Viroid diseases in pome and stone fruit trees and Koch s postulates: a critical assessment

[EN] Composed of a naked circular non-protein-coding genomic RNA, counting only a few hundred nucleotides, viroids¿the smallest infectious agents known so far¿are able to replicate and move systemically in herbaceous and woody host plants, which concomitantly may develop specific diseases or remain symptomless. Several viroids have been reported to naturally infect pome and stone fruit trees, showing symptoms on leaves, fruits and/or bark. However, Koch¿s postulates required for establishing on firm grounds the viroid etiology of these diseases, have not been met in all instances. Here, pome and stone fruit tree diseases, conclusively proven to be caused by viroids, are reviewed, and the need to pay closer attention to fulfilling Koch¿s postulates is emphasized. View Full-TextThis project has received funding from the European Union's Horizon 2020 Research and Innovation Scientific Exchange Program under the Marie Sklodowska-Curie grant agreement No. 734736. This publication reflects only the authors' view. The Agency is not responsible for any use that may be made of the information it contains.Di Serio, F.; Ambros Palaguerri, S.; Sano, T.; Flores Pedauye, R.; Navarro, B. (2018). Viroid diseases in pome and stone fruit trees and Koch s postulates: a critical assessment. Viruses. 10(11). https://doi.org/10.3390/v101106121011Diener, T. O. (1971). Potato spindle tuber «virus». Virology, 45(2), 411-428. doi:10.1016/0042-6822(71)90342-4Flores, R., Minoia, S., Carbonell, A., Gisel, A., Delgado, S., López-Carrasco, A., … Di Serio, F. (2015). Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Research, 209, 136-145. doi:10.1016/j.virusres.2015.02.027López-Carrasco, A., & Flores, R. (2016). Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A «naked» rod-like conformation similar but not identical to that observed in vitro. RNA Biology, 14(8), 1046-1054. doi:10.1080/15476286.2016.1223005López-Carrasco, A., & Flores, R. (2017). The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins. Journal of General Virology, 98(7), 1913-1922. doi:10.1099/jgv.0.000846Flores, R., Hernández, C., Alba, A. E. M. de, Daròs, J.-A., & Serio, F. D. (2005). Viroids and Viroid-Host Interactions. Annual Review of Phytopathology, 43(1), 117-139. doi:10.1146/annurev.phyto.43.040204.140243Di Serio, F., Flores, R., Verhoeven, J. T. J., Li, S.-F., Pallás, V., Randles, J. W., … Owens, R. A. (2014). Current status of viroid taxonomy. Archives of Virology, 159(12), 3467-3478. doi:10.1007/s00705-014-2200-6Di Serio, F., Li, S.-F., Matoušek, J., Owens, R. A., Pallás, V., … Randles, J. W. (2018). ICTV Virus Taxonomy Profile: Avsunviroidae. Journal of General Virology, 99(5), 611-612. doi:10.1099/jgv.0.001045Diener, T. O., Smith, D. R., & O’Brien, M. J. (1972). Potato spindle tuber viroid. Virology, 48(3), 844-846. doi:10.1016/0042-6822(72)90166-3Diener, T. O. (1972). Potato spindle tuber viroid. Virology, 50(2), 606-609. doi:10.1016/0042-6822(72)90412-6Semancik, J. S. (1970). Properties of the Infectious Forms of Exocortis Virus of Citrus. Phytopathology, 60(4), 732. doi:10.1094/phyto-60-732Semancik, J. S., Morris, T. J., & Weathers, L. G. (1973). Structure and conformation of low molecular weight pathogenic RNA from exocortis disease. Virology, 53(2), 448-456. doi:10.1016/0042-6822(73)90224-9Bos, L. (1981). Hundred years of Koch’s