Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1979 Feb;6(2):575–592. doi: 10.1093/nar/6.2.575

Sequence of the gene for isoleucine tRNA1 and the surrounding region in a ribosomal RNA operon of Escherichia coli

Takao Sekiya 1, Susumu Nishimura 1
PMCID: PMC327714  PMID: 370791

Abstract

A DNA fragment of about 2000 base pairs carrying the gene for tRNA1Ile has been cloned from a total Eco RI endonuclease digest of Escherichia coli DNA. Sequence analyses revealed that about the first 850 base pairs from one end of the fragment contain a nucleotide sequence corresponding to that in the 3'-end of 16S rRNA. The gene for tRNAIle follows the 16S rRNA gene and both genes flank a spacer sequence of 68 base pairs. The spacer region contains a repeating, a hair pin and a symmetrical structure when the sequence is viewed in the single stranded form. A notable hair pin structure is also observed in the region adjacent to the 3'-end of the tRNA1Ile gene. In addition, about 850 base pairs from the other end of the DNA fragment have been found to contain the nucleotide sequence of the 5'-end of 23S rRNA. The presence of the genes for tRNA1Ile, 16S and 23S rRNA and the hybridization to tRNA1Ala suggest that this cloned DNA is part of one of the E. coli rRNA operons carrying these two tRNA genes as a spacer.

