Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1978 Jun;75(6):2859–2863. doi: 10.1073/pnas.75.6.2859

Conservation of ribosomal protein binding sites in prokaryotic 16S RNAs.

D L Thurlow, R A Zimmermann
PMCID: PMC392664  PMID: 351619

Abstract

The Escherichia coli 30S ribosomal subunit proteins S4, S7, S8, S15, S17, and S20 that interact independently with 16S RNA from E. coli formed specific heterologous complexes with 16S RNAs extracted from 11 different prokaryotes covering a broad phylogenetic range. Complex formation was shown to be specific by saturation of binding in the presence of excess protein. Binding stoichiometries and the apparent affinities for a given protein varied depending on which 16S RNA was used, although the pattern of binding was not strictly correlated with phylogenetic relationships. The size-distribution of fragments resulting from limited hydrolysis of free prokaryotic 16S RNAs with T1 and pancreatic ribonucleases indicated that the structural organization of 16S RNA from E. coli is similar to that of 16S RNAs from closely related species, but differs, although to an unknown extent, from that of 16S RNAs from other prokaryotes tested. Digestions of RNA-protein complexes under similar conditions indicated that the proteins remain bound to specific RNA fragments. For those 16S RNAs isolated from species closely related to E. coli, the fragments were comparable to those generated by hydrolysis of the homologous complex.

Full text

PDF
2860

Selected References

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

  1. Cammack K. A., Wade H. E. The sedimentation behaviour of ribonuclease-active and -inactive ribosomes from bacteria. Biochem J. 1965 Sep;96(3):671–680. doi: 10.1042/bj0960671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Daya-Grosjean L., Geisser M., Stöffler G., Garret R. A. Heterologous protein-RNA interactions in bacterial ribosomes. FEBS Lett. 1973 Nov 15;37(1):17–20. doi: 10.1016/0014-5793(73)80416-8. [DOI] [PubMed] [Google Scholar]
  3. Dickerson R. E., Timkovich R., Almassy R. J. The cytochrome fold and the evolution of bacterial energy metabolism. J Mol Biol. 1976 Feb 5;100(4):473–491. doi: 10.1016/s0022-2836(76)80041-1. [DOI] [PubMed] [Google Scholar]
  4. Ehresmann B., Backendorf C., Ehresmann C., Ebel J. P. Characterization of the regions from E. coli 16 S RNA covalently linked to ribosomal proteins S4 and S20 after ultraviolet irradiation. FEBS Lett. 1977 Jun 15;78(2):261–266. doi: 10.1016/0014-5793(77)80319-0. [DOI] [PubMed] [Google Scholar]
  5. Ehresmann C., Stiegler P., Fellner P., Ebel J. P. The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. III. Further studies. Biochimie. 1975;57(6-7):711–748. doi: 10.1016/s0300-9084(75)80047-2. [DOI] [PubMed] [Google Scholar]
  6. Fischel J. L., Krol A., Ehresmann C., Fellner P., Ebel J. P. Comparative study of the 16S RNA's of Escherichia coli and Proteus vulgaris. Biochimie. 1975;57(8):885–897. doi: 10.1016/s0300-9084(75)80211-2. [DOI] [PubMed] [Google Scholar]
  7. Garrett R. A., Rak K. H., Daya L., Stöffler G. Ribosomal proteins. XXIX. Specific protein binding sites on 16S rRNA of Escherichia coli. Mol Gen Genet. 1972;114(2):112–124. doi: 10.1007/BF00332782. [DOI] [PubMed] [Google Scholar]
  8. Geisser M., Mackie G. A. The binding site of Escherichia coli ribosomal protein S4 on 16-S ribosomal RNA from different bacterial species. Eur J Biochem. 1976 Nov 1;70(1):159–170. doi: 10.1111/j.1432-1033.1976.tb10966.x. [DOI] [PubMed] [Google Scholar]
  9. Hori H. Molecular evolution of 5S RNA. Mol Gen Genet. 1976 May 7;145(2):119–123. doi: 10.1007/BF00269583. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Mizushima S., Nomura M. Assembly mapping of 30S ribosomal proteins from E. coli. Nature. 1970 Jun 27;226(5252):1214–1214. doi: 10.1038/2261214a0. [DOI] [PubMed] [Google Scholar]
  12. Muto A., Ehresmann C., Fellner P., Zimmermann R. A. RNA-protein interactions in the ribosome. I. Characterization and ribonuclease digestion of 16 S RNA-ribosomal protein complexes. J Mol Biol. 1974 Jun 25;86(2):411–432. doi: 10.1016/0022-2836(74)90028-x. [DOI] [PubMed] [Google Scholar]
  13. Nomura M., Traub P., Bechmann H. Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins. Nature. 1968 Aug 24;219(5156):793–799. doi: 10.1038/219793b0. [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. Schaup H. W., Green M., Kurland C. G. Molecular interactions of ribosomal components. II. Site-specific complex formation between 30S proteins and ribosomal RNA. Mol Gen Genet. 1971;112(1):1–8. doi: 10.1007/BF00266926. [DOI] [PubMed] [Google Scholar]
  16. Schaup H. W., Sogin M. L., Kurland C. G., Woese C. R. Localization of a binding site for ribosomal protein S8 within the 16S ribosomal ribonucleic acid of Escherichia coli. J Bacteriol. 1973 Jul;115(1):82–87. doi: 10.1128/jb.115.1.82-87.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Schaup H. W., Sogin M., Woese C. Characterization of an RNA "binding site" for a specific ribosomal protein of Escherichia coli. Mol Gen Genet. 1972;114(1):1–8. doi: 10.1007/BF00268740. [DOI] [PubMed] [Google Scholar]
  18. Spicer E., Schwarzbauer J., Craven G. R. Isolation of ribosomal protein-RNA complexes by nitrocellulose membrane filtration: equilibrium binding studies. Nucleic Acids Res. 1977 Feb;4(2):491–499. doi: 10.1093/nar/4.2.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stanley J., Ebel J. P. The binding site of ribosomal protein s8 on the 16-S ribosomal RNA from Bacillus stearothermophilus. Eur J Biochem. 1977 Jul 15;77(2):357–366. doi: 10.1111/j.1432-1033.1977.tb11675.x. [DOI] [PubMed] [Google Scholar]
  20. Traub P., Nomura M. Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins. Proc Natl Acad Sci U S A. 1968 Mar;59(3):777–784. doi: 10.1073/pnas.59.3.777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Ungewickell E., Garrett R., Ehresmann C., Stiegler P., Fellner P. An investigation of the 16-S RNA binding sites of ribosomal proteins S4, S8, S15, and S20 FROM Escherichia coli. Eur J Biochem. 1975 Feb 3;51(1):165–180. doi: 10.1111/j.1432-1033.1975.tb03917.x. [DOI] [PubMed] [Google Scholar]
  23. Woese C. R., Fox G. E., Zablen L., Uchida T., Bonen L., Pechman K., Lewis B. J., Stahl D. Conservation of primary structure in 16S ribosomal RNA. Nature. 1975 Mar 6;254(5495):83–86. doi: 10.1038/254083a0. [DOI] [PubMed] [Google Scholar]
  24. Woese C. R., Sogin M. L., Bonen L., Stahl D. Sequence studies on 16S ribosomal RNA from a blue-green alga. J Mol Evol. 1975 Mar 24;4(4):307–315. doi: 10.1007/BF01732533. [DOI] [PubMed] [Google Scholar]
  25. Woese C. R., Sogin M. L., Sutton L. A. Procaryote phylogeny. I. Concerning the relatedness of Aerobacter aerogenes to Escherichia coli. J Mol Evol. 1974;3(4):293–299. doi: 10.1007/BF01796044. [DOI] [PubMed] [Google Scholar]
  26. Woese C., Sogin M., Stahl D., Lewis B. J., Bonen L. A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: some modifications in the Sanger method for RNA sequencing. J Mol Evol. 1976 Apr 9;7(3):197–213. doi: 10.1007/BF01731489. [DOI] [PubMed] [Google Scholar]
  27. Zimmermann R. A., Mackie G. A., Muto A., Garrett R. A., Ungewickell E., Ehresmann C., Stiegler P., Ebel J. P., Fellner P. Location and characteristics of ribosomal protein binding sites in the 16S RNA of Escherichia coli. Nucleic Acids Res. 1975 Feb;2(2):279–302. doi: 10.1093/nar/2.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Zimmermann R. A., Muto A., Fellner P., Ehresmann C., Branlant C. Location of ribosomal protein binding sites on 16S ribosomal RNA. Proc Natl Acad Sci U S A. 1972 May;69(5):1282–1286. doi: 10.1073/pnas.69.5.1282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Zimmermann R. A., Muto A., Mackie G. A. RNA-protein interactions in the ribosome. II. Binding of ribosomal proteins to isolated fragments of the 16 S RNA. J Mol Biol. 1974 Jun 25;86(2):433–450. doi: 10.1016/0022-2836(74)90029-1. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES