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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.
Nucleic Acids Res. 2006; 34(19):5613-22.NA

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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Authors+Show Affiliations

Carbonell A
Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Avenida de los Naranjos s/n, 46022 Valencia, Spain.
De la Peña M
No affiliation info available
Flores R
No affiliation info available
Gago S
No affiliation info available

MeSH

Base SequenceCatalysisKineticsMagnesiumModels, MolecularMolecular Sequence DataMutationNucleic Acid ConformationNucleotidesOligodeoxyribonucleotides, AntisenseRNA Processing, Post-TranscriptionalRNA, CatalyticRNA, ViralViroids

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17028097

Citation

Carbonell, Alberto, et al. "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." Nucleic Acids Research, vol. 34, no. 19, 2006, pp. 5613-22.
Carbonell A, De la Peña M, Flores R, et al. 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. Nucleic Acids Res. 2006;34(19):5613-22.
Carbonell, A., De la Peña, M., Flores, R., & Gago, S. (2006). 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. Nucleic Acids Research, 34(19), 5613-22.
Carbonell A, et al. 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. Nucleic Acids Res. 2006;34(19):5613-22. PubMed PMID: 17028097.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Carbonell,Alberto, AU - De la Peña,Marcos, AU - Flores,Ricardo, AU - Gago,Selma, Y1 - 2006/10/05/ PY - 2006/10/10/pubmed PY - 2006/12/21/medline PY - 2006/10/10/entrez SP - 5613 EP - 22 JF - Nucleic acids research JO - Nucleic Acids Res VL - 34 IS - 19 N2 - 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. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/17028097/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_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl717 DB - PRIME DP - Unbound Medicine ER -