ArticleNucleic acids research2006
Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 34 citations in OpenAlex.
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- Understanding metric-related pitfalls in image analysis validation.Nature methods · 2024Review
- A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations.Virus evolution · 2022Review
- How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host.RNA biology · 2019Article
- Mutational Analysis ofFrontiers in microbiology · 2018Article
- Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing.PLoS pathogens · 2017Article
- The Hammerhead Ribozyme: A Long History for a Short RNA.Molecules (Basel, Switzerland) · 2017Review
- Eggplant latent viroid: a friendly experimental system in the family Avsunviroidae.Molecular plant pathology · 2016Review
- The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their in vivo RNA conformations.RNA biology · 2016Article
- Complete RNA inverse folding: computational design of functional hammerhead ribozymes.Nucleic acids research · 2014Article
- Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change.RNA (New York, N.Y.) · 2012Article
- Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.Frontiers in microbiology · 2012Article
- Trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA.Nucleic acids research · 2011Article
- Article
- Catalytic diversity of extended hammerhead ribozymes.Biochemistry · 2008Article
- Hammerhead redux: does the new structure fit the old biochemical data?RNA (New York, N.Y.) · 2008Review
- Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.RNA (New York, N.Y.) · 2008Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eggplant latent viroid (ELVd) can form stable hammerhead structures in its (+) and (-) strands. These ribozymes have the longest helices I reported in natural hammerheads, with that of the ELVd (+) hammerhead being particularly stable (5/7 bp are G-C). Moreover, the trinucleotide preceding the self-cleavage site of this hammerhead is AUA, which together with GUA also found in some natural hammerheads, deviate from the GUC present in most natural hammerheads including the ELVd (-) hammerhead. When the AUA trinucleotide preceding the self-cleavage site of the ELVd (+) hammerhead was substituted by GUA and GUC, as well as by AUC (essentially absent in natural hammerheads), the values of the self-cleavage rate constants at low magnesium of the purified hammerheads were: ELVd-(+)-AUC approximately ELVd-(+)-GUC>ELVd-(+)-GUA> ELVd-(+)-AUA. However, the ELVd-(+)-AUC hammerhead was the catalytically less efficient during in vitro transcription, most likely because of the transient adoption of catalytically-inactive metastable structures. These results suggest that natural hammerheads have been evolutionary selected to function co-transcriptionally, and provide a model explaining the lack of trinucleotide AUC preceding the self-cleavage site of most natural hammerheads. Comparisons with other natural hammerheads showed that the ELVd-(+)-GUC and ELVd-(+)-AUC hammerheads are the catalytically most active in a post-transcriptional context with low magnesium.
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