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. 1985 Jan 11;13(1):31–43. doi: 10.1093/nar/13.1.31

Common structural features of the genes for two stable RNAs from Halobacterium halobium.

A Moritz, B Lankat-Buttgereit, H J Gross, W Goebel
PMCID: PMC340972  PMID: 2582351

Abstract

The genes coding for the 5S rRNA and another stable RNA, termed 7S RNA, in Halobacterium halobium were isolated from a genomic library of this archaebacterium and their nucleotide sequences determined. Both genes are colinear with their transcripts (5S rRNA and 7S RNA), but 5S rRNA and possibly also 7S RNA isolated from other halobacteria carry additional nucleotides within the RNA transcript. Both genes are located in the G + C rich chromosomal fraction I of H. halobium. Comparison of the 3' non-coding regions of both genes shows a 20 bp sequence of high homology immediately at the 3' ends which is almost symmetrically flanked by two stem-loop structures, one being situated close to the 3' end but within the coding region and the other downstream of the common 20 bp sequence.

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Selected References

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

  1. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981 May 15;148(2):107–127. doi: 10.1016/0022-2836(81)90508-8. [DOI] [PubMed] [Google Scholar]
  2. Collins J., Hohn B. Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4242–4246. doi: 10.1073/pnas.75.9.4242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dassarma S., Rajbhandary U. L., Khorana H. G. Bacterio-opsin mRNA in wild-type and bacterio-opsin-deficient Halobacterium halobium strains. Proc Natl Acad Sci U S A. 1984 Jan;81(1):125–129. doi: 10.1073/pnas.81.1.125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Doolittle W. F., Pace N. R. Transcriptional organization of the ribosomal RNA cistrons in Escherichia coli. Proc Natl Acad Sci U S A. 1971 Aug;68(8):1786–1790. doi: 10.1073/pnas.68.8.1786. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gillum A. M., Urquhart N., Smith M., RajBhandary U. L. Nucleotide sequence of salmon testes and salmon liver cytoplasmic initiator tRNA. Cell. 1975 Nov;6(3):395–405. doi: 10.1016/0092-8674(75)90189-0. [DOI] [PubMed] [Google Scholar]
  7. Goebel W. Studies on extrachromosomal DNA elements. Replication of the colicinogenic factor Col E1 in two temperature sensitive mutants of Escherichia coli defective in DNA replication. Eur J Biochem. 1970 Aug;15(2):311–320. doi: 10.1111/j.1432-1033.1970.tb01009.x. [DOI] [PubMed] [Google Scholar]
  8. Gross H. J., Domdey H., Lossow C., Jank P., Raba M., Alberty H., Sänger H. L. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature. 1978 May 18;273(5659):203–208. doi: 10.1038/273203a0. [DOI] [PubMed] [Google Scholar]
  9. Gross H. J., Krupp G., Domdey H., Raba M., Jank P., Lossow C., Alberty H., Ramm K., Sänger H. L. Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid. Eur J Biochem. 1982 Jan;121(2):249–257. doi: 10.1111/j.1432-1033.1982.tb05779.x. [DOI] [PubMed] [Google Scholar]
  10. Haseloff J., Symons R. H. Chrysanthemum stunt viroid: primary sequence and secondary structure. Nucleic Acids Res. 1981 Jun 25;9(12):2741–2752. doi: 10.1093/nar/9.12.2741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hofman J. D., Lau R. H., Doolittle W. F. The number, physical organization and transcription of ribosomal RNA cistrons in an archaebacterium: Halobacterium halobium. Nucleic Acids Res. 1979 Nov 10;7(5):1321–1333. doi: 10.1093/nar/7.5.1321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hohn B., Collins J. A small cosmid for efficient cloning of large DNA fragments. Gene. 1980 Nov;11(3-4):291–298. doi: 10.1016/0378-1119(80)90069-4. [DOI] [PubMed] [Google Scholar]
  13. Huet J., Schnabel R., Sentenac A., Zillig W. Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type. EMBO J. 1983;2(8):1291–1294. doi: 10.1002/j.1460-2075.1983.tb01583.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jay E., Bambara R., Padmanabhan R., Wu R. DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping. Nucleic Acids Res. 1974 Mar;1(3):331–353. doi: 10.1093/nar/1.3.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kaine B. P., Gupta R., Woese C. R. Putative introns in tRNA genes of prokaryotes. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3309–3312. doi: 10.1073/pnas.80.11.3309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lockard R. E., Alzner-Deweerd B., Heckman J. E., MacGee J., Tabor M. W., RajBhandary U. L. Sequence analysis of 5'[32P] labeled mRNA and tRNA using polyacrylamide gel electrophoresis. Nucleic Acids Res. 1978 Jan;5(1):37–56. doi: 10.1093/nar/5.1.37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Luehrsen K. R., Fox G. E., Kilpatrick M. W., Walker R. T., Domdey H., Krupp G., Gross H. J. The nucleotide sequence of the 5S rRNA from the archaebacterium Thermoplasma acidophilum. Nucleic Acids Res. 1981 Feb 25;9(4):965–970. doi: 10.1093/nar/9.4.965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Luehrsen K. R., Nicholson D. E., Eubanks D. C., Fox G. E. An archaebacterial 5S rRNA contains a long insertion sequence. Nature. 1981 Oct 29;293(5835):755–756. doi: 10.1038/293755a0. [DOI] [PubMed] [Google Scholar]
  19. Maniatis T., Efstratiadis A. Fractionation of low molecular weight DNA or RNA in polyacrylamide gels containing 98% formamide or 7 M urea. Methods Enzymol. 1980;65(1):299–305. doi: 10.1016/s0076-6879(80)65040-x. [DOI] [PubMed] [Google Scholar]
  20. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  21. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  24. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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]
  26. Thayer R. E. An improved method for detecting foreign DNA in plasmids of Escherichia coli. Anal Biochem. 1979 Sep 15;98(1):60–63. doi: 10.1016/0003-2697(79)90705-x. [DOI] [PubMed] [Google Scholar]
  27. Tyc K., Kikuchi Y., Konarska M., Filipowicz W., Gross H. J. Ligation of endogenous tRNA 3' half molecules to their corresponding 5' halves via 2'-phosphomonoester,3',5'-phosphodiester bonds in extracts of Chlamydomonas. EMBO J. 1983;2(4):605–610. doi: 10.1002/j.1460-2075.1983.tb01470.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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]
  29. Zillig W., Stetter K. O., Janeković D. DNA-dependent RNA polymerase from the archaebacterium Sulfolobus acidocaldarius. Eur J Biochem. 1979 Jun 1;96(3):597–604. doi: 10.1111/j.1432-1033.1979.tb13074.x. [DOI] [PubMed] [Google Scholar]

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