Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1975 Feb;2(2):265–278. doi: 10.1093/nar/2.2.265

Primary sequence of the 16S ribosomal RNA of Escherichia coli.

C Ehresmann, P Stiegler, G A Mackie, R A Zimmermann, J P Ebel, P Fellner
PMCID: PMC342831  PMID: 1091918

Abstract

Recent progress in the nucleotide sequence analysis of the 16S ribosomal RNA from E. coli is described. The sequence which has been partially or completely determined so far encompasses 1520 nucleotides, i.e. about 95% of the molecule. Possible features of the secondary structure are suggested on the basis of the nucleotide sequence and data on sequence heterogeneities, repetitions and the location of modified nucleotides are presented. In the accompanying paper, the use of the nucleotide sequence data in studies of the ribosomal protein binding sites is described.

Full text

PDF
265

Selected References

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

  1. ARONSON A. I., HOLOWCZYK M. A. COMPOSITION OF BACTERIAL RIBOSOMAL RNA. HETEROGENEITY WITHIN A GIVEN ORGANISM. Biochim Biophys Acta. 1965 Feb 8;95:217–231. doi: 10.1016/0005-2787(65)90487-9. [DOI] [PubMed] [Google Scholar]
  2. Adesnik M., Levinthal C. Synthesis and maturation of ribosomal RNA in Escherichia coli. J Mol Biol. 1969 Dec 14;46(2):281–303. doi: 10.1016/0022-2836(69)90422-7. [DOI] [PubMed] [Google Scholar]
  3. Attardi G., Huang P. C., Kabat S. Recognition of ribosomal RNA sites in DNA. I. Analysis of the E. coli system. Proc Natl Acad Sci U S A. 1965 Jun;53(6):1490–1498. doi: 10.1073/pnas.53.6.1490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Avery R. J., Midgley J. E., Pigott G. H. An analysis of the ribosomal ribonucleic acids of Escherichia coli by hybridization techniques. Biochem J. 1969 Nov;115(3):395–403. doi: 10.1042/bj1150395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brownlee G. G., Sanger F., Barrell B. G. Nucleotide sequence of 5S-ribosomal RNA from Escherichia coli. Nature. 1967 Aug 12;215(5102):735–736. doi: 10.1038/215735a0. [DOI] [PubMed] [Google Scholar]
  6. Cotter R. I., McPhie P., Gratzer W. B. Internal organization of the ribosome. Nature. 1967 Dec 2;216(5118):864–868. doi: 10.1038/216864a0. [DOI] [PubMed] [Google Scholar]
  7. Cox R. A., Bonanou S. A. A possible structure of the rabbit reticulocyte ribosome. An exercise in model building. Biochem J. 1969 Oct;114(4):769–774. doi: 10.1042/bj1140769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cox R. A., Pratt H., Huvos P., Higginson B., Hirst W. A study of the thermal stability of ribosomes and biologically active subribosomal particles. Biochem J. 1973 Jul;134(3):775–793. doi: 10.1042/bj1340775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Cramer F., Erdmann V. A. Amount of adenine and uracil base pairs in E. coli 23S, 16S and 5S ribosomal RNA. Nature. 1968 Apr 6;218(5136):92–93. doi: 10.1038/218092a0. [DOI] [PubMed] [Google Scholar]
  11. Dahlberg A. E., Dingman C. W., Peacock A. C. Electrophoretic characterization of bacterial polyribosomes in agarose-acrylamide composite gels. J Mol Biol. 1969 Apr 14;41(1):139–147. doi: 10.1016/0022-2836(69)90131-4. [DOI] [PubMed] [Google Scholar]
  12. Doty P., Boedtker H., Fresco J. R., Haselkorn R., Litt M. SECONDARY STRUCTURE IN RIBONUCLEIC ACIDS. Proc Natl Acad Sci U S A. 1959 Apr;45(4):482–499. doi: 10.1073/pnas.45.4.482. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ehresmann C., Stiegler P., Fellner P., Ebel J. P. The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. 2. Nucleotide sequences of products from partial enzymatic hydrolysis. Biochimie. 1972;54(7):901–967. doi: 10.1016/s0300-9084(72)80007-5. [DOI] [PubMed] [Google Scholar]
  14. FRESCO J. R., ALBERTS B. M., DOTY P. Some molecular details of the secondary structure of ribonucleic acid. Nature. 1960 Oct 8;188:98–101. doi: 10.1038/188098a0. [DOI] [PubMed] [Google Scholar]
  15. Fellner P., Ebel J. P., Blasi O. The 3'-terminal nucleotide sequence of the 23 S ribosomal RNA from Escherichia coli. FEBS Lett. 1970 Jan 26;6(2):102–104. doi: 10.1016/0014-5793(70)80012-6. [DOI] [PubMed] [Google Scholar]
  16. Fellner P., Ebel J. P. Observations on the primary structure of the 23S ribosomal RNA from E. coli. Nature. 1970 Mar 21;225(5238):1131–1132. doi: 10.1038/2251131a0. [DOI] [PubMed] [Google Scholar]
  17. Fellner P., Ehresmann C., Ebel J. P. Nucleotide sequences present within the 16S ribosomal RNA of Escherichia coli. Nature. 1970 Jan 3;225(5227):26–29. doi: 10.1038/225026a0. [DOI] [PubMed] [Google Scholar]