Postulates and the history of etiology in plant virus research. Netherlands Journal of Plant Pathology, 87(3), 91-110. doi:10.1007/bf01976645Schumacher, J., Randles, J. W., & Riesner, D. (1983). A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids. Analytical Biochemistry, 135(2), 288-295. doi:10.1016/0003-2697(83)90685-1Flores, R., Duran-Vila, N., Pallas, V., & Semancik, J. S. (1985). Detection of Viroid and Viroid-like RNAs from Grapevine. Journal of General Virology, 66(10), 2095-2102. doi:10.1099/0022-1317-66-10-2095Serio, F. D., Malfitano, M., Alioto, D., Ragozzino, A., Desvignes, J. C., & Flores, R. (2001). Apple dimple fruit viroid: Fulfillment of Koch’s Postulates and Symptom Characteristics. Plant Disease, 85(2), 179-182. doi:10.1094/pdis.2001.85.2.179Pallas, V., Navarro, A., & Flores, R. (1987). Isolation of a Viroid-like RNA from Hop Different from Hop Stunt Viroid. Journal of General Virology, 68(12), 3201-3205. doi:10.1099/0022-1317-68-12-3201Navarro, B., & Flores, R. (1997). Chrysanthemum chlorotic mottle viroid: Unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proceedings of the National Academy of Sciences, 94(21), 11262-11267. doi:10.1073/pnas.94.21.11262De la Pena, M., Navarro, B., & Flores, R. (1999). Mapping the molecular determinant of pathogenicity in a hammerhead viroid: A tetraloop within the in vivo branched RNA conformation. Proceedings of the National Academy of Sciences, 96(17), 9960-9965. doi:10.1073/pnas.96.17.9960Bellamy, A. R., & Ralph, R. K. (1968). [104] Recovery and purification of nucleic acids by means of cetyltrimethylammonium bromide. Nucleic Acids, Part B, 156-160. doi:10.1016/0076-6879(67)12125-3Codoñer, F. M., Darós, J.-A., Solé, R. V., & Elena, S. F. (2006). The Fittest versus the Flattest: Experimental Confirmation of the Quasispecies Effect with Subviral Pathogens. PLoS Pathogens, 2(12), e136. doi:10.1371/journal.ppat.0020136Hashimoto, J., & Koganezawa, H. (1987). Nucleotide sequence and secondary structure of apple scar skin viroid. Nucleic Acids Research, 15(17), 7045-7052. doi:10.1093/nar/15.17.7045Zhu, S. F., Hadidi, A., & Hammond, R. W. (1998). AGROINFECTION OF PEAR AND APPLE WITH DAPPLE APPLE VIROID RESULTS IN SYSTEMIC INFECTION. Acta Horticulturae, (472), 613-616. doi:10.17660/actahortic.1998.472.81OSAKI, H., KUDO, A., & OHTSU, Y. (1996). Japanese Pear Fruit Dimple Disease Caused by Apple Scar Skin Viroid (ASSVd). Japanese Journal of Phytopathology, 62(4), 379-385. doi:10.3186/jjphytopath.62.379Ito, T., & Yoshida, K. (1998). REPRODUCTION OF APPLE FRUIT CRINKLE DISEASE SYMPTOMS BY APPLE FRUIT CRINKLE VIROID. Acta Horticulturae, (472), 587-594. doi:10.17660/actahortic.1998.472.78Hadidi, A., & Yang, X. (1990). Detection of pome fruit viroids by enzymatic cDNA amplification. Journal of Virological Methods, 30(3), 261-269. doi:10.1016/0166-0934(90)90068-qKyriakopoulou, P. E., & Hadidi, A. (1998). NATURAL INFECTION OF WILD AND CULTIVATED PEARS WITH APPLE SCAR SKIN VIROID IN GREECE. Acta Horticulturae, (472), 617-626. doi:10.17660/actahortic.1998.472.82Ambros, S., Desvignes, J. C., Llacer, G., & Flores, R. (1995). Pear blister canker viroid: sequence variability and causal role in pear blister canker disease. Journal of General Virology, 76(10), 2625-2629. doi:10.1099/0022-1317-76-10-2625Sano, T., Hataya, T., Terai, Y., & Shikata, E. (1989). Hop Stunt Viroid Strains from Dapple Fruit Disease of Plum and Peach in Japan. Journal