Home LiteratureArticle Details
PMID: 9592132 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The environment of 5S rRNA in the ribosome: cross-links to the GTPase-associated area of 23S rRNA.

Nucleic acids research ·Vol. 26 ·No. 11 ·1998-06-01 ·Pages 2519-25

Sergiev P, Dokudovskaya S, Romanova E, Topin A, Bogdanov A, Brimacombe R, Dontsova O

Abstract

Two photoreactive diazirine derivatives of uridine were used to study contacts between 5S rRNA and 23 rRNA in situ in Escherichia coli ribosomes. 2'-Amino-2'-deoxy-uridine or 5-methyleneaminouridine were introduced into 5S rRNA by T7 transcription. After incorporation of these uridine analogues into the transcript their amino groups were modified with 4-[3-(trifluoromethyl)-3 H -diazirin-3-yl]benzyl isothiocyanate or the N -hydroxysuccinimide ester of 4-[3-(trifluoromethyl)-3 H -diazirin-3-yl]benzoic acid respectively. 5S rRNA carrying the photoreactive diazirine groups (referred to as the 2'-aminoribose derivative and the 5-methyleneamino derivative respectively) was reconstituted into 50S subunits or 70S ribosomes. After mild UV irradiation cross-links formed to 23S rRNA were analysed by standard procedures. All of the observed cross-links involved residue U89 of the 5S rRNA. Three nucleotides of 23S rRNA were cross-linked to this residue with the 5-methyleneamino derivative, namely U958, G1022 and G1138. With the 2'-aminoribose derivative a single cross-link was found, to U958. The significance of these cross-links for our understanding of the structure and function of 5S rRNA and its environment in the ribosome are discussed.

