Abstract
We have found a linear, 16 kb, double-stranded RNA (dsRNA) in symptomless Japonica rice (Oryza sativa L.) that is not found in Indica rice (Oryza sativa L.). The dsRNA was detected in every tissue and at every developmental stage, and its copy number was approximately constant (about 20 copies/cell). Double-stranded RNA was also detected in two strains of Oryza rufipogon (an ancestor of O. sativa). Hybridization experiments indicated that the dsRNA of O. rufipogon was homologous but not identical to that of O. sativa. The sequence of about 13.2 kb of the dsRNA was determined and two open reading frames (ORFs) were found. The larger ORF (ORF B) was more than 12 351 nucleotides long and encoded more than 4 117 amino acid residues.
Similar content being viewed by others
References
Boccardo G, Lisa V, Luisoni E, Milne RG: Cryptic plant viruses. Adv Virus Res 32: 171–214 (1987).
Cordesse F, Second G, Delseny M: Ribosomal gene spacer lenght variability in cultivated and wild rice species. Theor Appl Genet 79: 81–88 (1990).
Dekochko A, Kiefer MC, Cordesse F, Reddy AS, Delseny M: Distribution and organization of a tandemly repeated 352-bp sequence in the Oryzae family. Theor Appl Genet 82: 57–64 (1991).
Dodds JA, Morris TJ, Jordan RL: Plant viral double-stranded RNA. Annu Rev Phytopath 22: 151–168 (1984).
Dodds JA, Valverde RA, Mathews DM: Detection and interpretation of dsRNA. In: Koltin Y, Leibowitz MJ (eds) Viruses of Fungi and Simple Eukaryotes, pp. 309–326. Marcel Dekker, New York (1988).
Fairbanks DJ, Smith SE, Brown JK: Inheritance of large mitochondrial RNA's in alfalfa. Theor Appl Genet 76: 619–622 (1988).
Gabriel CJ, Walsh R, Nolt BL: Evidence for a latent viruslike agent in cassava. Phytopathology 77: 92–95 (1987).
Grill LK, Garger SJ: Identification and characterization of double-stranded RNA associated with cytoplasmic male sterility in Vicia faba. Proc Natl Acad Sci USA 78: 7043–7046 (1981).
Hanahan D: Techniques for transformation of E. coli. In: Glover DM (ed) DNA Cloning: A Practical Approach, vol. 1, pp. 109–135. IRL Press, Oxford/Washington DC (1985).
Icho T, Wickner RB: The double-stranded RNA genome of yeast virus L-A encodes its own putative RNA polymerase by fusing two open reading frames. J Biol Chem 264: 6716–6723 (1989).
International Rice Research Institute (IRRI): Rice Genetics, Proceedings of the International Rice Genetics Symposium, Los Banos, Philippines, (1986).
Ishihara J, Pak JK, Fukuhara T, Nitta T: Association of particles that contain double-stranded RNAs with algal chloroplasts and mitochondria. Planta 187: 475–482 (1992).
Kadowaki K, Yazaki K, Osumi T, Harada K, Katsuta M, Nakagahara M: Distribution of mitochondrial plasmid-like DNA in cultivated rice (Oryza sativa L.) and its relationship with varietal groups. Theor Appl Genet 76: 809–814 (1988).
Lefebvre A, Scalla R, Pfeiffer P: The double-stranded RNA associated with the ‘447’ cytoplasmic male sterility in Vicia faba is packaged together with its replicase in cytplasmic membranous vesicles. Plant Mol Biol 14: 477–490 (1990).
Mackenzie SA, Pring DR, Bassett MJ: Large double-stranded RNA molecules in Phaseolus vulgaris L. are not associated with cytoplasmic male sterility. Theor Appl Genet 76: 59–63 (1988).
McCrae MA: Double-stranded RNA viruses. In: Mahy BWJ (ed) Virology: A Practical Approach, pp. 151–168. IRL Press, Oxford/Washington DC (1985).
Morris TJ, Dodds JA: Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69: 854–858 (1979).
Nuss DL, Dall DJ: Structural and functional properties of plant reovirus genomes. Adv Virus Res 38: 249–306 (1990).
Rogers SO, Bendich AJ: Extraction of DNA from plant tissues. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual, pp. A6/1-A6/10. Kluwer Academic Publishers, Dordrecht (1988).
Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).
Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467 (1977).
Sano Y, Sano R: Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33: 209–218 (1990).
Schuster AM, Sisco PH: Isolation and characterization of single-stranded and double-stranded RNAs in mitochondria. Meth Enzymol 118: 497–507 (1986).
Second G: Origin of the genic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57: 25–57 (1982).
Shapira R, Choi GH, Nuss DL: Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight. EMBO J 10: 731–739 (1991).
Turpen T, Garger SJ, Grill LK: On the mechanism of cytoplasmic male sterility in the 447 line of Vicia faba. Plant Mol Biol 10: 489–497 (1988).
Valverde RA, Fontenot JF: Variation in double-stranded ribonucleic acid among pepper cultivars. J Amer Soc Hort Sci 116: 903–905 (1990).
Valverde RA, Nameth S, Abdallha O, Al-Musa O, Desjardins P, Dodds JA: Indigenous double-stranded RNA from pepper (Capsicum annuum). Plant Sci 67: 195–201 (1990).
Wakarchuk DA, Hamilton RI: Cellular double-stranded RNA in Phaseolus vulgaris. Plant Mol Biol 5: 55–63 (1985).
Wakarchuk DA, Hamilton RI: Partial nucleotide sequence from enigmatic dsRNAs in Phaseolus vulgaris. Plant Mol Biol 14: 637–639 (1990).
Wang B, Li YN, Zhang XW, Hu L, Wang JZ: Double-stranded RNA and male sterility in rice. Theor Appl Genet 79: 556–560 (1990).
Zabalgogeazcoa IA, Gildow FE: Double-stranded ribonucleic acid in ‘Barsoy’ barley. Plant Sci 83: 187–194 (1992).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Fukuhara, T., Moriyama, H., Pak, J. et al. Enigmatic double-stranded RNA in Japonica rice. Plant Mol Biol 21, 1121–1130 (1993). https://doi.org/10.1007/BF00023608
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00023608