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Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

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Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

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Serra Alfonso, P.; Bertolini, E.; Martinez, MC.; Cambra, M.; Flores Pedauye, R. (2017). Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection. Scientific Reports. 7. https://doi.org/10.1038/srep42825

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Título: Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection
Autor: Serra Alfonso, Pedro Bertolini, Edson Martinez, M. Carmen Cambra, Mariano Flores Pedauye, Ricardo
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Natural populations of peach latent mosaic viroid (PLMVd) are complex mixtures of variants. During routine testing, TaqMan rtRT-PCR and RNA gel-blot hybridization produced discordant results with some PLMVd isolates. ...[+]
Derechos de uso: Reconocimiento (by)
Fuente:
Scientific Reports. (issn: 2045-2322 )
DOI: 10.1038/srep42825
Editorial:
Nature Publishing Group
Versión del editor: https://doi.org/10.1038/srep42825
Código del Proyecto:
info:eu-repo/grantAgreement/MINECO//BFU2014-56812-P/ES/VIROIDES, LOS PARASITOS EXTREMOS: EVOLUCION ESPACIO-TEMPORAL, PATOGENESIS MEDIADA POR SILENCIAMIENTO VIA RNA, Y DEGRADACION/
info:eu-repo/grantAgreement/MINECO//INIA-CCA2011-2016
Agradecimientos:
We thank A. Ahuir for excellent technical assistance and Dr. Francesco Di Serio for suggestions. This work was supported by grant BFU2014-56812-P (to R.F.) from Ministerio de Economia y Competitividad (MINECO) of Spain. ...[+]
Tipo: Artículo

References

Diener, T. O. Discovering viroids - a personal perspective. Nat. Rev. Microbiol. 1, 75–80 (2003).

Flores, R., Hernández, C., Martínez de Alba, A. E., Daròs, J. A. & Di Serio, F. Viroids and viroid–host interactions. Annu. Rev. Phytopathol. 43, 117–139 (2005).

Tsagris, E. M., Martínez de Alba, A. E., Gozmanova, M. & Kalantidis, K. Viroids. Cell Microbiol. 10, 2168–2179 (2008). [+]
Diener, T. O. Discovering viroids - a personal perspective. Nat. Rev. Microbiol. 1, 75–80 (2003).

Flores, R., Hernández, C., Martínez de Alba, A. E., Daròs, J. A. & Di Serio, F. Viroids and viroid–host interactions. Annu. Rev. Phytopathol. 43, 117–139 (2005).

Tsagris, E. M., Martínez de Alba, A. E., Gozmanova, M. & Kalantidis, K. Viroids. Cell Microbiol. 10, 2168–2179 (2008).

Ding, B. The biology of viroid–host interactions. Annu. Rev. Phytopathol. 47, 105–131 (2009).

Kovalskaya, N. & Hammond, R. W. Molecular biology of viroid-host interactions and disease control strategies. Plant Sci. 228, 48–60 (2014).

Palukaitis, P. What has been happening with viroids? Virus Genes 49, 175–184 (2014).

Flores, R. et al. Viroids, the simplest RNA replicons: how they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res. 209, 136–145 (2015).

Hernández, C. & Flores, R. Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proc. Natl. Acad. Sci. USA 89, 3711–3715 (1992).

Flores, R. et al. Peach latent mosaic viroid: not so latent. Mol. Plant Pathol. 4, 209–221 (2006).

Ambrós, S., Hernández, C., Desvignes, J. C. & Flores, R. Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasi-species. J. Virol. 72, 7397–7406 (1998).

Ambrós, S., Hernández, C. & Flores, R. Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host. J. Gen. Virol. 80, 2239–2252 (1999).

Malfitano, M. et al. Peach latent mosaic viroid variants inducing peach calico contain a characteristic insertion that is responsible for this symptomatology. Virology 313, 492–501 (2003).

Rodio, M. E., Delgado, S., Flores, R. & Di Serio, F. Variants of peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant. J. Gen. Virol. 87, 231–240 (2006).

