Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.
<h4>Background</h4>Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation o...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-11-01
|
| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19890399/?tool=EBI |
| _version_ | 1818736630368829440 |
|---|---|
| author | Beatriz Navarro Vitantonio Pantaleo Andreas Gisel Simon Moxon Tamas Dalmay György Bisztray Francesco Di Serio József Burgyán |
| author_facet | Beatriz Navarro Vitantonio Pantaleo Andreas Gisel Simon Moxon Tamas Dalmay György Bisztray Francesco Di Serio József Burgyán |
| author_sort | Beatriz Navarro |
| collection | DOAJ |
| description | <h4>Background</h4>Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21-24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms.<h4>Methodology/principal findings</h4>To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (-) viroid RNAs, with a prevalence of those from the (-) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots.<h4>Conclusions/significance</h4>These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression. |
| first_indexed | 2024-12-18T00:40:12Z |
| format | Article |
| id | doaj.art-82a5a8173127439eb7be0e12bf1ce24b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-18T00:40:12Z |
| publishDate | 2009-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-82a5a8173127439eb7be0e12bf1ce24b2022-12-21T21:26:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-11-01411e768610.1371/journal.pone.0007686Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.Beatriz NavarroVitantonio PantaleoAndreas GiselSimon MoxonTamas DalmayGyörgy BisztrayFrancesco Di SerioJózsef Burgyán<h4>Background</h4>Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21-24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms.<h4>Methodology/principal findings</h4>To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (-) viroid RNAs, with a prevalence of those from the (-) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots.<h4>Conclusions/significance</h4>These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19890399/?tool=EBI |
| spellingShingle | Beatriz Navarro Vitantonio Pantaleo Andreas Gisel Simon Moxon Tamas Dalmay György Bisztray Francesco Di Serio József Burgyán Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS ONE |
| title | Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. |
| title_full | Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. |
| title_fullStr | Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. |
| title_full_unstemmed | Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. |
| title_short | Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. |
| title_sort | deep sequencing of viroid derived small rnas from grapevine provides new insights on the role of rna silencing in plant viroid interaction |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19890399/?tool=EBI |
| work_keys_str_mv | AT beatriznavarro deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT vitantoniopantaleo deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT andreasgisel deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT simonmoxon deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT tamasdalmay deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT gyorgybisztray deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT francescodiserio deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction AT jozsefburgyan deepsequencingofviroidderivedsmallrnasfromgrapevineprovidesnewinsightsontheroleofrnasilencinginplantviroidinteraction |