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. 1985 Mar;161(3):1162–1170. doi: 10.1128/jb.161.3.1162-1170.1985

Escherichia coli 6S RNA gene is part of a dual-function transcription unit.

L M Hsu, J Zagorski, Z Wang, M J Fournier
PMCID: PMC215021  PMID: 2579060

Abstract

The gene coding for the metabolically stable 6S RNA of Escherichia coli has been cloned, sequenced, and partially characterized in expression analyses. The DNA sequence results confirm the accuracy of the previously established RNA sequence and, with genomic hybridization data, reveal that there is only one copy of the 6S DNA in the chromosome. Consistent with its relaxed mode of expression, the promoter region of the 6S RNA gene was found to lack the hypothetical GC-rich discriminator domain common to other stable RNA genes under stringent control. The sequence results also revealed the occurrence of a 540-base-pair open reading frame immediately downstream from the 6S RNA coding region. Results from the expression analyses show that the protein and RNA coding regions are cotranscribed in vitro and that the open reading frame is translated in vivo.

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Selected References

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

  1. Altman S., Model P., Dixon G. H., Wosnick N. A. An E. coli gene coding for a protamine-like protein. Cell. 1981 Nov;26(3 Pt 1):299–304. doi: 10.1016/0092-8674(81)90198-7. [DOI] [PubMed] [Google Scholar]
  2. Alwine J. C., Kemp D. J., Parker B. A., Reiser J., Renart J., Stark G. R., Wahl G. M. Detection of specific RNAs or specific fragments of DNA by fractionation in gels and transfer to diazobenzyloxymethyl paper. Methods Enzymol. 1979;68:220–242. doi: 10.1016/0076-6879(79)68017-5. [DOI] [PubMed] [Google Scholar]
  3. Amann E., Brosius J., Ptashne M. Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli. Gene. 1983 Nov;25(2-3):167–178. doi: 10.1016/0378-1119(83)90222-6. [DOI] [PubMed] [Google Scholar]
  4. An G., Friesen J. D. The nucleotide sequence of tufB and four nearby tRNA structural genes of Escherichia coli. Gene. 1980 Dec;12(1-2):33–39. doi: 10.1016/0378-1119(80)90013-x. [DOI] [PubMed] [Google Scholar]
  5. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  6. Brosius J., Holy A. Regulation of ribosomal RNA promoters with a synthetic lac operator. Proc Natl Acad Sci U S A. 1984 Nov;81(22):6929–6933. doi: 10.1073/pnas.81.22.6929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brownlee G. G. Sequence of 6S RNA of E. coli. Nat New Biol. 1971 Feb 3;229(5):147–149. doi: 10.1038/newbio229147a0. [DOI] [PubMed] [Google Scholar]
  8. Bruni C. B., Colantuoni V., Sbordone L., Cortese R., Blasi F. Biochemical and regulatory properties of Escherichia coli K-12 hisT mutants. J Bacteriol. 1977 Apr;130(1):4–10. doi: 10.1128/jb.130.1.4-10.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976 Sep;9(1):91–99. doi: 10.1016/0092-8674(76)90055-6. [DOI] [PubMed] [Google Scholar]
  11. Duester G., Campen R. K., Holmes W. M. Nucleotide sequence of an Escherichia coli tRNA (Leu 1) operon and identification of the transcription promoter signal. Nucleic Acids Res. 1981 May 11;9(9):2121–2139. doi: 10.1093/nar/9.9.2121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Goldstein J., Harewood K. Another species of ribonucleic acid in Escherichia coli. J Mol Biol. 1969 Jan;39(2):383–387. doi: 10.1016/0022-2836(69)90325-8. [DOI] [PubMed] [Google Scholar]
  13. Griffin B. E., Baillie D. L. Precursors of stable RNA accumulated in a mutant of E. coli. FEBS Lett. 1973 Aug 15;34(2):273–279. doi: 10.1016/0014-5793(73)80811-7. [DOI] [PubMed] [Google Scholar]
  14. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Helling R. B., Goodman H. M., Boyer H. W. Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. J Virol. 1974 Nov;14(5):1235–1244. doi: 10.1128/jvi.14.5.1235-1244.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Holmes W. M., Platt T., Rosenberg M. Termination of transcription in E. coli. Cell. 1983 Apr;32(4):1029–1032. doi: 10.1016/0092-8674(83)90287-8. [DOI] [PubMed] [Google Scholar]
  17. Hsu L. M., Klee H. J., Zagorski J., Fournier M. J. Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs. J Bacteriol. 1984 Jun;158(3):934–942. doi: 10.1128/jb.158.3.934-942.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hsu L. M., Zagorski J., Fournier M. J. Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene. J Mol Biol. 1984 Sep 25;178(3):509–531. doi: 10.1016/0022-2836(84)90236-5. [DOI] [PubMed] [Google Scholar]