of General Virology, 70(6), 1311-1319. doi:10.1099/0022-1317-70-6-1311Flores, R., Hernández, C., Desvignes, J. C., & Llácer, G. (1990). Some properties of the viroid inducing peach latent mosaic disease. Research in Virology, 141(1), 109-118. doi:10.1016/0923-2516(90)90060-vMalfitano, M., Di Serio, F., Covelli, L., Ragozzino, A., Hernández, C., & Flores, R. (2003). Peach latent mosaic viroid variants inducing peach calico (extreme chlorosis) contain a characteristic insertion that is responsible for this symptomatology. Virology, 313(2), 492-501. doi:10.1016/s0042-6822(03)00315-5Puchta, H., Luckinger, R., Yang, X., Hadidi, A., & S�nger, H. L. (1990). Nucleotide sequence and secondary structure of apple scar skin viroid (ASSVd) from China. Plant Molecular Biology, 14(6), 1065-1067. doi:10.1007/bf00019406KOGANEZAWA, H. (1985). Transmission to apple seedlings of a low molecular weight RNA extracted from apple scar skin diseased trees. Japanese Journal of Phytopathology, 51(2), 176-182. doi:10.3186/jjphytopath.51.176Koganezawa, H. (1986). FURTHER EVIDENCE FOR VIROID ETIOLOGY OF APPLE SCAR SKIN AND DAPPLE APPLE DISEASES. Acta Horticulturae, (193), 29-34. doi:10.17660/actahortic.1986.193.2Yamaguch, A., & Yanase, H. (1976). POSSIBLE RELATIONSHIP BETWEEN THE CAUSAL AGENT OF DAPPLE APPLE AND SCAR SKIN. Acta Horticulturae, (67), 249-254. doi:10.17660/actahortic.1976.67.31Desvignes, J. C., Grasseau, N., Boyé, R., Cornaggia, D., Aparicio, F., Di Serio, F., & Flores, R. (1999). Biological Properties of Apple Scar Skin Viroid: Isolates, Host Range, Different Sensitivity of Apple Cultivars, Elimination, and Natural Transmission. Plant Disease, 83(8), 768-772. doi:10.1094/pdis.1999.83.8.768Walia, Y., Dhir, S., Bhadoria, S., Hallan, V., & Zaidi, A. A. (2011). Molecular characterization of Apple scar skin viroid from Himalayan wild cherry. Forest Pathology, 42(1), 84-87. doi:10.1111/j.1439-0329.2011.00723.xDi Serio, F., Aparicio, F., Alioto, D., Ragozzino, A., & Flores, R. (1996). Identification and molecular properties of a 306 nucleotide viroid associated with apple dimple fruit disease. Journal of General Virology, 77(11), 2833-2837. doi:10.1099/0022-1317-77-11-2833Di Serio, F., Giunchedi, L., Alioto, D., Ragozzino, A., & Flores, R. (1998). IDENTIFICATION OF APPLE DIMPLE FRUIT VIROID IN DIFFERENT COMMERCIAL VARIETIES OF APPLE GROWN IN ITALY. Acta Horticulturae, (472), 595-602. doi:10.17660/actahortic.1998.472.79Roumi, V., Gazel, M., & Caglayan, K. (2017). First report of Apple dimple fruit viroid in apple trees in Iran. New Disease Reports, 35, 3. doi:10.5197/j.2044-0588.2017.035.003He, Y.-H., Isono, S., Kawaguchi-Ito, Y., Taneda, A., Kondo, K., Iijima, A., … Sano, T. (2010). Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees. Journal of General Plant Pathology, 76(5), 324-330. doi:10.1007/s10327-010-0258-xChiumenti, M., Torchetti, E. M., Di Serio, F., & Minafra, A. (2014). Identification and characterization of a viroid resembling apple dimple fruit viroid in fig (Ficus carica L.) by next generation sequencing of small RNAs. Virus Research, 188, 54-59. doi:10.1016/j.virusres.2014.03.026ITO, T., KANEMATSU, S., KOGANEZAWA, H., TSUCHIZAKI, T., & YOSHIDA, K. (1993). Detection of a Viroid Associated with Apple Fruit Crinkle Disease. Japanese Journal of Phytopathology, 59(5), 520-527. doi:10.3186/jjphytopath.59.520Sano, T., Yoshida, H., Goshono, M., Monma, T., Kawasaki, H., & Ishizaki, K. (2004). Characterization