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. 1991 Oct 1;88(19):8826–8830. doi: 10.1073/pnas.88.19.8826

RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript.

B J Saville 1, R A Collins 1
PMCID: PMC52603  PMID: 1833766

Abstract

Neurospora VS RNA is a mitochondrial single-stranded RNA that combines certain features of catalytic RNAs and group I introns. We report here that monomeric VS RNA synthesized in vitro by self-cleavage of a multimeric transcript can perform an RNA-mediated self-ligation reaction producing circular RNAs indistinguishable from those isolated from mitochondria. We conclude that the active site for the ligation reaction is present in the RNA itself. Also, the mechanism for aligning the termini to be ligated may be different from mechanisms previously described. The lack of sequence similarity between VS RNA and previously characterized catalytic RNAs suggests that VS RNA is an independently evolved ribozyme capable of both cleavage and ligation.

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Selected References

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  1. Akins R. A., Grant D. M., Stohl L. L., Bottorff D. A., Nargang F. E., Lambowitz A. M. Nucleotide sequence of the Varkud mitochondrial plasmid of Neurospora and synthesis of a hybrid transcript with a 5' leader derived from mitochondrial RNA. J Mol Biol. 1988 Nov 5;204(1):1–25. doi: 10.1016/0022-2836(88)90594-3. [DOI] [PubMed] [Google Scholar]
  2. Branch A. D., Robertson H. D. A replication cycle for viroids and other small infectious RNA's. Science. 1984 Feb 3;223(4635):450–455. doi: 10.1126/science.6197756. [DOI] [PubMed] [Google Scholar]
  3. Bruce A. G., Uhlenbeck O. C. Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res. 1978 Oct;5(10):3665–3677. doi: 10.1093/nar/5.10.3665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Buzayan J. M., Gerlach W. L., Bruening G. Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc Natl Acad Sci U S A. 1986 Dec;83(23):8859–8862. doi: 10.1073/pnas.83.23.8859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cech T. R. Self-splicing RNA: implications for evolution. Int Rev Cytol. 1985;93:3–22. doi: 10.1016/s0074-7696(08)61370-4. [DOI] [PubMed] [Google Scholar]
  6. Cech T. R. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543–568. doi: 10.1146/annurev.bi.59.070190.002551. [DOI] [PubMed] [Google Scholar]
  7. Collins R. A., Saville B. J. Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora. Nature. 1990 May 10;345(6271):177–179. doi: 10.1038/345177a0. [DOI] [PubMed] [Google Scholar]
  8. Collins R. A., Stohl L. L., Cole M. D., Lambowitz A. M. Characterization of a novel plasmid DNA found in mitochondria of N. crassa. Cell. 1981 May;24(2):443–452. doi: 10.1016/0092-8674(81)90335-4. [DOI] [PubMed] [Google Scholar]
  9. Diener T. O. Circular RNAs: relics of precellular evolution? Proc Natl Acad Sci U S A. 1989 Dec;86(23):9370–9374. doi: 10.1073/pnas.86.23.9370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dinter-Gottlieb G. Viroids and virusoids are related to group I introns. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6250–6254. doi: 10.1073/pnas.83.17.6250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Epstein L. M., Gall J. G. Self-cleaving transcripts of satellite DNA from the newt. Cell. 1987 Feb 13;48(3):535–543. doi: 10.1016/0092-8674(87)90204-2. [DOI] [PubMed] [Google Scholar]
  12. Feldstein P. A., Buzayan J. M., Bruening G. Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene. 1989 Oct 15;82(1):53–61. doi: 10.1016/0378-1119(89)90029-2. [DOI] [PubMed] [Google Scholar]
  13. Feldstein P. A., Buzayan J. M., van Tol H., deBear J., Gough G. R., Gilham P. T., Bruening G. Specific association between an endoribonucleolytic sequence from a satellite RNA and a substrate analogue containing a 2'-5' phosphodiester. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2623–2627. doi: 10.1073/pnas.87.7.2623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Field D. J., Sommerfield A., Saville B. J., Collins R. A. A group II intron in the Neurospora mitochondrial coI gene: nucleotide sequence and implications for splicing and molecular evolution. Nucleic Acids Res. 1989 Nov 25;17(22):9087–9099. doi: 10.1093/nar/17.22.9087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Filipowicz W., Konarska M., Gross H. J., Shatkin A. J. RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 1983 Mar 11;11(5):1405–1418. doi: 10.1093/nar/11.5.1405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Forster A. C., Symons R. H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987 Apr 24;49(2):211–220. doi: 10.1016/0092-8674(87)90562-9. [DOI] [PubMed] [Google Scholar]
  17. Forster A. C., Symons R. H. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell. 1987 Jul 3;50(1):9–16. doi: 10.1016/0092-8674(87)90657-x. [DOI] [PubMed] [Google Scholar]
  18. Garriga G., Bertrand H., Lambowitz A. M. RNA splicing in Neurospora mitochondria: nuclear mutants defective in both splicing and 3' end synthesis of the large rRNA. Cell. 1984 Mar;36(3):623–634. doi: 10.1016/0092-8674(84)90342-8. [DOI] [PubMed] [Google Scholar]
