. [PubMed]
  • Yuki A, Brimacombe R. Nucleotide sequences of Escherichia coli 16-S RNA associated with ribosomal proteins S7, S9, S10, S14 and S19. Eur J Biochem. 1975 Aug 1;56(1):23–34. [PubMed]
  • Rinke J, Yuki A, Brimacombe R. Studies on the environment of protein S7 within the 30-S subunit Escherichia coli ribosomes. Eur J Biochem. 1976 Apr 15;64(1):77–89. [PubMed]
  • Rubtsov PM, Musakhanov MM, Batchikova NV, Skriabin KS, Baev AA. Opredelenie pervichnoi struktury fragmentov ribosomnogo operona pekarskikh drozhzhei, kodiruiushchikh 18 S rRNK. Dokl Akad Nauk SSSR. 1979;248(3):760–762. [PubMed]
  • Vasilenko SK, Ryte VC. [Isolation of highly purified ribonuclease from cobra (Naja oxiana) venom]. Biokhimiia. 1975 May-Jun;40(3):578–583. [PubMed]
  • de Wachter R, Fiers W. Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA. Anal Biochem. 1972 Sep;49(1):184–197. [PubMed]
  • Peattie DA. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760–1764. [PMC free article] [PubMed]
  • Rich A, RajBhandary UL. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. [PubMed]
  • Jack A, Ladner JE, Klug A. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution. J Mol Biol. 1976 Dec 25;108(4):619–649. [PubMed]
  • Zimmermann RA, Singh-Bergmann K. Binding sites for ribosomal proteins S8 and S15 in the 16 S RNA of Escherichia coli. Biochim Biophys Acta. 1979 Jul 26;563(2):422–431. [PubMed]
  • Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4537–4541. [PMC free article] [PubMed]
  • Möller K, Zwieb C, Brimacombe R. Identification of the oligonucleotide and oligopeptide involved in an RNA--protein crosslink induced by ultraviolet irradiation of Escherichia coli 30 S ribosomal subunits. J Mol Biol. 1978 Dec 15;126(3):489–506. [PubMed]
  • Shimizu M, Craven GR. Chemical inactivation of Escherichia coli 30-S ribosomes by iodination. Identification of proteins involved in tRNA binding. Eur J Biochem. 1976 Jan 2;61(1):307–315. [PubMed]
  • Hagenbüchle O, Santer M, Steitz JA, Mans RJ. Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells. Cell. 1978 Mar;13(3):551–563. [PubMed]
  • Poldermans B, Bakker H, Van Knippenberg PH. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16S ribosomal RNA of Escherichia coli. IV. The effect of the methylgroups on ribosomal subunit interaction. Nucleic Acids Res. 1980 Jan 11;8(1):143–151. [PMC free article] [PubMed]
  • Van Duin J, Kurland CG, Dondon J, Grunberg-Mangago M, Branlant C, Ebel JP. New aspects of the IF3-ribosome interaction. FEBS Lett. 1976 Feb 15;62(2):111–114. [PubMed]
  • Ross A, Brimacombe R. Experimental determination of interacting sequences in ribosomal RNA. Nature. 1979 Sep 27;281(5729):271–276. [PubMed]

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


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Gene
    Gene links
  • GEO Profiles
    GEO Profiles
    Related GEO records
  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...