Home LiteratureArticle Details
PMID: 6359058 Published · ppublish English Comparative Study Journal Article

Refined secondary structure models for the 16S and 23S ribosomal RNA of Escherichia coli.

Nucleic acids research ·Vol. 11 ·No. 21 ·1983-11-11 ·Pages 7263-86

Maly P, Brimacombe R

Abstract

The complete range of published sequences for ribosomal RNA (or rDNA), totalling well over 50,000 bases, has been used to derive refined models for the secondary structures of both 16S and 23S RNA from E. coli. Particular attention has been paid to resolving the differences between the various published secondary structures for these molecules. The structures are described in terms of 133 helical regions (45 for 16S RNA and 88 for 23S RNA). Of these, approximately 20 are still tentative or unconfirmed. A further 20 represent helical regions which definitely exist, but where the detailed base-pairing is still open to discussion. Over 90 of the helical regions are however now precisely established, at least to within one or two base pairs.

MeSH Terms
Animals Base Composition Escherichia coli/genetics Humans Macromolecular Substances Models, Molecular Nucleic Acid Conformation RNA, Ribosomal/genetics Species Specificity
Chemicals
Macromolecular Substances RNA, Ribosomal
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Maly P
Brimacombe R
References (40)
40 references, click to expand
  1. Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria.
    Nucleic Acids Res. 1983 Jan 25;11(2):339-48 PMID: 6298722
  2. Sequence of the 16S Ribosomal RNA from Halobacterium volcanii, an Archaebacterium.
    Science. 1983 Aug 12;221(4611):656-9 PMID: 17787735
  3. Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function.
    J Mol Biol. 1983 Jan 5;163(1):27-46 PMID: 6834429
  4. The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisae.
    Nucleic Acids Res. 1981 Dec 21;9(24):6953-8 PMID: 6460984
  5. Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species.
    Nucleic Acids Res. 1981 Aug 11;9(15):3621-40 PMID: 7024918
  6. Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure.
    Nucleic Acids Res. 1981 May 11;9(9):2153-72 PMID: 6170942
  7. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.
    Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801-5 PMID: 368799
  8. The structure of ribosomal RNA and its organization relative to ribosomal protein.
    Prog Nucleic Acid Res Mol Biol. 1983;28:1-48 PMID: 6348873
  9. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli.
    Proc Natl Acad Sci U S A. 1980 Jan;77(1):201-4 PMID: 6153795
  10. Sequence of the chloroplast 16S rRNA gene and its surrounding regions of Chlamydomonas reinhardii.
    Nucleic Acids Res. 1982 Dec 11;10(23):7609-20 PMID: 6296784
  11. Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence.
    Nature. 1981 May 21;291(5812):205-8 PMID: 7015146
  12. The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae.
    Nucleic Acids Res. 1980 Dec 11;8(23):5779-94 PMID: 7008030
  13. The complete nucleotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans.
    Mol Gen Genet. 1983;191(1):46-50 PMID: 6412038
  14. [Nucleotide sequence of the gene for the mitochondrial 15S ribosomal RNA of yeast].
    C R Seances Acad Sci D. 1980 Dec 8;291(12):933-6 PMID: 6261980
  15. Distinctive sequence of human mitochondrial ribosomal RNA genes.
    Nature. 1980 Jul 31;286(5772):460-7 PMID: 6157106
  16. Nuclease mapping of the secondary structure of the 49-nucleotide 3' terminal cloacin fragment of Escherichia coli 16s RNA and its interactions with initiation factor 3.
    Nucleic Acids Res. 1983 Apr 11;11(7):2035-52 PMID: 6340066
  17. Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes.
    Cell. 1980 Nov;22(1 Pt 1):157-70 PMID: 7428037
  18. The nucleotide sequence of the large ribosomal RNA gene and the adjacent tRNA genes from rat mitochondria.
    Nucleic Acids Res. 1981 Aug 25;9(16):4139-48 PMID: 6913863
  19. Nucleotide sequence of the Aspergillus nidulans mitochondrial gene coding for the small ribosomal subunit RNA: homology to E. coli 16S rRNA.
    Nucleic Acids Res. 1981 Nov 11;9(21):5689-96 PMID: 6273804
  20. Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes.
    Nucleic Acids Res. 1981 Jul 24;9(14):3287-306 PMID: 7024913
  21. The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts.
    Eur J Biochem. 1982 May;124(1):13-9 PMID: 6177532
  22. Modification of 18 S rRNA in the 40 S ribosomal subunit of yeast with dimethyl sulfate.
    FEBS Lett. 1981 Nov 2;134(1):11-4 PMID: 9222313
  23. The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E.coli 23S rDNA.
    Nucleic Acids Res. 1981 Jun 25;9(12):2853-69 PMID: 7024906
  24. The sequence of the ribosomal 16S RNA from Proteus vulgaris. Sequence comparison with E. coli 16S RNA and its use in secondary model building.
    Nucleic Acids Res. 1981 May 25;9(10):2325-33 PMID: 7019853
  25. Secondary structure model for 23S ribosomal RNA.
    Nucleic Acids Res. 1981 Nov 25;9(22):6167-89 PMID: 7031608
  26. A 5.8 S rRNA-like sequence in prokaryotic 23 S rRNA.
    FEBS Lett. 1980 Oct 6;119(2):212-4 PMID: 6159235
  27. Secondary structure of 16S ribosomal RNA.
    Science. 1981 Apr 24;212(4493):403-11 PMID: 6163215
  28. Structure and sequence of the mitochondrial 20S rRNA and tRNA tyr gene of Paramecium primaurelia.
    Nucleic Acids Res. 1981 Dec 11;9(23):6391-406 PMID: 6275359
  29. Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA.
    Gene. 1981 Dec;16(1-3):297-307 PMID: 6282697
  30. The primary and secondary structure of yeast 26S rRNA.
    Nucleic Acids Res. 1981 Dec 21;9(24):6935-52 PMID: 7335496
  31. The complete nucleotide sequence of 16S ribosomal RNA gene from tobacco chloroplasts.
    Gene. 1982 Feb;17(2):213-8 PMID: 7044901
  32. Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs.
    Nucleic Acids Res. 1981 Sep 11;9(17):4303-24 PMID: 6170936
  33. Methylated regions of hamster mitochondrial ribosomal RNA: structural and functional correlates.
    Nucleic Acids Res. 1981 Jan 24;9(2):323-37 PMID: 6782552
  34. 5S RNA secondary structure.
    Nature. 1975 Aug 7;256(5517):505-7 PMID: 808733
  35. Localisation of a series of intra-RNA cross-links in the secondary and tertiary structure of 23S RNA, induced by ultraviolet irradiation of Escherichia coli 50S ribosomal subunits.
    Nucleic Acids Res. 1983 Mar 25;11(6):1687-706 PMID: 6340065
  36. Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA.
    Nucleic Acids Res. 1982 Oct 25;10(20):6369-81 PMID: 6294602
  37. A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem.
    EMBO J. 1983;2(8):1309-21 PMID: 10872325
  38. Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: its significance in gene evolution.
    Proc Natl Acad Sci U S A. 1983 Jun;80(11):3163-7 PMID: 6304693
  39. An unusual 5S rRNA, from Sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure.
    Nucleic Acids Res. 1981 Nov 25;9(22):6129-37 PMID: 6273825
  40. The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E. coli.
    Cell. 1980 Feb;19(2):393-401 PMID: 6153577
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/11.21.7263
Published
1983-11-11
Pages
7263-86
Language
English
Region
England
NLM ID
0411011
PMCID
PMC326482
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/11.21.7263 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2