  19. Greer C. L., Peebles C. L., Gegenheimer P., Abelson J. Mechanism of action of a yeast RNA ligase in tRNA splicing. Cell. 1983 Feb;32(2):537–546. doi: 10.1016/0092-8674(83)90473-7. [DOI] [PubMed] [Google Scholar]
  20. Hampel A., Tritz R., Hicks M., Cruz P. 'Hairpin' catalytic RNA model: evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res. 1990 Jan 25;18(2):299–304. doi: 10.1093/nar/18.2.299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Haseloff J., Gerlach W. L. Sequences required for self-catalysed cleavage of the satellite RNA of tobacco ringspot virus. Gene. 1989 Oct 15;82(1):43–52. doi: 10.1016/0378-1119(89)90028-0. [DOI] [PubMed] [Google Scholar]
  22. Hutchins C. J., Rathjen P. D., Forster A. C., Symons R. H. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 1986 May 12;14(9):3627–3640. doi: 10.1093/nar/14.9.3627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jacquier A. Self-splicing group II and nuclear pre-mRNA introns: how similar are they? Trends Biochem Sci. 1990 Sep;15(9):351–354. doi: 10.1016/0968-0004(90)90075-m. [DOI] [PubMed] [Google Scholar]
  24. Kiberstis P. A., Haseloff J., Zimmern D. 2' phosphomonoester, 3'-5' phosphodiester bond at a unique site in a circular viral RNA. EMBO J. 1985 Mar;4(3):817–822. doi: 10.1002/j.1460-2075.1985.tb03703.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Konarska M., Filipowicz W., Domdey H., Gross H. J. Formation of a 2'-phosphomonoester, 3',5'-phosphodiester linkage by a novel RNA ligase in wheat germ. Nature. 1981 Sep 10;293(5828):112–116. doi: 10.1038/293112a0. [DOI] [PubMed] [Google Scholar]
  26. Kuo M. Y., Sharmeen L., Dinter-Gottlieb G., Taylor J. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J Virol. 1988 Dec;62(12):4439–4444. doi: 10.1128/jvi.62.12.4439-4444.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lambowitz A. M. Infectious introns. Cell. 1989 Feb 10;56(3):323–326. doi: 10.1016/0092-8674(89)90232-8. [DOI] [PubMed] [Google Scholar]
  28. Lambowitz A. M. Preparation and analysis of mitochondrial ribosomes. Methods Enzymol. 1979;59:421–433. doi: 10.1016/0076-6879(79)59103-4. [DOI] [PubMed] [Google Scholar]
  29. Nargang F. E., Bell J. B., Stohl L. L., Lambowitz A. M. The DNA sequence and genetic organization of a Neurospora mitochondrial plasmid suggest a relationship to introns and mobile elements. Cell. 1984 Sep;38(2):441–453. doi: 10.1016/0092-8674(84)90499-9. [DOI] [PubMed] [Google Scholar]
  30. Prody G. A., Bakos J. T., Buzayan J. M., Schneider I. R., Bruening G. Autolytic processing of dimeric plant virus satellite RNA. Science. 1986 Mar 28;231(4745):1577–1580. doi: 10.1126/science.231.4745.1577. [DOI] [PubMed] [Google Scholar]
  31. Rosenstein S. P., Been M. D. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry. 1990 Sep 4;29(35):8011–8016. doi: 10.1021/bi00487a002. [DOI] [PubMed] [Google Scholar]
  32. Saville B. J., Collins R. A. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell. 1990 May 18;61(4):685–696. doi: 10.1016/0092-8674(90)90480-3. [DOI] [PubMed] [Google Scholar]
  33. Sharmeen L., Kuo M. Y., Dinter-Gottlieb G., Taylor J. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol. 1988 Aug;62(8):2674–2679. doi: 10.1128/jvi.62.8.2674-2679.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sharmeen L., Kuo M. Y., Taylor J. Self-ligating RNA sequences on the antigenome of human hepatitis delta virus. J Virol. 1989 Mar;63(3):1428–1430. doi: 10.1128/jvi.63.3.1428-1430.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sharp P. A. On the origin of RNA splicing and introns. Cell. 1985 Sep;42(2):397–400. doi: 10.1016/0092-8674(85)90092-3. [DOI] [PubMed] [Google Scholar]
  36. Symons R. H. Self-cleavage of RNA in the replication of small pathogens of plants and animals. Trends Biochem Sci. 1989 Nov;14(11):445–450. doi: 10.1016/0968-0004(89)90103-5. [DOI] [PubMed] [Google Scholar]
  37. Usher D. A., McHale A. H. Nonenzymic joining of oligoadenylates on a polyuridylic acid template. Science. 1976 Apr 2;192(4234):53–54. doi: 10.1126/science.1257755. [DOI] [PubMed] [Google Scholar]
  38. Woodson S. A., Cech T. R. Reverse self-splicing of the tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell. 1989 Apr 21;57(2):335–345. doi: 10.1016/0092-8674(89)90971-9. [DOI] [PubMed] [Google Scholar]
  39. Wu H. N., Lai M. M. RNA conformational requirements of self-cleavage of hepatitis delta virus RNA. Mol Cell Biol. 1990 Oct;10(10):5575–5579. doi: 10.1128/mcb.10.10.5575. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wu H. N., Lai M. M. Reversible cleavage and ligation of hepatitis delta virus RNA. Science. 1989 Feb 3;243(4891):652–654. doi: 10.1126/science.2492677. [DOI] [PubMed] [Google Scholar]
  41. Wu H. N., Lin Y. J., Lin F. P., Makino S., Chang M. F., Lai M. M. Human hepatitis delta virus RNA subfragments contain an autocleavage activity. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1831–1835. doi: 10.1073/pnas.86.6.1831. [DOI] [PMC free article] [PubMed] [Google Scholar]

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