Rodio, M. E. et al. A viroid RNA with a specific structural motif inhibits chloroplast development. Plant Cell 19, 3610–3626 (2007).

Navarro, B. et al. Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. Plant J. 70, 991–1003 (2012).

Yazarlou, A., Jafarpour, B., Tarighi, S., Habili, N. & Randles, J. W. New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution. Arch. Virol. 157, 343–347 (2012).

Wang, L. P. et al. 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 Res. 177, 171–178 (2013).

Desvignes, J. C. The virus diseases detected in greenhouse and in the field by the peach seedling GF 305 indicator. Acta Hortic. 67, 315–323 (1976).

Flores, R. & Llácer, G. Isolation of a viroid-like RNA associated with peach latent mosaic disease. Acta Hortic. 235, 325–332 (1988).

Flores, R., Hernández, C., Desvignes, J. C. & Llácer, G. Some properties of the viroid inducing the peach latent mosaic disease. Res. Virol. 141, 109–118 (1990).

Ambrós, S., Desvignes, J. C., Llácer, G. & Flores, R. Peach latent mosaic and pear blister canker viroids: detection by molecular hybridization and relationships with specific maladies affecting peach and pear trees. Acta Hortic. 386, 515–521 (1995).

Loreti, S., Faggioli, F. & Barba, M. A rapid extraction method to detect peach latent mosaic viroid by molecular hybridization. Acta Hortic. 386, 560–564 (1995).

Skrzeczkowski, L. J., Howell, W. E. & Mink, G. I. Occurrence of peach latent mosaic viroid in commercial peach and nectarine cultivars in the US. Plant Dis. 80, 823 (1996).

Hadidi, A., Giunchedi, L., Shamloul, A. M., Poggi-Pollini, C. & Amer, M. A. Occurrence of peach latent mosaic viroid in stone fruits and its transmission with contaminated blades. Plant Dis. 81, 154–158 (1997).

Xu, W. X. et al. Probe binding to host proteins: a cause for false positive signals in viroid detection by tissue hybridization. Virus Res. 145, 26–30 (2009).

Shamloul, A. M. et al. Peach latent mosaic viroid: nucleotide sequence of an Italian isolate, sensitive detection using RT-PCR and geographic distribution. Acta Hortic. 386, 522–530 (1995).

Shamloul, A. M. & Hadidi, A. Sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization. J. Virol. Methods 80, 145–155 (1999).

Shamloul, A. M., Faggioli, F., Keith, J. M. & Hadidi, A. A novel multiplex RT-PCR probe capture hybridization (RT-PCR-ELISA) for simultaneous detection of six viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid, and Pospiviroid . J. Virol. Methods 105, 115–121 (2002).

Ragozzino, E., Faggioli, F. & Barba, M. Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid and Pospiviroid. J. Virol. Methods 121, 25–29 (2004).

Luigi, M. & Faggioli, F. Development of quantitative real-time RT-PCR for the detection and quantification of peach latent mosaic viroid. Eur. J. Plant Pathol. 130, 109–116 (2011).

Parisi, O., Lepoivre, P. & Jijakli, M. H. Development of a quick quantitative real-time PCR for the in vivo detection and quantification of peach latent mosaic viroid. Plant Dis. 95, 137–142 (2011).

Lin, L., Li, R., Bateman, M., Mock, R. & Kinard, G. Development of a multiplex TaqMan real-time RT-PCR assay for simultaneous detection of Asian prunus viruses, plum bark necrosis stem pitting associated virus, and peach latent mosaic viroid. Eur. J. Plant Pathol. 137, 797–804 (2013).

Zhang, Y. J. et al. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level. PLoS One 8, e64474 (2013).

Di Serio, F. et al. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 4, e7539 (2009).

Bolduc, F., Hoareau, C., St-Pierre, P. & Perreault, J. P. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol. Biol. 11, 16 (2010).

Glouzon, J. P. S., Bolduc, F., Wang, S., Najmanovich, R. J. & Perreault, J. P. Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity. PLoS One 9, e87297 (2014).