  18. Fellner P., Ehresmann C., Ebel J. P. The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. 1. Nucleotide sequence analysis of T 1 and pancreatic ribonuclease digestion products. Biochimie. 1972;54(7):853–900. doi: 10.1016/s0300-9084(72)80006-3. [DOI] [PubMed] [Google Scholar]
  19. Fellner P., Sanger F. Sequence analysis of specific areas of the 16S and 23S ribosomal RNAs. Nature. 1968 Jul 20;219(5151):236–238. doi: 10.1038/219236a0. [DOI] [PubMed] [Google Scholar]
  20. Hecht N. B., Woese C. R. Separation of bacterial ribosomal ribonucleic acid from its macromolecular precursors by polyacrylamide gel electrophoresis. J Bacteriol. 1968 Mar;95(3):986–990. doi: 10.1128/jb.95.3.986-990.1968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Helser T. L., Davies J. E., Dahlberg J. E. Mechanism of kasugamycin resistance in Escherichia coli. Nat New Biol. 1972 Jan 5;235(53):6–9. doi: 10.1038/newbio235006a0. [DOI] [PubMed] [Google Scholar]
  22. Jarry B., Rosset R. Heterogeneity of 5S RNA in Escherichia coli. Mol Gen Genet. 1971;113(1):43–50. doi: 10.1007/BF00335006. [DOI] [PubMed] [Google Scholar]
  23. Mangiarotti G., Apirion D., Schlessinger D., Silengo L. Biosynthetic precursors of 30S and 50S ribosomal particles in Escherichia coli. Biochemistry. 1968 Jan;7(1):456–472. doi: 10.1021/bi00841a058. [DOI] [PubMed] [Google Scholar]
  24. McIlreavy D. J., Midgley J. E. The chemical structure of bacterial ribosomal RNA. I. Terminal nucleotide sequences of Escherichia coli ribosomal RNA. Biochim Biophys Acta. 1967 Jun 20;142(1):47–64. doi: 10.1016/0005-2787(67)90514-x. [DOI] [PubMed] [Google Scholar]
  25. Midgley J. E. The estimation of polynucleotide chain length by a chemical method. Biochim Biophys Acta. 1965 Nov 8;108(3):340–347. doi: 10.1016/0005-2787(65)90026-2. [DOI] [PubMed] [Google Scholar]
  26. Min Jou W., Haegeman G., Ysebaert M., Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature. 1972 May 12;237(5350):82–88. doi: 10.1038/237082a0. [DOI] [PubMed] [Google Scholar]
  27. Muto A. Nucleotide distribution of Escherichia coli 16S ribosomal ribonucleic acid. Biochemistry. 1970 Sep 15;9(19):3683–3694. doi: 10.1021/bi00821a006. [DOI] [PubMed] [Google Scholar]
  28. Noller H. F. Topography of 16S RNA in 30S ribosomal subunits. Nucleotide sequences and location of sites of reaction with kethoxal. Biochemistry. 1974 Nov 5;13(23):4694–4703. doi: 10.1021/bi00720a003. [DOI] [PubMed] [Google Scholar]
  29. Nomura M. Assembly of bacterial ribosomes. Science. 1973 Mar 2;179(4076):864–873. doi: 10.1126/science.179.4076.864. [DOI] [PubMed] [Google Scholar]
  30. Ortega J. P., Hill W. E. A molecular weight determination of the 16S ribosomal ribonucleic acid from Escherichia coli. Biochemistry. 1973 Aug 14;12(17):3241–3243. doi: 10.1021/bi00741a015. [DOI] [PubMed] [Google Scholar]
  31. STARR J. L., FEFFERMAN R. THE OCCURRENCE OF METHYLATED BASES IN RIBOSOMAL RIBONUCLEIC ACID OF ESCHERICHIA COLI K12 W-6. J Biol Chem. 1964 Oct;239:3457–3461. [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. Santer U. V., Santer M. The sequence of the 3'-OH end of the 16 S RNA of Escherichia coli. FEBS Lett. 1972 Apr 1;21(3):311–314. doi: 10.1016/0014-5793(72)80191-1. [DOI] [PubMed] [Google Scholar]
  35. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Spadari S., Ritossa F. Clustered genes for ribosomal ribonucleic acids in Escherichia coli. J Mol Biol. 1970 Nov 14;53(3):357–367. doi: 10.1016/0022-2836(70)90071-9. [DOI] [PubMed] [Google Scholar]
  37. Stanley W. M., Jr, Bock R. M. Isolation and physical properties of the ribosomal ribonucleic acid of Escherichia coli. Biochemistry. 1965 Jul;4(7):1302–1311. doi: 10.1021/bi00883a014. [DOI] [PubMed] [Google Scholar]
  38. Takanami M. Analysis of the 5'-terminal nucleotide sequences of ribonucleic acids 1. the 5'-termini of Excherichia coli ribosomal RNA. J Mol Biol. 1967 Jan 28;23(2):135–148. doi: 10.1016/s0022-2836(67)80022-6. [DOI] [PubMed] [Google Scholar]
  39. Tinoco I., Jr, Uhlenbeck O. C., Levine M. D. Estimation of secondary structure in ribonucleic acids. Nature. 1971 Apr 9;230(5293):362–367. doi: 10.1038/230362a0. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. Young R. J. The fractionation of quaternary ammonium complexes of nucleic acids. Evidence for heterogeneity of ribosomal ribonucleic acid. Biochemistry. 1968 Jun;7(6):2263–2272. doi: 10.1021/bi00846a032. [DOI] [PubMed] [Google Scholar]
  42. 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]

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

RESOURCES