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Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations
Replication of viroids, small non-protein-coding plant pathogenic RNAs, entails reiterative transcription of their incoming single-stranded circular genomes, to which the (+) polarity is arbitrarily assigned, cleavage of the oligomeric strands of one or both polarities to unit-length, and ligation t...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2098832/ https://www.ncbi.nlm.nih.gov/pubmed/18052530 http://dx.doi.org/10.1371/journal.ppat.0030182 |
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author | Gas, María-Eugenia Hernández, Carmen Flores, Ricardo Daròs, José-Antonio |
author_facet | Gas, María-Eugenia Hernández, Carmen Flores, Ricardo Daròs, José-Antonio |
author_sort | Gas, María-Eugenia |
collection | PubMed |
description | Replication of viroids, small non-protein-coding plant pathogenic RNAs, entails reiterative transcription of their incoming single-stranded circular genomes, to which the (+) polarity is arbitrarily assigned, cleavage of the oligomeric strands of one or both polarities to unit-length, and ligation to circular RNAs. While cleavage in chloroplastic viroids (family Avsunviroidae) is mediated by hammerhead ribozymes, where and how cleavage of oligomeric (+) RNAs of nuclear viroids (family Pospiviroidae) occurs in vivo remains controversial. Previous in vitro data indicated that a hairpin capped by a GAAA tetraloop is the RNA motif directing cleavage and a loop E motif ligation. Here we have re-examined this question in vivo, taking advantage of earlier findings showing that dimeric viroid (+) RNAs of the family Pospiviroidae transgenically expressed in Arabidopsis thaliana are processed correctly. Using this methodology, we have mapped the processing site of three members of this family at equivalent positions of the hairpin I/double-stranded structure that the upper strand and flanking nucleotides of the central conserved region (CCR) can form. More specifically, from the effects of 16 mutations on Citrus exocortis viroid expressed transgenically in A. thaliana, we conclude that the substrate for in vivo cleavage is the conserved double-stranded structure, with hairpin I potentially facilitating the adoption of this structure, whereas ligation is determined by loop E and flanking nucleotides of the two CCR strands. These results have deep implications on the underlying mechanism of both processing reactions, which are most likely catalyzed by enzymes different from those generally assumed: cleavage by a member of the RNase III family, and ligation by an RNA ligase distinct from the only one characterized so far in plants, thus predicting the existence of at least a second plant RNA ligase. |
format | Text |
id | pubmed-2098832 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-20988322007-11-29 Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations Gas, María-Eugenia Hernández, Carmen Flores, Ricardo Daròs, José-Antonio PLoS Pathog Research Article Replication of viroids, small non-protein-coding plant pathogenic RNAs, entails reiterative transcription of their incoming single-stranded circular genomes, to which the (+) polarity is arbitrarily assigned, cleavage of the oligomeric strands of one or both polarities to unit-length, and ligation to circular RNAs. While cleavage in chloroplastic viroids (family Avsunviroidae) is mediated by hammerhead ribozymes, where and how cleavage of oligomeric (+) RNAs of nuclear viroids (family Pospiviroidae) occurs in vivo remains controversial. Previous in vitro data indicated that a hairpin capped by a GAAA tetraloop is the RNA motif directing cleavage and a loop E motif ligation. Here we have re-examined this question in vivo, taking advantage of earlier findings showing that dimeric viroid (+) RNAs of the family Pospiviroidae transgenically expressed in Arabidopsis thaliana are processed correctly. Using this methodology, we have mapped the processing site of three members of this family at equivalent positions of the hairpin I/double-stranded structure that the upper strand and flanking nucleotides of the central conserved region (CCR) can form. More specifically, from the effects of 16 mutations on Citrus exocortis viroid expressed transgenically in A. thaliana, we conclude that the substrate for in vivo cleavage is the conserved double-stranded structure, with hairpin I potentially facilitating the adoption of this structure, whereas ligation is determined by loop E and flanking nucleotides of the two CCR strands. These results have deep implications on the underlying mechanism of both processing reactions, which are most likely catalyzed by enzymes different from those generally assumed: cleavage by a member of the RNase III family, and ligation by an RNA ligase distinct from the only one characterized so far in plants, thus predicting the existence of at least a second plant RNA ligase. Public Library of Science 2007-11 2007-11-30 /pmc/articles/PMC2098832/ /pubmed/18052530 http://dx.doi.org/10.1371/journal.ppat.0030182 Text en © 2007 Gas et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Gas, María-Eugenia Hernández, Carmen Flores, Ricardo Daròs, José-Antonio Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title | Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title_full | Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title_fullStr | Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title_full_unstemmed | Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title_short | Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations |
title_sort | processing of nuclear viroids in vivo: an interplay between rna conformations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2098832/ https://www.ncbi.nlm.nih.gov/pubmed/18052530 http://dx.doi.org/10.1371/journal.ppat.0030182 |
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