Jo, Y. et al. Complete genome sequences of peach latent mosaic viroid from a single peach cultivar. Genome Announc. 3, e01098–15 (2015).

Pelchat, M. et al. Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure. Virology 271, 37–45 (2000).

Bussière, F., Ouellet, J., Côté, F., Lévesque, D. & Perreault, J. P. Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure. J. Virol. 74, 2647–2654 (2000).

Dubé, A., Baumstark, T., Bisaillon, M. & Perreault, J. P. The RNA strands of the plus and minus polarities of peach latent mosaic viroid fold into different structures. RNA 16, 463–473 (2010).

Dubé, A., Bolduc, F., Bisaillon, M. & Perreault, J. P. Mapping studies of the peach latent mosaic viroid reveal novel structural features. Mol. Plant Pathol. 12, 688–701 (2011).

Gago, S., De la Peña, M. & Flores, R. A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability. RNA 11, 1073–1083 (2005).

Olmos, A., Bertolini, E., Gil, M. & Cambra, M. Real-time assay for quantitative detection of non-persistently transmitted plum pox virus RNA targets in single aphids. J. Virol. Methods 128, 151–155 (2005).

Ruffner, D. E., Stormo, G. D. & Uhlenbeck, O. C. Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695–10702 (1990).

Symons, R. H. Plant pathogenic RNAs and RNA catalysis. Nucleic Acids Res. 25, 2683–2689 (1997).

Flores, R., Hernández, C., De la Peña, M., Vera, A. & Daròs, J. A. Hammerhead ribozyme structure and function in plant RNA replication. Meth. Enzymol. 341, 540–552 (2001).

Hutchins, C., Rathjen, P. D., Forster, A. C. & Symons, R. H. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 14, 3627–3640 (1986).

Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R. & Bruening, G. Autolytic processing of dimeric plant virus satellite RNA. Science 231, 1577–1580 (1986).

Giguère, T., Adkar-Purushothamam, C., Bolduc, F. & Perreault, J. P. Elucidation of the structures of all members of the Avsunviroidae family. Mol. Plant Pathol. 15, 767–779 (2014).

Sheldon, C. C. & Symons, R. H. Is hammerhead self-cleavage involved in the replication of a virusoid in vivo? Virology 194, 463–474 (1993).

Biebricher, C. K. & Eigen, M. What is a quasispecies? Curr. Top. Microbiol. Immunol. 299, 1–31 (2006).

Ojosnegros, S., Perales, C., Mas, A. & Domingo, E. Quasispecies as a matter of fact: viruses and beyond. Virus Res. 162, 203–215 (2011).

Fekih Hassen, I. et al. Molecular features of new Peach latent mosaic viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology 360, 50–57 (2007).

Gazel, M., Ulubas Serce, C., Caglayan, K., Luigi, M. & Faggioli, F. Incidence and genetic diversity of peach latent mosaic viroid isolates in Turkey. J. Plant Pathol. 90, 495–503 (2008).

Niblett, C. L., Dickson, E., Fernow, K. H., Horst, R. K. & Zaitlin, M. Cross-protection among four viroids. Virology 91, 198–203 (1978).

Navarro, B. & Flores, R. Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proc. Natl. Acad. Sci. USA 94, 11262–11267 (1997).

De la Peña, M. & Flores, R. Chrysanthemum chlorotic mottle viroid RNA: dissection of the pathogenicity determinant and comparative fitness of symptomatic and non-symptomatic variants. J. Mol. Biol. 321, 411–421 (2002).

Carbonell, A., Martínez de Alba, A. E., Flores, R. & Gago, S. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families. Virology 371, 44–53 (2008).

Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

Nei, M. & Li, J. Variances of the average numbers of nucleotide substitutions within and between populations. Mol. Biol. Evol. 6, 290–300 (1989).

Capote, N. et al. Direct sample preparation methods for the detection of Plum pox virus by real-time RT-PCR. Interntl. Microbiol. 12, 1–6 (1999).

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