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Hammann C.,TU Darmstadt | Hammann C.,Jacobs University Bremen | Luptak A.,University of California at Irvine | Perreault J.,Center Institute Armand Frappier | De La Pena M.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic
RNA | Year: 2012

The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-) cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast self-scission under physiological conditions. Originally discovered in subviral plant pathogens, its presence in several eukaryotic genomes has been reported since. More recently, this catalytic RNA motif has been shown to reside in a large number of genomes. We review the different approaches in discovering these new hammerhead ribozyme sequences and discuss possible biological functions of the genomic motifs. Published by Cold Spring Harbor Laboratory Press. Copyright © 2012 RNA Society.

Flores R.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic
Acta Horticulturae | Year: 2011

With a genome composed of a small (246-401 nt), single-stranded, circular RNA, viroids are a special class of replicons infecting plants, including some ornamentals, in which they may induce specific diseases. In striking contrast to plant viruses, which encode proteins mediating their own replication and movement, viroids depend on host factors for these purposes and can be regarded as parasites of their host transcription machinery. The about 30 known viroids are classified into the families Pospiviroidae, type species Potato spindle tuber viroid (PSTVd), and Avsunviroidae, type species Avocado sunblotch viroid (ASBVd). PSTVd and ASBVd replicate (and accumulate) in the nucleus and the chloroplast, respectively, and the other members of both families most likely behave as their type species. Viroids replicate through an RNA-based rolling-circle mechanism that entails reiterative transcription of the incoming circular template to generate complementary longerthan- unit strands that, by themselves or after cleavage and ligation, prime the second half of the cycle finally leading to the mature circular forms. Remarkably, processing of the multimeric replicative intermediates is catalyzed by hammerhead ribozymes in the family Avsunviroidae. To complete their infectious cycle, viroids must recruit host factors for intracellular, cell-to-cell and long-distance movement within the plant. Viroid-derived RNAs with the typical properties of the small interfering RNAs, the hallmarks of RNA silencing, have been detected in plants infected by members of both families. This finding indicates that viroids are inducers and targets (and perhaps even suppressors) of RNA silencing, a regulatory layer that may mediate many aspects of viroid biology including pathogenesis. Chrysanthemum stunt was one of the first diseases in which the inciting agent was identified as a viroid, Chrysanthemum stunt viroid, a member of the family Pospiviroidae that also infects other ornamentals. Chrysanthemum was additionally suspected to host a second viroid, although identification and characterization of the corresponding RNA, Chrysanthemum chlorotic mottle viroid (CChMVd), a member of the family Avsunviroidae, had to wait more than 20 years due to its low accumulation level. There are CChMVd non-symptomatic strains that cross-protect against challenge inoculation with severe strains, with the pathogenicity determinant mapping at a tetraloop of the CChMVd branched conformation. Other viroids infecting ornamentals include Columnea latent viroid, Iresine viroid and Coleus blumei viroid 1, 2 and 3, all belonging to the family Pospiviroidae. Additionally, a retroviroidlike element has been found in carnation. Some ornamental viroids are seed-transmissible. Viroids are usually detected by nucleic acid-based techniques (PAGE, molecular hybridization and RT-PCR). Control measures include the use of viroidfree propagating material together with the regular decontamination of pruning tools. Some viroids can be removed from infected material by in vitro micrografting.

De La Pena M.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic | Garcia-Robles I.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic
RNA | Year: 2010

Examples of small self-cleaving RNAs embedded in noncoding regions already have been found to be involved in the control of gene expression, although their origin remains uncertain. In this work, we show the widespread occurrence of the hammerhead ribozyme (HHR) motif among genomes from the Bacteria, Chromalveolata, Plantae, and Metazoa kingdoms. Intergenic HHRs were detected in three different bacterial genomes, whereas metagenomic data from Galapagos Islands showed the occurrence of similar ribozymes that could be regarded as direct relics from the RNA world. Among eukaryotes, HHRs were detected in the genomes of three water molds as well as 20 plant species, ranging from unicellular algae to vascular plants. These HHRs were very similar to those previously described in small RNA plant pathogens and, in some cases, appeared as close tandem repetitions. A parallel situation of tandemly repeated HHR motifs was also detected in the genomes of lower metazoans from cnidarians to invertebrates, with special emphasis among hematophagous and parasitic organisms. Altogether, these findings unveil the HHR as a widespread motif in DNA genomes, which would be involved in new forms of retrotransposable elements.

Di Serio F.,National Research Council Italy | Flores R.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic | Verhoeven J.T.J.,National Reference Center | Li S.-F.,Chinese Academy of Agricultural Sciences | And 5 more authors.
Archives of Virology | Year: 2014

Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized viroids. © 2014, Springer-Verlag Wien.

Cervera A.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic | De La Pena M.,Institute Biologia Molecular Y Celular Of Plantas Upv Csic
Molecular Biology and Evolution | Year: 2014

Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes. © 2014 The Author.

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