  19. Hudson L., Rossi J., Landy A. Dual function transcripts specifying tRNA and mRNA. Nature. 1981 Dec 3;294(5840):422–427. doi: 10.1038/294422a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Humphreys G. O., Willshaw G. A., Anderson E. S. A simple method for the preparation of large quantities of pure plasmid DNA. Biochim Biophys Acta. 1975 Apr 2;383(4):457–463. doi: 10.1016/0005-2787(75)90318-4. [DOI] [PubMed] [Google Scholar]
  21. Ikemura T., Dahlberg J. E. Small ribonucleic acids of Escherichia coli. II. Noncoordinate accumulation during stringent control. J Biol Chem. 1973 Jul 25;248(14):5033–5041. [PubMed] [Google Scholar]
  22. Ishii S., Kuroki K., Imamoto F. tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jan;81(2):409–413. doi: 10.1073/pnas.81.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lee C. A., Fournier M. J., Beckwith J. Escherichia coli 6S RNA is not essential for growth or protein secretion. J Bacteriol. 1985 Mar;161(3):1156–1161. doi: 10.1128/jb.161.3.1156-1161.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lee S. Y., Bailey S. C., Apirion D. Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA. J Bacteriol. 1978 Feb;133(2):1015–1023. doi: 10.1128/jb.133.2.1015-1023.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Li W. Y., Reddy R., Henning D., Epstein P., Busch H. Nucleotide sequence of 7 S RNA. Homology to Alu DNA and La 4.5 S RNA. J Biol Chem. 1982 May 10;257(9):5136–5142. [PubMed] [Google Scholar]
  26. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  27. McKenney K., Shimatake H., Court D., Schmeissner U., Brady C., Rosenberg M. A system to study promoter and terminator signals recognized by Escherichia coli RNA polymerase. Gene Amplif Anal. 1981;2:383–415. [PubMed] [Google Scholar]
  28. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. O'Farrell P. H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PMC free article] [PubMed] [Google Scholar]
  30. Peacock A. C., Dingman C. W. Molecular weight estimation and separation of ribonucleic acid by electrophoresis in agarose-acrylamide composite gels. Biochemistry. 1968 Feb;7(2):668–674. doi: 10.1021/bi00842a023. [DOI] [PubMed] [Google Scholar]
  31. Rice P. W., Dahlberg J. E. A gene between polA and glnA retards growth of Escherichia coli when present in multiple copies: physiological effects of the gene for spot 42 RNA. J Bacteriol. 1982 Dec;152(3):1196–1210. doi: 10.1128/jb.152.3.1196-1210.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Robertson M. Membrane traffic and the problem of protein secretion. Nature. 1984 Feb 16;307(5952):594–595. doi: 10.1038/307594a0. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. 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]
  35. Simoncsits A., Brownlee G. G., Brown R. S., Rubin J. R., Guilley H. New rapid gel sequencing method for RNA. Nature. 1977 Oct 27;269(5631):833–836. doi: 10.1038/269833a0. [DOI] [PubMed] [Google Scholar]
  36. Smith H. O., Birnstiel M. L. A simple method for DNA restriction site mapping. Nucleic Acids Res. 1976 Sep;3(9):2387–2398. doi: 10.1093/nar/3.9.2387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Smith H. O. Recovery of DNA from gels. Methods Enzymol. 1980;65(1):371–380. doi: 10.1016/s0076-6879(80)65048-4. [DOI] [PubMed] [Google Scholar]
  38. 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]
  39. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  40. Travers A. A. Conserved features of coordinately regulated E. coli promoters. Nucleic Acids Res. 1984 Mar 26;12(6):2605–2618. doi: 10.1093/nar/12.6.2605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ullu E., Murphy S., Melli M. Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence. Cell. 1982 May;29(1):195–202. doi: 10.1016/0092-8674(82)90103-9. [DOI] [PubMed] [Google Scholar]
  42. Walter P., Blobel G. Disassembly and reconstitution of signal recognition particle. Cell. 1983 Sep;34(2):525–533. doi: 10.1016/0092-8674(83)90385-9. [DOI] [PubMed] [Google Scholar]
  43. Walter P., Blobel G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature. 1982 Oct 21;299(5885):691–698. doi: 10.1038/299691a0. [DOI] [PubMed] [Google Scholar]

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