Home LiteratureArticle Details
PMID: 1712293 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

A functional pseudoknot in 16S ribosomal RNA.

The EMBO journal ·Vol. 10 ·No. 8 ·1991-08-00 ·Pages 2203-14

Powers T, Noller HF

Abstract

Several lines of evidence indicate that the universally conserved 530 loop of 16S ribosomal RNA plays a crucial role in translation, related to the binding of tRNA to the ribosomal A site. Based upon limited phylogenetic sequence variation, Woese and Gutell (1989) have proposed that residues 524-526 in the 530 hairpin loop are base paired with residues 505-507 in an adjoining bulge loop, suggesting that this region of 16S rRNA folds into a pseudoknot structure. Here, we demonstrate that Watson-Crick interactions between these nucleotides are essential for ribosomal function. Moreover, we find that certain mild perturbations of the structure, for example, creation of G-U wobble pairs, generate resistance to streptomycin, an antibiotic known to interfere with the decoding process. Chemical probing of mutant ribosomes from streptomycin-resistant cells shows that the mutant ribosomes have a reduced affinity for streptomycin, even though streptomycin is thought to interact with a site on the 30S subunit that is distinct from the 530 region. Data from earlier in vitro assembly studies suggest that the pseudoknot structure is stabilized by ribosomal protein S12, mutations in which have long been known to confer streptomycin resistance and dependence.