of a new viroid strain from hops: evidence for viroid speciation by isolation in different host species. Journal of General Plant Pathology, 70(3), 181-187. doi:10.1007/s10327-004-0105-zNakaune, R., & Nakano, M. (2008). Identification of a new Apscaviroid from Japanese persimmon. Archives of Virology, 153(5), 969-972. doi:10.1007/s00705-008-0073-2Hernandez, C., Elena, S. F., Moya, A., & Flores, R. (1992). Pear Blister Canker Viroid is a Member of the Apple Scar Skin Subgroup (apscaviroids) and also has Sequence Homology with Viroids from other Subgroups. Journal of General Virology, 73(10), 2503-2507. doi:10.1099/0022-1317-73-10-2503Lemoine, J. (1986). PROBLEMS REGARDING THE DETECTION OF GRAFT TRANSMITTED PEAR CANKER. Acta Horticulturae, (193), 251-260. doi:10.17660/actahortic.1986.193.43Ambrós, S., Llácer, G., Desvignes, J. C., & Flores, R. (1995). PEACH LATENT MOSAIC AND PEAR BLISTER CANKER VIROIDS: DETECTION BY MOLECULAR HYBRIDIZATION AND RELATIONSHIPS WITH SPECIFIC MALADIES AFFECTING PEACH AND PEAR TREES. Acta Horticulturae, (386), 515-521. doi:10.17660/actahortic.1995.386.74Flores, R., Hernandez, C., Llacer, G., & Desvignes, J. C. (1991). Identification of a new viroid as the putative causal agent of pear blister canker disease. Journal of General Virology, 72(6), 1199-1204. doi:10.1099/0022-1317-72-6-1199Desvignes, J. C., Cornaggia, D., Grasseau, N., Ambrós, S., & Flores, R. (1999). Pear Blister Canker Viroid: Host Range and Improved Bioassay with Two New Pear Indicators, Fieud 37 and Fieud 110. Plant Disease, 83(5), 419-422. doi:10.1094/pdis.1999.83.5.419SASAKI, M., & SHIKATA, E. (1977). On Some Properties of Hop Stunt Disease Agent, a Viroid. Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 53(3), 109-112. doi:10.2183/pjab.53.109Ohno, T., Takamatsu, N., Meshi, T., & Okada, Y. (1983). Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy. Nucleic Acids Research, 11(18), 6185-6197. doi:10.1093/nar/11.18.6185Kofalvi, S. A., Pall√°s, V., Marcos, J. F., Candresse, T., & Ca√±izares, M. C. (1997). Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates. Journal of General Virology, 78(12), 3177-3186. doi:10.1099/0022-1317-78-12-3177Amari, K., Gomez, G., Myrta, A., Di Terlizzi, B., & Pallás, V. (2001). The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule The sequences described in this work have been deposited in the EMBL database and received accession numbers AJ297825 to AJ297840. Journal of General Virology, 82(4), 953-962. doi:10.1099/0022-1317-82-4-953SANO, T., HATAYA, T., TERAI, Y., & SHIKATA, E. (1986). Association of a viroid-like RNA from plum dapple disease occurring in Japan. Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 62(3), 98-101. doi:10.2183/pjab.62.98Hernandez, C., & Flores, R. (1992). Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proceedings of the National Academy of Sciences, 89(9), 3711-3715. doi:10.1073/pnas.89.9.3711Ambros, S. (1998). In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket. Nucleic Acids Research, 26(8), 1877-1883. doi:10.1093/nar/26.8.1877Ambrós, S., Hernández, C., & Flores, R. (1999). Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host The data reported in this paper are in the EMBL nucleotide sequence database and assigned the accession nos AJ241818–AJ241850. Journal of General Virology, 80(8), 2239-2252. doi:10.1099/0022-1317-80-8-2239Fekih Hassen, I., Massart, S., Motard, J., Roussel, S., Parisi, O., Kummert, J., … Jijakli, M. H. (2007). Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology, 360(1), 50-57. doi:10.1016/j.virol.2006.10.021DUBÉ, A., BOLDUC, F., BISAILLON, M., & PERREAULT, J.-P. (2011). Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Molecular Plant Pathology, 12(7), 688-701. doi:10.1111/j.1364-3703.2010.00703.xBussière, F., Ouellet, J., Côté, F., Lévesque, D., & Perreault, J. P. (2000). Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure. Journal of Virology, 74(6), 2647-2654. doi:10.1128/jvi.74.6.2647-2654.2000FLORES, R., DELGADO, S., RODIO, M.-E., AMBRÓS, S., HERNÁNDEZ, C., & SERIO, F. D. (2006). Peach latent mosaic viroid: not so latent. Molecular Plant Pathology, 7(4), 209-221. doi:10.1111/j.1364-3703.2006.00332.xDesvignes, J. C. (1976). THE VIRUS DISEASES DETECTED IN GREENHOUSE AND IN FIELD BY THE PEACH SEEDLING GF 305 INDICATOR. Acta Horticulturae, (67), 315-323. doi:10.17660/actahortic.1976.67.41DESVIGNES, J. C. (1986). PEACH LATENT MOSAIC AND ITS RELATION TO PEACH MOSAIC AND PEACH YELLOW MOSAIC VIRUS DISEASES. Acta Horticulturae, (193), 51-58. doi:10.17660/actahortic.1986.193.6Flores, R., & Llácer, G. (1989). ISOLATION OF A VIROID-LIKE RNA ASSOCIATED WITH PEACH LATENT MOSAIC DISEASE. Acta Horticulturae, (235), 325-332. doi:10.17660/actahortic.1989.235.47Rodio, M.-E., Delgado, S., Flores, R., & Serio, F. D. (2006). Variants of Peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant. Journal of General Virology, 87(1), 231-240. doi:10.1099/vir.0.81356-0Rodio, M.-E., Delgado, S., De Stradis, A., Gómez, M.-D., Flores, R., & Di Serio, F. (2007). A Viroid RNA with a Specific Structural Motif Inhibits Chloroplast Development. The Plant Cell, 19(11), 3610-3626. doi:10.1105/tpc.106.049775Navarro, B., Gisel, A., Rodio, M. E., Delgado, S., Flores, R., & Di Serio, F. (2012). Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. The Plant Journal, 70(6), 991-1003. doi:10.1111/j.1365-313x.2012.04940.xWang, L., He, Y., Kang, Y., Hong, N., Farooq, A. B. U., Wang, G., & Xu, W. (2013). Virulence determination and molecular features of peach latent mosaic viroid isolates derived from phenotypically different peach leaves: A nucleotide polymorphism in L11 contributes to symptom alteration. Virus Research, 177(2), 171-178. doi:10.1016/j.virusres.2013.08.005Zhang, Z., Qi, S., Tang, N., Zhang, X., Chen, S., Zhu, P., … Wu, Q. (2014). Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms. PLoS Pathogens, 10(12), e1004553. doi:10.1371/journal.ppat.1004553Serra, P., Messmer, A., Sanderson, D., James, D., & Flores, R. (2018). Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Research, 249, 8-15. doi:10.1016/j.virusres.2018.03.001Messmer, A., Sanderson, D., Braun, G., Serra, P., Flores, R., & James, D. (2017). Molecular and phylogenetic identification of unique isolates of hammerhead viroid-like RNA from ‘Pacific Gala’ apple (Malus domestica) in Canada. Canadian Journal of Plant Pathology, 39(3), 342-353. doi:10.1080/07060661.2017.1354334Wu, Q., Wang, Y., Cao, M., Pantaleo, V., Burgyan, J., Li, W.-X., & Ding, S.-W. (2012). Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proceedings of the National Academy of Sciences, 109(10), 3938-3943. doi:10.1073/pnas.1117815109Hadidi, A., Flores, R., Candresse, T., & Barba, M. (2016). Next-Generation Sequencing and Genome Editing in Plant Virology. Frontiers in Microbiology, 7. doi:10.3389/fmicb.2016.0132