MeSH Terms
Base Sequence Binding Sites Cross-Linking Reagents Deoxyuridine GTP Phosphohydrolases/metabolism Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial RNA, Ribosomal, 23S/metabolism RNA, Ribosomal, 5S/metabolism Ribosomes/metabolism Uridine/analogs & derivatives Uridine Triphosphate/analogs & derivatives
Chemicals
5-methyleneaminouridine triphosphate Cross-Linking Reagents RNA, Bacterial RNA, Ribosomal, 23S RNA, Ribosomal, 5S GTP Phosphohydrolases Uridine Triphosphate Deoxyuridine Uridine
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Sergiev P
A. N. Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Moscow State University, Moscow 119899, Russia.
Dokudovskaya S
Romanova E
Topin A
Bogdanov A
Brimacombe R
Dontsova O
References (42)
42 references, click to expand
  1. Investigation of the tertiary folding of Escherichia coli ribosomal RNA by intra-RNA cross-linking in vivo.
    J Mol Biol. 1986 Sep 5;191(1):135-8 PMID: 2432273
  2. Construction and functional analysis of ribosomal 5S RNA from Escherichia coli with single base changes in the ribosomal protein binding sites.
    Biol Chem Hoppe Seyler. 1986 Aug;367(8):769-80 PMID: 2429677
  3. Transient association of newly synthesized unfolded proteins with the heat-shock GroEL protein.
    Nature. 1988 Nov 17;336(6196):254-7 PMID: 2904124
  4. A model for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome.
    EMBO J. 1988 Nov;7(11):3571-6 PMID: 2463164
  5. The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyl transfer centre of Escherichia coli 23S ribosomal RNA.
    EMBO J. 1988 Nov;7(11):3577-87 PMID: 3061800
  6. Characterization of the binding sites of protein L11 and the L10.(L12)4 pentameric complex in the GTPase domain of 23 S ribosomal RNA from Escherichia coli.
    J Mol Biol. 1990 May 20;213(2):275-88 PMID: 1692883
  7. Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents.
    Nucleic Acids Res. 1990 Dec 11;18(23):6755-60 PMID: 1702198
  8. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling.
    J Mol Biol. 1991 Sep 5;221(1):293-308 PMID: 1717695
  9. Higher order interactions in 23s rRNA.
    Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):5044-8 PMID: 1375755
  10. Application of 3-[3-(3-(trifluoromethyl)diazirin-3-yl)phenyl]-2,3- dihydroxypropionic acid, carbene-generating, cleavable cross-linking reagent for photoaffinity labeling.
    Anal Biochem. 1992 Jul;204(1):90-5 PMID: 1381157
  11. [Oligodeoxyribonucleotides containing 2'-amino-2'-deoxypyrimidine nucleosides].
    Bioorg Khim. 1993 Apr;19(4):455-66 PMID: 8494568
  12. The antibiotics micrococcin and thiostrepton interact directly with 23S rRNA nucleotides 1067A and 1095A.
    Nucleic Acids Res. 1994 Feb 11;22(3):357-63 PMID: 8127673
  13. Stem-loop IV of 5S rRNA lies close to the peptidyltransferase center.
    Proc Natl Acad Sci U S A. 1994 May 10;91(10):4125-9 PMID: 7514294
  14. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site.
    Science. 1995 Jan 13;267(5195):234-7 PMID: 7528943
  15. Pseudoknot in domain II of 23 S rRNA is essential for ribosome function.
    J Mol Biol. 1995 May 26;249(1):59-68 PMID: 7776376
  16. The structure of ribosomal RNA: a three-dimensional jigsaw puzzle.
    Eur J Biochem. 1995 Jun 1;230(2):365-83 PMID: 7607205
  17. Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.
    RNA. 1995 Aug;1(6):575-83 PMID: 7489517
  18. The ribosomal environment of tRNA: crosslinks to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P, or E site.
    RNA. 1995 Dec;1(10):1018-28 PMID: 8595557
  19. Loop IV of 5S ribosomal RNA has contacts both to domain II and to domain V of the 23S RNA.
    RNA. 1996 Feb;2(2):146-52 PMID: 8601281
  20. 5S rRNA sugar-phosphate backbone protection in complexes with specific ribosomal proteins.
    FEBS Lett. 1996 Sep 23;394(1):71-5 PMID: 8925931
  21. Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy.
    Cell. 1997 Jan 10;88(1):19-28 PMID: 9019401
  22. The path of mRNA through the bacterial ribosome: a site-directed crosslinking study using new photoreactive derivatives of guanosine and uridine.
    RNA. 1997 May;3(5):464-75 PMID: 9149228
  23. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A.
    J Mol Biol. 1997 Aug 29;271(4):524-44 PMID: 9281424
  24. [Apropos of the presence of weak molecular weight RNA in the ribosomes of Escherichia Coli].
    Biochim Biophys Acta. 1963 Apr 30;68:653-6 PMID: 13975159
  25. Letters to the editor: Accessibility of 5 S RNA in 50 S ribosomal subunits.
    J Mol Biol. 1974 Nov 25;90(1):181-4 PMID: 4616097
  26. 5S RNA secondary structure.
    Nature. 1975 Aug 7;256(5517):505-7 PMID: 808733
  27. Total reconstitution and assembly of 50 S subunits from Escherichia coli Ribosomes in vitro.
    J Mol Biol. 1976 Nov 15;107(4):585-99 PMID: 794489
  28. RNA sequences associated with proteins L1, L9, and L5, L18, L25, in ribonucleoprotein fragments isolated from the 50-S subunit of Escherichia coli ribosomes.
    Eur J Biochem. 1976 Nov 15;70(2):483-92 PMID: 827440
  29. A micromethod for base analysis of 32P-labeled oligoribonulcleotides.
    Anal Biochem. 1977 Nov;83(1):222-7 PMID: 920941
  30. Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin-Dahlem, GFR.
    Nucleic Acids Res. 1979;6(5):1775-90 PMID: 377231
  31. Protection of specific sites in 23 S and 5 S RNA from chemical modification by association of 30 S and 50 S ribosomes.
    J Mol Biol. 1979 Jun 5;130(4):421-32 PMID: 384002
  32. Structure of 5 S ribosomal RNA from Escherichia coli: identification of kethoxal-reactive sites in the A and B conformations.
    J Mol Biol. 1979 Aug 25;132(4):621-36 PMID: 393828
  33. Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA.
    J Mol Biol. 1979 Aug 25;132(4):637-48 PMID: 393829
  34. Topography of RNA in the ribosome: location of the 3'-end of 5 S RNA on the central protuberance of the 50 S subunit.
    FEBS Lett. 1980 Nov 17;121(1):97-100 PMID: 7007079
  35. A "bulged" double helix in a RNA-protein contact site.
    Proc Natl Acad Sci U S A. 1981 Dec;78(12):7331-5 PMID: 7038676
  36. A structural model of 5S RNA from E. coli based on intramolecular crosslinking evidence.
    Nucleic Acids Res. 1982 Feb 25;10(4):1257-69 PMID: 7041089
  37. Chemical crosslinking of elongation factor G to the 23S RNA in 70S ribosomes from Escherichia coli.
    Nucleic Acids Res. 1983 Jul 25;11(14):4923-32 PMID: 6348702
  38. Nuclease protection analysis of ribonucleoprotein complexes: use of the cytotoxic ribonuclease alpha-sarcin to determine the binding sites for Escherichia coli ribosomal proteins L5, L18, and L25 on 5S rRNA.
    Proc Natl Acad Sci U S A. 1984 Jan;81(2):322-6 PMID: 6364140
  39. Escherichia coli 5S RNA A and B conformers. Characterisation by enzymatic and chemical methods.
    Eur J Biochem. 1984 Oct 1;144(1):25-34 PMID: 6207022
  40. Topography of RNA in the ribosome: location of the 5 S RNA residues A39 and U40 on the central protuberance of the 50 S subunit.
    FEBS Lett. 1985 Jun 3;185(1):57-62 PMID: 2581815
  41. 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
  42. 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
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/26.11.2519
Published
1998-06-01
Pages
2519-25
Language
English
Region
England
NLM ID
0411011
PMCID
PMC147597
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/26.11.2519 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