Full text

PDF
575

Images in this article

579Image
on p.579
580Image
on p.580
582Image
on p.582

Selected References

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

  1. Allet B., Bukhari A. I. Analysis of bacteriophage mu and lambda-mu hybrid DNAs by specific endonucleases. J Mol Biol. 1975 Mar 15;92(4):529–540. doi: 10.1016/0022-2836(75)90307-1. [DOI] [PubMed] [Google Scholar]
  2. Altman S., Smith J. D. Tyrosine tRNA precursor molecule polynucleotide sequence. Nat New Biol. 1971 Sep 8;233(36):35–39. doi: 10.1038/newbio233035a0. [DOI] [PubMed] [Google Scholar]
  3. Bolivar F., Rodriguez R. L., Betlach M. C., Boyer H. W. Construction and characterization of new cloning vehicles. I. Ampicillin-resistant derivatives of the plasmid pMB9. Gene. 1977;2(2):75–93. doi: 10.1016/0378-1119(77)90074-9. [DOI] [PubMed] [Google Scholar]
  4. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  5. Branlant C., Ebel J. P. Studies on the primary structure of Escherichia coli 23 SRNA. Nucleotide sequence of the ribonuclease T1 digestion products containing more than one uridine residue. J Mol Biol. 1977 Apr 15;111(3):215–256. doi: 10.1016/s0022-2836(77)80050-8. [DOI] [PubMed] [Google Scholar]
  6. Branlant C., Sri Widada J., Krol A., Ebel J. P. RNA sequences in ribonucleoprotein fragments of the complex formed from ribosomal 23-S RNA and ribosomal protein L24 of Escherichia coli. Eur J Biochem. 1977 Mar 15;74(1):155–170. doi: 10.1111/j.1432-1033.1977.tb11377.x. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Carbon P., Ehresmann C., Ehresmann B., Ebel J. P. The sequence of Escherichia coli ribosomal 16 S RNA determined by new rapid gel methods. FEBS Lett. 1978 Oct 1;94(1):152–156. doi: 10.1016/0014-5793(78)80926-0. [DOI] [PubMed] [Google Scholar]
  9. Chang S., Carbon J. The nucleotide sequence of a precursor to the glycine- and threonine-specific transfer ribonucleic acids of Escherichia coli. J Biol Chem. 1975 Jul 25;250(14):5542–5555. [PubMed] [Google Scholar]
  10. Clewell D. B., Helinski D. R. Properties of a supercoiled deoxyribonucleic acid-protein relaxation complex and strand specificity of the relaxation event. Biochemistry. 1970 Oct 27;9(22):4428–4440. doi: 10.1021/bi00824a026. [DOI] [PubMed] [Google Scholar]
  11. Contreras R., Küpper H., Landy A., Khorana H. G. Escherichia coli tyrosine transfer ribonucleic acid genes. Nucleotide sequences of their promoters and of the regions adjoining C-C-A ends. J Biol Chem. 1976 Sep 10;251(17):5124–5140. [PubMed] [Google Scholar]
  12. 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]
  13. Ginsburg D., Steitz J. A. The 30 S ribosomal precursor RNA from Escherichia coli. A primary transcript containing 23 S, 16 S, and 5 S sequences. J Biol Chem. 1975 Jul 25;250(14):5647–5654. [PubMed] [Google Scholar]
  14. Ikemura T., Dahlberg J. E. Small ribonucleic acids of Escherichia coli. I. Characterization by polyacrylamide gel electrophoresis and fingerprint analysis. J Biol Chem. 1973 Jul 25;248(14):5024–5032. [PubMed] [Google Scholar]
  15. Ikemura T., Nomura M. Expression of spacer tRNA genes in ribosomal RNA transcription units carried by hybrid Col E1 plasmids in E. coli. Cell. 1977 Aug;11(4):779–793. doi: 10.1016/0092-8674(77)90291-4. [DOI] [PubMed] [Google Scholar]
  16. Ikemura T., Ozeki H. Gross map location of Escherichia coli transfer RNA genes. J Mol Biol. 1977 Dec 5;117(2):419–446. doi: 10.1016/0022-2836(77)90136-x. [DOI] [PubMed] [Google Scholar]
  17. Küpper H., Sekiya T., Rosenberg M., Egan J., Landy A. A rho-dependent termination site in the gene coding for tyrosine tRNA su3 of Escherichia coli. Nature. 1978 Mar 30;272(5652):423–428. doi: 10.1038/272423a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Loewen P. C., Sekiya T., Khorana H. G. The nucleotide sequence adjoining the CCA end of an Escherichia coli tyrosine transfer ribonucleic acid gene. J Biol Chem. 1974 Jan 10;249(1):217–226. [PubMed] [Google Scholar]
  19. Lund E., Dahlberg J. E., Lindahl L., Jaskunas S. R., Dennis P. P., Nomura M. Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli. Cell. 1976 Feb;7(2):165–177. doi: 10.1016/0092-8674(76)90016-7. [DOI] [PubMed] [Google Scholar]
  20. Lund E., Dahlberg J. E. Spacer transfer RNAs in ribosomal RNA transcripts of E. coli: processing of 30S ribosomal RNA in vitro. Cell. 1977 Jun;11(2):247–262. doi: 10.1016/0092-8674(77)90042-3. [DOI] [PubMed] [Google Scholar]
  21. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Morgan E. A., Ikemura T., Nomura M. Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2710–2714. doi: 10.1073/pnas.74.7.2710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Ohmori H., Tomizawa J. I., Maxam A. M. Detection of 5-methylcytosine in DNA sequences. Nucleic Acids Res. 1978 May;5(5):1479–1485. doi: 10.1093/nar/5.5.1479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Perry R. P. Processing of RNA. Annu Rev Biochem. 1976;45:605–629. doi: 10.1146/annurev.bi.45.070176.003133. [DOI] [PubMed] [Google Scholar]
  25. Sekiya T., Gait M. J., Noris K., Ramamoorthy B., Khorana H. G. The nucleotide sequence in the promoter region of the gene for an Escherichia coli tyrosine transfer ribonucleic acid. J Biol Chem. 1976 Aug 10;251(15):4481–4489. [PubMed] [Google Scholar]
  26. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  27. Sprinzl M., Grüter F., Gauss D. H. Collection of published tRNA sequences. Nucleic Acids Res. 1978 May;5(5):r15–r27. [PMC free article] [PubMed] [Google Scholar]
  28. Stark B. C., Kole R., Bowman E. J., Altman S. Ribonuclease P: an enzyme with an essential RNA component. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3717–3721. doi: 10.1073/pnas.75.8.3717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Studies on bacteriophage fd DNA I. A cleavage map of the fd genome. J Mol Biol. 1975 Jun 15;95(1):21–31. [PubMed] [Google Scholar]
  30. Vögeli G., Grosjean H., Söll D. A method for the isolation of specific tRNA precursors. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4790–4794. doi: 10.1073/pnas.72.12.4790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Vögeli G., Stewart T. S., McCutchan T., Söll D. Isolation of Escherichia coli precursor tRNAs containing modified nucleoside Q. J Biol Chem. 1977 Apr 10;252(7):2311–2318. [PubMed] [Google Scholar]
  32. Yang R. C., Van de Voorde A., Fiers W. Cleavage map of the simian-virus-40 genome by the restriction endonuclease III of Haemopholus aegyptius. Eur J Biochem. 1976 Jan 2;61(1):101–117. doi: 10.1111/j.1432-1033.1976.tb10002.x. [DOI] [PubMed] [Google Scholar]
  33. Yarus M., Barrell B. G. The sequence of nucleotides in tRNA Ile from E. coli B. Biochem Biophys Res Commun. 1971 May 21;43(4):729–734. doi: 10.1016/0006-291x(71)90676-0. [DOI] [PubMed] [Google Scholar]
  34. Young R. A., Steitz J. A. Complementary sequences 1700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3593–3597. doi: 10.1073/pnas.75.8.3593. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES