Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 Jan 24;14(2):659–673. doi: 10.1093/nar/14.2.659

The tertiary folding of Escherichia coli 16S RNA, as studied by in situ intra-RNA cross-linking of 30S ribosomal subunits with bis-(2-chloroethyl)-methylamine.

J Atmadja, W Stiege, M Zobawa, B Greuer, M Osswald, R Brimacombe
PMCID: PMC339456  PMID: 2418415

Abstract

Intra-RNA cross-links were introduced into E. coli 30S ribosomal subunits by treatment with bis-(2-chloroethyl)methylamine. The subunits were partially digested with cobra venom nuclease, and the cross-linked complexes were separated by two-dimensional electrophoresis and analysed according to our published procedures. Tertiary structural cross-links in the 16S RNA were identified between nucleotides 31 and 306, and between the tetranucleotide 693-696 and nucleotides 794 or 799. Secondary structural cross-links, lying at the ends of double-helical regions, were found between nucleotides 46 and the trinucleotide 362-364, and between the dinucleotide 148-149 and nucleotide 174. Cross-links within double-helical elements were identified between the tetranucleotide 128-131 and nucleotide 232, between nucleotide 250 and the dinucleotide 274-275, and between nucleotides 1413 and 1486. Adenine as well as guanine residues were involved in the cross-links.

Full text

PDF
659

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Atmadja J., Brimacombe R., Blöcker H., Frank R. Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits. Nucleic Acids Res. 1985 Oct 11;13(19):6919–6936. doi: 10.1093/nar/13.19.6919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. doi: 10.1073/pnas.75.10.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Carbon P., Ehresmann C., Ehresmann B., Ebel J. P. 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. doi: 10.1111/j.1432-1033.1979.tb04183.x. [DOI] [PubMed] [Google Scholar]
  4. Expert-Bezançon A., Milet M., Carbon P. Precise localization of several covalent RNA-RNA cross-link in Escherichia coli 16S RNA. Eur J Biochem. 1983 Nov 2;136(2):267–274. doi: 10.1111/j.1432-1033.1983.tb07737.x. [DOI] [PubMed] [Google Scholar]
  5. Glotz C., Zwieb C., Brimacombe R., Edwards K., Kössel H. 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):3287–3306. doi: 10.1093/nar/9.14.3287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Maly P., Brimacombe R. Refined secondary structure models for the 16S and 23S ribosomal RNA of Escherichia coli. Nucleic Acids Res. 1983 Nov 11;11(21):7263–7286. doi: 10.1093/nar/11.21.7263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Noller H. F. Structure of ribosomal RNA. Annu Rev Biochem. 1984;53:119–162. doi: 10.1146/annurev.bi.53.070184.001003. [DOI] [PubMed] [Google Scholar]
  8. Stiege W., Glotz C., Brimacombe R. 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):1687–1706. doi: 10.1093/nar/11.6.1687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Stiege W., Zwieb C., Brimacombe R. Precise localisation of three intra-RNA cross-links in 23S RNA and one in 5S RNA, induced by treatment of Escherichia coli 50S ribosomal subunits with bis-(2-chloroethyl)-methylamine. Nucleic Acids Res. 1982 Nov 25;10(22):7211–7229. doi: 10.1093/nar/10.22.7211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Thompson J. F., Hearst J. E. Structure of E. coli 16S RNA elucidated by psoralen crosslinking. Cell. 1983 Apr;32(4):1355–1365. doi: 10.1016/0092-8674(83)90316-1. [DOI] [PubMed] [Google Scholar]
  11. Vasilenko S. K., Ryte V. C. [Isolation of highly purified ribonuclease from cobra (Naja oxiana) venom]. Biokhimiia. 1975 May-Jun;40(3):578–583. [PubMed] [Google Scholar]
  12. Vassilenko S. K., Carbon P., Ebel J. P., Ehresmann C. Topography of 16 S RNA in 30 S subunits and 70 S ribosomes accessibility to cobra venom ribonuclease. J Mol Biol. 1981 Nov 15;152(4):699–721. doi: 10.1016/0022-2836(81)90123-6. [DOI] [PubMed] [Google Scholar]
  13. Volckaert G., Fiers W. Micro thin-layer techniques for rapid sequence analysis of 32P-labeled RNA: double digestion and pancreatic ribonuclease analyses. Anal Biochem. 1977 Nov;83(1):228–239. doi: 10.1016/0003-2697(77)90531-0. [DOI] [PubMed] [Google Scholar]
  14. Wollenzien P. L., Cantor C. R. Gel electrophoretic technique for separating crosslinked RNAs. Application to improved electron microscopic analysis of psoralen crosslinked 16 S ribosomal RNA. J Mol Biol. 1982 Jul 25;159(1):151–166. doi: 10.1016/0022-2836(82)90036-5. [DOI] [PubMed] [Google Scholar]
  15. Wollenzien P. L., Murphy R. F., Cantor C. R., Expert-Bezançon A., Hayes D. H. Structure of the Escherichia coli 16 S ribosomal RNA. Psoralen crosslinks and N-acetyl-N'-(p-glyoxylylbenzoyl)cystamine crosslinks detected by electron microscopy. J Mol Biol. 1985 Jul 5;184(1):67–80. doi: 10.1016/0022-2836(85)90044-0. [DOI] [PubMed] [Google Scholar]
  16. Zwieb C., Brimacombe R. Localisation of a series of intra-RNA cross-links in 16S RNA, induced by ultraviolet irradiation of Escherichia coli 30S ribosomal subunits. Nucleic Acids Res. 1980 Jun 11;8(11):2397–2411. doi: 10.1093/nar/8.11.2397. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES