Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis
| Autor: | Angel Emilio Martínez de Alba, Ricardo Flores, Beatriz Navarro, Giacinto Donvito, Sonia Delgado, Francesco Di Serio, Andreas Gisel |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: |
Cytoplasm
Chloroplasts Viroid Oligonucleotides lcsh:Medicine RNA-dependent RNA polymerase peach Silencing pathways Illumina Self-cleavage Biochemistry/RNA Structure Small nucleolar RNA lcsh:Science Virology/Effects of Virus Infection on Host Gene Expression Genetics Dicer-like proteins Multidisciplinary Models Genetic biology Sequence Analysis RNA lcsh:R Genetic Variation RNA Argonaute Blotting Northern RNA-Dependent RNA Polymerase biology.organism_classification Virology Viroids Long non-coding RNA RNA silencing Genetic Techniques Virology/Viral Replication and Gene Regulation Infected tomato plants Nucleic Acid Conformation lcsh:Q RNA Interference Prunus Molecular Biology/RNA-Protein Interactions Virology/Host Antiviral Responses Peach latent mosaic viroid Software Research Article |
| Zdroj: | PLoS ONE PLoS ONE, Vol 4, Iss 10, p e7539 (2009) Digital.CSIC. Repositorio Institucional del CSIC instname PloS one 4 (2009): e7539. doi:10.1371/journal.pone.0007539 info:cnr-pdr/source/autori:Di Serio F.(1); Gisel A.(2); Navarro B.(1), Delgado S.(3); Martínez de Alba Á.E. (3); Donvito G. (4); Flores R. (3)/titolo:Deep Sequencing of the Small RNAs Derived from two Symptomatic Variants of a Chloroplastic Viroid: Implications for their Genesis and for Viroid Pathogenesis/doi:10.1371%2Fjournal.pone.0007539/rivista:PloS one/anno:2009/pagina_da:e7539/pagina_a:/intervallo_pagine:e7539/volume:4 |
| DOI: | 10.1371/journal.pone.0007539 |
| Popis: | Northern-blot hybridization and low-scale sequencing have revealed that plants infected by viroids, non-protein-coding RNA replicons, accumulate 21–24 nt viroid-derived small RNAs (vd-sRNAs) similar to the small interfering RNAs, the hallmarks of RNA silencing. These results strongly support that viroids are elicitors and targets of the RNA silencing machinery of their hosts. Low-scale sequencing, however, retrieves partial datasets and may lead to biased interpretations. To overcome this restraint we have examined by deep sequencing (Solexa-Illumina) and computational approaches the vdsRNAs accumulating in GF-305 peach seedlings infected by two molecular variants of Peach latent mosaic viroid (PLMVd) inciting peach calico (albinism) and peach mosaic. Our results show in both samples multiple PLMVd-sRNAs, with prevalent 21-nt (+) and (2) RNAs presenting a biased distribution of their 59 nucleotide, and adopting a hotspot profile along the genomic (+) and (2) RNAs. Dicer-like 4 and 2 (DCL4 and DCL2, respectively), which act hierarchically in antiviral defense, likely also mediate the genesis of the 21- and 22-nt PLMVd-sRNAs. More specifically, because PLMVd replicates in plastids wherein RNA silencing has not been reported, DCL4 and DCL2 should dice the PLMVd genomic RNAs during their cytoplasmic movement or the PLMVd-dsRNAs generated by a cytoplasmic RNA-dependent RNA polymerase (RDR), like RDR6, acting in concert with DCL4 processing. Furthermore, given that vd-sRNAs derived from the 12–14-nt insertion containing the pathogenicity determinant of peach calico are underrepresented, it is unlikely that symptoms may result from the accidental targeting of host mRNAs by vd-sRNAs from this determinant guiding the RNA silencing machinery. This work was supported by the Ministerio de Ciencia e Innovacio´n and the Generalidad Valenciana of Spain (BFU2008-03154/BMC and ACOMP/2009/ 151, respectively, to R.F.) and the Dipartimento Agroalimentare of the CNR of Italy (A. Leone and D. Mariotti 2008 award for advanced research in agriculture to F.D.S.). Funding for open access charge: Universidad Polite´cnica de Valencia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. |
| Databáze: | OpenAIRE |
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