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. 1978 Aug;5(8):2705–2720. doi: 10.1093/nar/5.8.2705

Evidence for RNA-RNA cross-link formation in Escherichia coli ribosomes.

C Zwieb, A Ross, J Rinke, M Meinke, R Brimacombe
PMCID: PMC342201  PMID: 358146

Abstract

Evidence is presented in three separate cases for the formation of RNA-RNA cross-links in intact E. coli ribosomes and ribosomal subunits. The first case is a cross-link between the 18S and 13S regions of the 23S RNA, induced by ultraviolet irradiation. The second is a cross-link at the subunit interface, generated by the bifunctional reagent bis-(2-chloroethyl)-amine. The third example is a cross-link between sections O'-D and P-A of the 16S RNA, induced as in the first case by ultraviolet irradiation. The RNA-RNA cross-links can be identified as such, despite the complications introduced by concomitant RNA-protein cross-linking reactions. The experiments represent a first attempt to introduce RNA-RNA cross-linking into studies of the topographical organization of the RNA within the ribosome.

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Selected References

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  1. Allet B., Spahr P. F. Binding sites of ribosomal proteins on two specific fragments derived from Escherichia coli 50 S ribosomes. Eur J Biochem. 1971 Mar 11;19(2):250–255. doi: 10.1111/j.1432-1033.1971.tb01311.x. [DOI] [PubMed] [Google Scholar]
  2. Dohme F., Nierhaus K. H. Role of 5S RNA in assembly and function of the 50S subunit from Escherichia coli. Proc Natl Acad Sci U S A. 1976 Jul;73(7):2221–2225. doi: 10.1073/pnas.73.7.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ehresmann C., Stiegler P., Carbon P., Ebel J. P. Recent progress in the determination of the primary sequence of the 16 S RNA of Escherichia coli. FEBS Lett. 1977 Dec 15;84(2):337–341. doi: 10.1016/0014-5793(77)80720-5. [DOI] [PubMed] [Google Scholar]
  4. Herr W., Noller H. F. Nucleotide sequences of accessible regions of 23S RNA in 50S ribosomal subunits. Biochemistry. 1978 Jan 24;17(2):307–315. doi: 10.1021/bi00595a018. [DOI] [PubMed] [Google Scholar]
  5. Mackie G. A., Zimmermann R. A. Characterization of fragments of 16 S ribonucleic acid protected against pancreatic ribonuclease digestion by ribosomal protein S4. J Biol Chem. 1975 Jun 10;250(11):4100–4112. [PubMed] [Google Scholar]
  6. Malbon R. M., Parish J. H. Fractions of RNA and ribonucleoprotein from bacterial polysomes. II. Reactions with sulphur mustard. Biochim Biophys Acta. 1971 Sep 24;246(3):542–552. doi: 10.1016/0005-2787(71)90791-x. [DOI] [PubMed] [Google Scholar]
  7. Mets L. J., Bogorad L. Two-dimensional polyacrylamide gel electrophoresis: an improved method for ribosomal proteins. Anal Biochem. 1974 Jan;57(1):200–210. doi: 10.1016/0003-2697(74)90065-7. [DOI] [PubMed] [Google Scholar]
  8. Morgan J., Brimacombe R. A series of specific ribonucleoprotein fragments from the 30-S subparticle of Escherichia coli ribosomes. Eur J Biochem. 1972 Sep 25;29(3):542–552. doi: 10.1111/j.1432-1033.1972.tb02020.x. [DOI] [PubMed] [Google Scholar]
  9. Möller K., Brimacombe R. Specific cross-linking of proteins S7 and L4 to ribosomal RNA, by UV irradiation of Escherichia coli ribosomal subunits. Mol Gen Genet. 1975 Dec 9;141(4):343–355. doi: 10.1007/BF00331455. [DOI] [PubMed] [Google Scholar]
