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. 1992 May 1;89(9):3711–3715. doi: 10.1073/pnas.89.9.3711

Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures.

C Hernández 1, R Flores 1
PMCID: PMC525560  PMID: 1373888

Abstract

Peach latent mosaic viroid (PLMVd), the causal agent of peach latent mosaic disease, has been sequenced and found to be a circular RNA molecule of 337 nucleotide residues, which adopts a branched conformation when it is folded in the model of lowest free energy. PLMVd exhibits limited homologies with other viroids and some satellite RNAs, but it does not have any of the central conserved sequences characteristic of the subgroups of typical viroids. However, a segment of approximately one-third of the PLMVd sequence has the elements required to form in the RNAs of both polarities the hammerhead structures proposed to act in the in vitro self-cleavage of avocado sunblotch viroid (ASBVd) and some satellite RNAs. Plus and minus partial- and full-length RNA transcripts of PLMVd containing the hammerhead structures displayed self-cleavage during transcription and after purification as predicted by these structures. These data are consistent with the high stability of the PLMVd hammerhead structures, more similar to the corresponding structures of some satellite RNAs than to those of ASBVd, and indicate that the self-cleavage reactions of PLMVd are most probably mediated by single hammerhead structures. Our results support the inclusion of PLMVd in a viroid subgroup represented by ASBVd, whose members are characterized by their ability to self-cleave in vitro, and probably in vivo, through hammerhead structures. A consensus phylogenetic tree has been obtained suggesting that PLMVd, together with ASBVd, may represent an evolutionary link between viroids and viroid-like satellite RNAs.

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Selected References

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  1. Bruening G. Compilation of self-cleaving sequences from plant virus satellite RNAs and other sources. Methods Enzymol. 1989;180:546–558. doi: 10.1016/0076-6879(89)80123-5. [DOI] [PubMed] [Google Scholar]
  2. Davies C., Haseloff J., Symons R. H. Structure, self-cleavage, and replication of two viroid-like satellite RNAs (virusoids) of subterranean clover mottle virus. Virology. 1990 Jul;177(1):216–224. doi: 10.1016/0042-6822(90)90475-7. [DOI] [PubMed] [Google Scholar]
  3. Davies C., Sheldon C. C., Symons R. H. Alternative hammerhead structures in the self-cleavage of avocado sunblotch viroid RNAs. Nucleic Acids Res. 1991 Apr 25;19(8):1893–1898. doi: 10.1093/nar/19.8.1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Elena S. F., Dopazo J., Flores R., Diener T. O., Moya A. Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5631–5634. doi: 10.1073/pnas.88.13.5631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Flores R., Hernández C., Desvignes J. C., Llácer G. Some properties of the viroid inducing peach latent mosaic disease. Res Virol. 1990 Jan-Feb;141(1):109–118. doi: 10.1016/0923-2516(90)90060-v. [DOI] [PubMed] [Google Scholar]
  7. Forster A. C., Davies C., Hutchins C. J., Symons R. H. Characterization of self-cleavage of viroid and virusoid RNAs. Methods Enzymol. 1990;181:583–607. doi: 10.1016/0076-6879(90)81153-l. [DOI] [PubMed] [Google Scholar]
  8. Forster A. C., Davies C., Sheldon C. C., Jeffries A. C., Symons R. H. Self-cleaving viroid and newt RNAs may only be active as dimers. Nature. 1988 Jul 21;334(6179):265–267. doi: 10.1038/334265a0. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Gubler U., Hoffman B. J. A simple and very efficient method for generating cDNA libraries. Gene. 1983 Nov;25(2-3):263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. 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]
  13. Koltunow A. M., Rezaian M. A. A scheme for viroid classification. Intervirology. 1989;30(4):194–201. doi: 10.1159/000150093. [DOI] [PubMed] [Google Scholar]
  14. Koltunow A. M., Rezaian M. A. Grapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Res. 1988 Feb 11;16(3):849–864. doi: 10.1093/nar/16.3.849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Puchta H., Ramm K., Sänger H. L. The molecular structure of hop latent viroid (HLV), a new viroid occurring worldwide in hops. Nucleic Acids Res. 1988 May 25;16(10):4197–4216. doi: 10.1093/nar/16.10.4197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
  18. Spieker R. L., Haas B., Charng Y. C., Freimüller K., Sänger H. L. Primary and secondary structure of a new viroid 'species' (CbVd 1) present in the Coleus blumei cultivar 'Bienvenue'. Nucleic Acids Res. 1990 Jul 11;18(13):3998–3998. doi: 10.1093/nar/18.13.3998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Steger G., Hofmann H., Förtsch J., Gross H. J., Randles J. W., Sänger H. L., Riesner D. Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. J Biomol Struct Dyn. 1984 Dec;2(3):543–571. doi: 10.1080/07391102.1984.10507591. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]

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