MeSH Terms
Base Sequence Drug Resistance, Microbial/genetics Escherichia coli/metabolism Molecular Sequence Data Mutagenesis, Site-Directed Mutation Nucleic Acid Conformation Plasmids Protein Biosynthesis RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Ribosomes/drug effects,metabolism Streptomycin/metabolism,pharmacology
Chemicals
RNA, Bacterial RNA, Ribosomal, 16S Streptomycin
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Powers T
Sinsheimer Laboratories, University of California, Santa Cruz 95064.
Noller H F
References (57)
57 references, click to expand
  1. Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance.
    J Mol Biol. 1989 Oct 20;209(4):655-65 PMID: 2685326
  2. Conservation of primary structure in 16S ribosomal RNA.
    Nature. 1975 Mar 6;254(5495):83-6 PMID: 1089909
  3. Evidence for several higher order structural elements in ribosomal RNA.
    Proc Natl Acad Sci U S A. 1989 May;86(9):3119-22 PMID: 2654936
  4. Antibiotic resistance mutations in the chloroplast 16S and 23S rRNA genes of Chlamydomonas reinhardtii: correlation of genetic and physical maps of the chloroplast genome.
    Genetics. 1989 Oct;123(2):281-92 PMID: 2583478
  5. Mapping of chloroplast mutations conferring resistance to antibiotics in Chlamydomonas: evidence for a novel site of streptomycin resistance in the small subunit rRNA.
    Mol Gen Genet. 1988 Oct;214(2):192-7 PMID: 3237207
  6. Development of an efficient method for generating and screening active trypsin and trypsin variants.
    Ann N Y Acad Sci. 1988;542:61-74 PMID: 3228244
  7. A pseudoknotted RNA oligonucleotide.
    Nature. 1988 Jan 21;331(6153):283-6 PMID: 3336440
  8. Hyper-accurate ribosomes inhibit growth.
    EMBO J. 1984 Nov;3(11):2575-80 PMID: 6391914
  9. Streptomycin resistance; a genetically recessive mutation.
    J Bacteriol. 1951 May;61(5):549-50 PMID: 14832197
  10. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA.
    Nature. 1988 Jul 28;334(6180):362-4 PMID: 2455872
  11. Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA.
    Cell. 1988 Nov 4;55(3):399-411 PMID: 2846180
  12. Streptomycin preferentially perturbs ribosomal proofreading.
    Mol Gen Genet. 1984;198(2):100-4 PMID: 6394958
  13. Streptomycin-resistance of Euglena gracilis chloroplasts: identification of a point mutation in the 16S rRNA gene in an invariant position.
    Nucleic Acids Res. 1985 Jun 25;13(12):4299-310 PMID: 3925438
  14. Comparative anatomy of 16-S-like ribosomal RNA.
    Prog Nucleic Acid Res Mol Biol. 1985;32:155-216 PMID: 3911275
  15. Rapid and efficient site-specific mutagenesis without phenotypic selection.
    Proc Natl Acad Sci U S A. 1985 Jan;82(2):488-92 PMID: 3881765
  16. A new principle of RNA folding based on pseudoknotting.
    Nucleic Acids Res. 1985 Mar 11;13(5):1717-31 PMID: 4000943
  17. A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome.
    EMBO J. 1990 Aug;9(8):2649-55 PMID: 2196177
  18. Effects of mutagenesis of a conserved base-paired site near the decoding region of Escherichia coli 16 S ribosomal RNA.
    J Mol Biol. 1990 Mar 5;212(1):127-33 PMID: 1690811
  19. Dominant lethal mutations in a conserved loop in 16S rRNA.
    Proc Natl Acad Sci U S A. 1990 Feb;87(3):1042-6 PMID: 2405392
  20. Interaction of antibiotics with functional sites in 16S ribosomal RNA.
    Nature. 1987 Jun 4-10;327(6121):389-94 PMID: 2953976
  21. Evidence that the G2661 region of 23S rRNA is located at the ribosomal binding sites of both elongation factors.
    Biochimie. 1987 Sep;69(9):911-23 PMID: 3126829
  22. E. coli ribosomes with a C912 to U base change in the 16S rRNA are streptomycin resistant.
    EMBO J. 1986 Dec 20;5(13):3705-8 PMID: 3104030
  23. A mutation in the 530 loop of Escherichia coli 16S ribosomal RNA causes resistance to streptomycin.
    Nucleic Acids Res. 1988 Oct 25;16(20):9631-9 PMID: 3054810
  24. Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli.
    Methods Enzymol. 1988;164:673-90 PMID: 3071688
  25. Mutations in 16S ribosomal RNA disrupt antibiotic--RNA interactions.
    EMBO J. 1989 Apr;8(4):1213-6 PMID: 2472961
  26. Substitution of an invariant nucleotide at the base of the highly conserved '530-loop' of 15S rRNA causes suppression of yeast mitochondrial ochre mutations.
    Nucleic Acids Res. 1989 Jun 26;17(12):4535-9 PMID: 2473436
  27. RNA pseudoknots that interact with components of the translation apparatus.
    Cell. 1989 Jul 14;58(1):9-12 PMID: 2473840
  28. Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA.
    J Mol Biol. 1989 Aug 5;208(3):457-68 PMID: 2477554
  29. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension.
    Methods Enzymol. 1988;164:481-9 PMID: 2468070
  30. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites.
    Cell. 1989 May 19;57(4):585-97 PMID: 2470511
  31. Model for the three-dimensional folding of 16 S ribosomal RNA.
    J Mol Biol. 1988 Nov 20;204(2):447-81 PMID: 2464693
  32. Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA.
    J Mol Biol. 1988 Jun 20;201(4):683-95 PMID: 2459389
  33. Spectinomycin resistance at site 1192 in 16S ribosomal RNA of E. coli: an analysis of three mutants.
    Biochimie. 1987 Aug;69(8):885-9 PMID: 2447957
  34. The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme.
    Cell. 1988 Jan 15;52(1):19-26 PMID: 2449969
  35. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes.
    Cell. 1986 Dec 26;47(6):985-94 PMID: 2430725
  36. Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension.
    J Mol Biol. 1986 Feb 5;187(3):399-416 PMID: 2422386
  37. Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli.
    J Mol Biol. 1989 Oct 20;209(4):645-53 PMID: 2531227
  38. The guanosine binding site of the Tetrahymena ribozyme.
    Nature. 1989 Nov 23;342(6248):391-5 PMID: 2685606
  39. Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs.
    Proc Natl Acad Sci U S A. 1990 Jan;87(2):663-7 PMID: 2300554
  40. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.
    Nucleic Acids Res. 1980 May 24;8(10):2275-93 PMID: 6159576
  41. Improved plasmid vectors with a thermoinducible expression and temperature-regulated runaway replication.
    Gene. 1983 Apr;22(1):103-13 PMID: 6305768
  42. Antibiotic resistance mutations in 16S and 23S ribosomal RNA genes of Escherichia coli.
    Nucleic Acids Res. 1984 Jun 11;12(11):4653-63 PMID: 6330677
  43. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids.
    Microbiol Rev. 1983 Dec;47(4):621-69 PMID: 6363901
  44. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli.
    J Mol Biol. 1981 May 15;148(2):107-27 PMID: 7028991
  45. Ribosomal ambiguity (ram) mutations facilitate diyhydrostreptomycin binding to ribosomes.
    FEBS Lett. 1979 Aug 15;104(2):317-21 PMID: 89972
  46. Dual interference of hygromycin B with ribosomal translocation and with aminoacyl-tRNA recognition.
    Eur J Biochem. 1978 Jun 1;87(1):21-7 PMID: 208837
  47. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  48. Simultaneous analysis of families of sigmoidal curves: application to bioassay, radioligand assay, and physiological dose-response curves.
    Am J Physiol. 1978 Aug;235(2):E97-102 PMID: 686171
  49. The effects of streptomycin or dihydrostreptomycin binding to 16S RNA or to 30S ribosomal subunits.
    Proc Natl Acad Sci U S A. 1974 Oct;71(10):3814-8 PMID: 4139702
  50. Protein involved in the binding of dihydrostreptomycin to ribosomes of Escherichia coli.
    J Mol Biol. 1973 Nov 25;81(1):71-82 PMID: 4129206
  51. Binding of dihydrostreptomycin to Escherichia coli ribosomes: characteristics and equilibrium of the reaction.
    Antimicrob Agents Chemother. 1972 Oct;2(4):294-307 PMID: 4133236
  52. Identification and functional characterization of the protein controlled by the streptomycin-resistant locus in E. coli.
    Nature. 1969 Apr 26;222(5191):333-9 PMID: 4181187
  53. Ribosomal protein S12 and 'non-enzymatic' translocation.
    FEBS Lett. 1974 Sep 1;45(1):324-8 PMID: 4607032
  54. Structure and function of ribosomes and their molecular components.
    Cold Spring Harb Symp Quant Biol. 1969;34:49-61 PMID: 4909519
  55. Altered ribosomal protein in streptomycin-dependent Escherichia coli.
    Science. 1969 Dec 5;166(3910):1282-4 PMID: 4900367
  56. A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates.
    J Mol Biol. 1966 Jun;18(1):48-57 PMID: 5337558
  57. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA.
    Science. 1989 May 19;244(4906):783-90 PMID: 2658053
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1991-08-00
Pages
2203-14
Language
English
Region
England
NLM ID
8208664
PMCID
PMC452909
Subset
IM
Grants
NIGMS NIH HHS · GM-17129 · United States
External Links
PubMed source 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: product@genelibs.com

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