  10. Möller K., Rinke J., Ross A., Buddle G., Brimacombe R. The use of formaldehyde in RNA-protein cross-linking studies with ribosomal subunits from Escherichia coli. Eur J Biochem. 1977 Jun 1;76(1):175–187. doi: 10.1111/j.1432-1033.1977.tb11583.x. [DOI] [PubMed] [Google Scholar]
  11. Newton I., Brimacombe R. Two specific ribonucleoprotein fragments from the 50-S sub-particle of Escherichia coli ribosomes. Eur J Biochem. 1974 Oct 2;48(2):513–518. doi: 10.1111/j.1432-1033.1974.tb03792.x. [DOI] [PubMed] [Google Scholar]
  12. Nolan J. C., Hartman K. A. RNase catalyzed hydrolysis of ribosomes in several functional states. Biochem Biophys Res Commun. 1973 Oct 1;54(3):1216–1223. doi: 10.1016/0006-291x(73)90822-x. [DOI] [PubMed] [Google Scholar]
  13. Rinke J., Ross A., Brimacombe R. Characterisation of RNA fragments obtained by mild nuclease digestion of 30-S ribosomal subunits from Escherichia coli. Eur J Biochem. 1977 Jun 1;76(1):189–196. doi: 10.1111/j.1432-1033.1977.tb11584.x. [DOI] [PubMed] [Google Scholar]
  14. 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. doi: 10.1111/j.1432-1033.1976.tb10276.x. [DOI] [PubMed] [Google Scholar]
  15. Sanger F., Brownlee G. G., Barrell B. G. A two-dimensional fractionation procedure for radioactive nucleotides. J Mol Biol. 1965 Sep;13(2):373–398. doi: 10.1016/s0022-2836(65)80104-8. [DOI] [PubMed] [Google Scholar]
  16. Santer M., Santer U. Action of ribonuclease T1 on 30S ribosomes of Escherichia coli and its role in sequence studies on 16S ribonucleic acid. J Bacteriol. 1973 Dec;116(3):1304–1313. doi: 10.1128/jb.116.3.1304-1313.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Uchida T., Bonen L., Schaup H. W., Lewis B. J., Zablen L., Woese C. The use of ribonuclease U2 in RNA sequence determination. Some corrections in the catalog of oligomers produced by ribonuclease T1 digestion of Escherichia coli 16S ribosomal RNA. J Mol Evol. 1974 Feb 28;3(1):63–77. doi: 10.1007/BF01795977. [DOI] [PubMed] [Google Scholar]
  18. Ulmer E., Meinke M., Ross A., Fink G., Brimacombe R. Chemical cross-linking of protein to RNA within intact ribosomal subunits from Escherichia coli. Mol Gen Genet. 1978 Apr 6;160(2):183–193. doi: 10.1007/BF00267480. [DOI] [PubMed] [Google Scholar]
  19. Ungewickell E., Ehresmann C., Stiegler P., Garrett R. Evidence for tertiary structural RNA-RNA interactions within the protein S4 binding site at the 5'-end of 16S ribosomal RNA of Escherichia coli.+. Nucleic Acids Res. 1975 Oct;2(10):1867–1888. doi: 10.1093/nar/2.10.1867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Van Duin J., Kurland C. G., Dondon J., Grunberg-Mangago M., Branlant C., Ebel J. P. New aspects of the IF3-ribosome interaction. FEBS Lett. 1976 Feb 15;62(2):111–114. doi: 10.1016/0014-5793(76)80030-0. [DOI] [PubMed] [Google Scholar]
  21. 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. doi: 10.1111/j.1432-1033.1975.tb02203.x. [DOI] [PubMed] [Google Scholar]
  22. Zwieb C., Brimacombe R. RNA-protein cross-linking in Eschericia coli 30S ribosomal subunits: a method for the direct analysis of the RNA regions involved in the cross-links. Nucleic Acids Res. 1978 Apr;5(4):1189–1206. doi: 10.1093/nar/5.4.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]

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