Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1986 May;83(10):3156–3160. doi: 10.1073/pnas.83.10.3156

Gene for lysine tRNA1 may be a progenitor of the highly repetitive and transcribable sequences present in the salmon genome.

K Matsumoto, K Murakami, N Okada
PMCID: PMC323471  PMID: 3458171

Abstract

When salmon total DNA was transcribed in a HeLa cell extract, a discrete 6S RNA was found to be synthesized by RNA polymerase III. We isolated several phage clones containing the 6S RNA gene from a salmon genomic library and determined the sequences of two representative clones. The 5' part of the gene showed remarkable sequence homology with the lysine tRNA1 molecule. This homology extended to secondary structures, and the numbers of nucleotides in the stem and loop structures in the 6S RNA were the same as those in lysine tRNA1. Further, the pseudouridylic acid residues synthesized by HeLa pseudouridylate synthase(s) were determined to be at uridine-27 and uridine-55, which are the positions of these modified nucleosides in lysine tRNA1. These results strongly suggest that the lysine tRNA1 gene is a progenitor of the highly repetitive and transcribable sequences in the salmon genome.

Full text

PDF
3156

Images in this article

3157Image
on p.3157
3157Image
on p.3157
3157Image
on p.3157
3158Image
on p.3158
3159Image
on p.3159
3159Image
on p.3159
3159Image
on p.3159

Selected References

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

  1. Allan M., Paul J. Transcription in vivo of an Alu family member upstream from the human epsilon-globin gene. Nucleic Acids Res. 1984 Jan 25;12(2):1193–1200. doi: 10.1093/nar/12.2.1193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ames B. N., Tsang T. H., Buck M., Christman M. F. The leader mRNA of the histidine attenuator region resembles tRNAHis: possible general regulatory implications. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5240–5242. doi: 10.1073/pnas.80.17.5240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  4. Blin N., Stafford D. W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976 Sep;3(9):2303–2308. doi: 10.1093/nar/3.9.2303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Daniels G. R., Deininger P. L. Repeat sequence families derived from mammalian tRNA genes. 1985 Oct 31-Nov 6Nature. 317(6040):819–822. doi: 10.1038/317819a0. [DOI] [PubMed] [Google Scholar]
  6. Duncan C., Biro P. A., Choudary P. V., Elder J. T., Wang R. R., Forget B. G., de Riel J. K., Weissman S. M. RNA polymerase III transcriptional units are interspersed among human non-alpha-globin genes. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5095–5099. doi: 10.1073/pnas.76.10.5095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Endoh H., Okada N. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci U S A. 1986 Jan;83(2):251–255. doi: 10.1073/pnas.83.2.251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jelinek W. R., Schmid C. W. Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem. 1982;51:813–844. doi: 10.1146/annurev.bi.51.070182.004121. [DOI] [PubMed] [Google Scholar]
  9. Lawrence C. B., McDonnell D. P., Ramsey W. J. Analysis of repetitive sequence elements containing tRNA-like sequences. Nucleic Acids Res. 1985 Jun 25;13(12):4239–4252. doi: 10.1093/nar/13.12.4239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
  11. Manley J. L., Fire A., Cano A., Sharp P. A., Gefter M. L. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3855–3859. doi: 10.1073/pnas.77.7.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Matsumoto K., Murakami K., Okada N. Pseudouridylic modification of a 6S RNA transcribed in vitro from highly repetitive and transcribable (Hirt) sequences of salmon total DNA. Biochem Biophys Res Commun. 1984 Oct 30;124(2):514–522. doi: 10.1016/0006-291x(84)91584-5. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Okada N., Nishimura S. Isolation and characterization of a guanine insertion enzyme, a specific tRNA transglycosylase, from Escherichia coli. J Biol Chem. 1979 Apr 25;254(8):3061–3066. [PubMed] [Google Scholar]
  15. Okada N., Sakamoto K., Kondo A. Total DNA transcription reveals the existence of highly repetitive transcribable sequences in higher animals. J Biochem. 1983 Mar;93(3):723–731. doi: 10.1093/jb/93.3.723. [DOI] [PubMed] [Google Scholar]
  16. Okada N., Yasuda T., Nishimura S. Detection of nucleoside Q precursor in methyl-deficient E.coli tRNA. Nucleic Acids Res. 1977 Dec;4(12):4063–4075. doi: 10.1093/nar/4.12.4063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Raba M., Limburg K., Burghagen M., Katze J. R., Simsek M., Heckman J. E., Rajbhandary U. L., Gross H. J. Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts. Eur J Biochem. 1979 Jun;97(1):305–318. doi: 10.1111/j.1432-1033.1979.tb13115.x. [DOI] [PubMed] [Google Scholar]
  18. Rogers J. H. The origin and evolution of retroposons. Int Rev Cytol. 1985;93:187–279. doi: 10.1016/s0074-7696(08)61375-3. [DOI] [PubMed] [Google Scholar]
  19. Rogers J. Origins of repeated DNA. 1985 Oct 31-Nov 6Nature. 317(6040):765–766. doi: 10.1038/317765a0. [DOI] [PubMed] [Google Scholar]
  20. Rubin C. M., Houck C. M., Deininger P. L., Friedmann T., Schmid C. W. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature. 1980 Mar 27;284(5754):372–374. doi: 10.1038/284372a0. [DOI] [PubMed] [Google Scholar]
  21. Sakamoto K., Kominami R., Mishima Y., Okada N. The 6S RNA transcribed from rodent total DNA in vitro is the transcript of the type 2 Alu family. Mol Gen Genet. 1984;194(1-2):1–6. doi: 10.1007/BF00383489. [DOI] [PubMed] [Google Scholar]
  22. Sakamoto K., Okada N. 5-Methylcytidylic modification of in vitro transcript from the rat identifier sequence; evidence that the transcript forms a tRNA-like structure. Nucleic Acids Res. 1985 Oct 25;13(20):7195–7206. doi: 10.1093/nar/13.20.7195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Sakamoto K., Okada N. Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J Mol Evol. 1985;22(2):134–140. doi: 10.1007/BF02101691. [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. Singer M. F. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982 Mar;28(3):433–434. doi: 10.1016/0092-8674(82)90194-5. [DOI] [PubMed] [Google Scholar]
  26. Ullu E., Tschudi C. Alu sequences are processed 7SL RNA genes. Nature. 1984 Nov 8;312(5990):171–172. doi: 10.1038/312171a0. [DOI] [PubMed] [Google Scholar]
  27. Weiner A. M. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell. 1980 Nov;22(1 Pt 1):209–218. doi: 10.1016/0092-8674(80)90169-5. [DOI] [PubMed] [Google Scholar]
  28. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES