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. 1980 Sep 11;8(17):3793–3807. doi: 10.1093/nar/8.17.3793

The distal end of the ribosomal RNA operon rrnD of Escherichia coli contains a tRNA1thr gene, two 5s rRNA genes and a transcription terminator.

G L Duester, W M Holmes
PMCID: PMC324195  PMID: 6255417

Abstract

The distal region of the Escherichia coli ribosomal RNA operon rrnD has been sequenced to identify transfer RNA genes which might be contained within this transcriptional unit, and to define a possible transcription termination site. A nucleotide sequence corresponding to the gene for tRNA1thr is located between two genes for 5S rRNA. The spacer region between the proximal 5S rRNA gene and the tRNA1thr gene is 12 base pairs long, whereas the spacer region between the distal 5S rRNA gene and the tRNA1thr gene is 37 base pairs. Possible sites for RNA processing are discussed, and the sequence of the tRNA1thr gene is found to possess the same anticodon as the tRNA3thr gene. A putative transcription termination site for rrnD was located about 25 base pairs distal to the 3' end of the second 5S rRNA gene. The rrnD and rrnC terminators are compared with each other and with other prokaryotic terminators. Located at exactly the same site on the complementary strand is another putative transcription termination site for a gene being transcribed towards rrnD. The possibility of overlapping terminators is discussed.

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Selected References

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

  1. Boros I., Kiss A., Venetianer P. Physical map of the seven ribosomal RNA genes of Escherichia coli. Nucleic Acids Res. 1979;6(5):1817–1830. doi: 10.1093/nar/6.5.1817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bram R. J., Young R. A., Steitz J. A. The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E. coli. Cell. 1980 Feb;19(2):393–401. doi: 10.1016/0092-8674(80)90513-9. [DOI] [PubMed] [Google Scholar]
  3. Brosius J., Dull T. J., Noller H. F. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):201–204. doi: 10.1073/pnas.77.1.201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Clewell D. B. Nature of Col E 1 plasmid replication in Escherichia coli in the presence of the chloramphenicol. J Bacteriol. 1972 May;110(2):667–676. doi: 10.1128/jb.110.2.667-676.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Crick F. H. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. doi: 10.1016/s0022-2836(66)80022-0. [DOI] [PubMed] [Google Scholar]
  7. Csordás-Tóth E., Boros I., Venetianer P. Structure of the promoter region for the rrnB gene in Escherichia coli. Nucleic Acids Res. 1979 Dec 20;7(8):2189–2197. doi: 10.1093/nar/7.8.2189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Egan J., Landy A. Structural analysis of the tRNA1Tyr gene of Escherichia coli. A 178 base pair sequence that is repeated 3.14 times. J Biol Chem. 1978 May 25;253(10):3607–3622. [PubMed] [Google Scholar]
  9. Erdmann V. A. Collection of published 5S and 5.8S RNA sequences and their precursors. Nucleic Acids Res. 1979 Jan;6(1):r29–r44. doi: 10.1093/nar/6.1.419-c. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gauss D. H., Grüter F., Sprinzl M. Compilation of tRNA sequences. Nucleic Acids Res. 1979 Jan;6(1):r1–r19. [PMC free article] [PubMed] [Google Scholar]
  11. Ghora B. K., Apirion D. Identification of a novel RNA molecule in a new RNA processing mutant of Escherichia coli which contains 5 S rRNA sequences. J Biol Chem. 1979 Mar 25;254(6):1951–1956. [PubMed] [Google Scholar]
  12. Gralla J., Crothers D. M. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol. 1973 Feb 5;73(4):497–511. doi: 10.1016/0022-2836(73)90096-x. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Korn L. J., Queen C. L., Wegman M. N. Computer analysis of nucleic acid regulatory sequences. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4401–4405. doi: 10.1073/pnas.74.10.4401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Madison J. T. Primary structure of RNA. Annu Rev Biochem. 1968;37:131–148. doi: 10.1146/annurev.bi.37.070168.001023. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Morgan E. A., Ikemura T., Lindahl L., Fallon A. M., Nomura M. Some rRNA operons in E. coli have tRNA genes at their distal ends. Cell. 1978 Feb;13(2):335–344. doi: 10.1016/0092-8674(78)90202-7. [DOI] [PubMed] [Google Scholar]
  18. Nomura M., Morgan E. A. Genetics of bacterial ribosomes. Annu Rev Genet. 1977;11:297–347. doi: 10.1146/annurev.ge.11.120177.001501. [DOI] [PubMed] [Google Scholar]
  19. Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc Natl Acad Sci U S A. 1975 Mar;72(3):784–788. doi: 10.1073/pnas.72.3.784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  21. Rossi J. J., Landy A. Structure and organization of the two tRNATyr gene clusters on the E. coli chromosome. Cell. 1979 Mar;16(3):523–534. doi: 10.1016/0092-8674(79)90027-8. [DOI] [PubMed] [Google Scholar]
  22. Smith J. D. Transcription and processing of transfer RNA precursors. Prog Nucleic Acid Res Mol Biol. 1976;16:25–73. doi: 10.1016/s0079-6603(08)60755-2. [DOI] [PubMed] [Google Scholar]
  23. Yamamoto M., Nomura M. Organization of genes for transcription and translation in the rif region of the Escherichia coli chromosome. J Bacteriol. 1979 Jan;137(1):584–594. doi: 10.1128/jb.137.1.584-594.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Young R. A., Macklis R., Steitz J. A. Sequence of the 16 S-23 s spacer region in two ribosomal RNA operons of Escherichia coli. J Biol Chem. 1979 May 10;254(9):3264–3271. [PubMed] [Google Scholar]
  25. Young R. A., Steitz J. A. Tandem promoters direct E. coli ribosomal RNA synthesis. Cell. 1979 May;17(1):225–234. doi: 10.1016/0092-8674(79)90310-6. [DOI] [PubMed] [Google Scholar]
  26. Young R. A. Transcription termination in the Escherichia coli ribosomal RNA operon rrnC. J Biol Chem. 1979 Dec 25;254(24):12725–12731. [PubMed] [Google Scholar]
  27. de Boer H. A., Gilbert S. F., Nomura M. DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):201–209. doi: 10.1016/0092-8674(79)90308-8. [DOI] [PubMed] [Google Scholar]

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