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. 1976 Aug;3(8):1883–1902. doi: 10.1093/nar/3.8.1883

Evidence that 16S RNA from E. coli can assume two different biologically active conformations.

H K Hochkeppel, G R Craven
PMCID: PMC343047  PMID: 787927

Abstract

We have recently shown that 16S RNA can be extracted from 30S ribosomes by an acetic acid-urea precipitation procedure which yields RNA capable of binding 13 individual ribosomal proteins. This is in contrast to phenol extracted 16S RNA which can specifically associate with only 7 proteins2-7. In the experiments reported here, we demonstrate that the difference in protein binding capacities is due to a relatiely more "open" configuration possessed by the acetic acid-urea 16S RNA. Under identical conditions, acetic acid-urea 16S RNA is more susceptible to limited T1-RNase digestion than is phenol-16S RNA. In addition, acetic acid-urea RNA shows a relatively slower electrophoretic mobility. The observable difference in conformation between the two types of RNA is lost by storage at-70 degrees C. This loss is accompanied by a reduction in protein binding capacity of the acetic acid-urea 16S RNA.

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Selected References

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

  1. Cox R. A. The secondary structure of ribosomal ribonucleic acid in solution. Biochem J. 1966 Mar;98(3):841–857. doi: 10.1042/bj0980841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Craven G. R., Gupta V. Three-dimensional organization of the 30S ribosomal proteins from Escherichia coli. I. Preliminary classification of the proteins. Proc Natl Acad Sci U S A. 1970 Nov;67(3):1329–1336. doi: 10.1073/pnas.67.3.1329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dingman C. W., Peacock A. C. Analytical studies on nuclear ribonucleic acid using polyacrylamide gel electrophoresis. Biochemistry. 1968 Feb;7(2):659–668. doi: 10.1021/bi00842a022. [DOI] [PubMed] [Google Scholar]
  4. Ehresmann C., Fellner P., Ebel J. P. Nucleotide sequences of sections of 16S ribosomal RNA. Nature. 1970 Sep 26;227(5265):1321–1323. doi: 10.1038/2271321a0. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Ginzburg I., Miskin R., Zamir A. N-ethyl maleimide as a probe for the study of functional sites and conformations of 30 S ribosomal subunits. J Mol Biol. 1973 Sep 25;79(3):481–494. doi: 10.1016/0022-2836(73)90400-2. [DOI] [PubMed] [Google Scholar]
  7. Hardy S. J., Kurland C. G., Voynow P., Mora G. The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry. 1969 Jul;8(7):2897–2905. doi: 10.1021/bi00835a031. [DOI] [PubMed] [Google Scholar]
  8. Held W. A., Ballou B., Mizushima S., Nomura M. Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem. 1974 May 25;249(10):3103–3111. [PubMed] [Google Scholar]
  9. Hochkeppel H. K., Spicer E., Craven G. R. A method of preparing Escherichia coli 16 S RNA possessing previously unobserved 30 S ribosomal protein binding sites. J Mol Biol. 1976 Feb 25;101(2):155–170. doi: 10.1016/0022-2836(76)90369-7. [DOI] [PubMed] [Google Scholar]
  10. LEBOY P. S., COX E. C., FLAKS J. G. THE CHROMOSOMAL SITE SPECIFYING A RIBOSOMAL PROTEIN IN ESCHERICHIA COLI. Proc Natl Acad Sci U S A. 1964 Dec;52:1367–1374. doi: 10.1073/pnas.52.6.1367. [DOI] [PMC free article] [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. Morris D. R., Dahlberg J. E., Dahlberg A. E. Detection of cation-specific conformational changes in ribosomal RNA by gel electrophoresis. Nucleic Acids Res. 1974 Oct;1(10):1249–1258. doi: 10.1093/nar/1.10.1249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Rice R. H., Means G. E. Radioactive labeling of proteins in vitro. J Biol Chem. 1971 Feb 10;246(3):831–832. [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. Traub P., Nomura M. Structure and function of Escherichia coli ribosomes. VI. Mechanism of assembly of 30 s ribosomes studied in vitro. J Mol Biol. 1969 Mar 28;40(3):391–413. doi: 10.1016/0022-2836(69)90161-2. [DOI] [PubMed] [Google Scholar]
  17. Voynow P., Kurland C. G. Stoichiometry of the 30S ribosomal proteins of Escherichia coli. Biochemistry. 1971 Feb 2;10(3):517–524. doi: 10.1021/bi00779a026. [DOI] [PubMed] [Google Scholar]
  18. Wittmann H. G., Stöfflet G., Hindennach I., Kurland C. G., Birge E. A., Randall-Hazelbauer L., Nomura M., Kaltschmidt E., Mizushima S., Traut R. R. Correlation of 30S ribosomal proteins of Escherichia coli isolated in different laboratories. Mol Gen Genet. 1971;111(4):327–333. doi: 10.1007/BF00569784. [DOI] [PubMed] [Google Scholar]
  19. Zamir A., Miskin R., Elson D. Inactivation and reactivation of ribosomal subunits: amino acyl-transfer RNA binding activity of the 30 s subunit of Escherichia coli. J Mol Biol. 1971 Sep 14;60(2):347–364. doi: 10.1016/0022-2836(71)90299-3. [DOI] [PubMed] [Google Scholar]

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