ArticleNucleic acids research2008
Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 46 citations in OpenAlex.
- Archaeal RNA processing and regulation: expanding the functional landscape.Microbiology and molecular biology reviews : MMBR · 2025Review
- Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus.Nucleic acids research · 2024Article
- Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs.Non-coding RNA · 2021Review
- H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.Frontiers in microbiology · 2021Review
- The presence of the ACA box in archaeal H/ACA guide RNAs promotes atypical pseudouridylation.RNA (New York, N.Y.) · 2020Article
- The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue.RNA (New York, N.Y.) · 2019Article
- Contribution of protein Gar1 to the RNA-guided and RNA-independent rRNA:Ψ-synthase activities of the archaeal Cbf5 protein.Scientific reports · 2018Article
- Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism.Genes · 2018Article
- Efficient RNA pseudouridylation by eukaryotic H/ACA ribonucleoproteins requires high affinity binding and correct positioning of guide RNA.Nucleic acids research · 2018Article
- Archaeal fibrillarin-Nop5 heterodimer 2'-RNA (New York, N.Y.) · 2017Article
- Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation.RNA (New York, N.Y.) · 2016Article
- Large-scale identification of small noncoding RNA with strand-specific deep sequencing and characterization of a novel virulence-related sRNA in Brucella melitensis.Scientific reports · 2016Article
- Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea.Nucleic acids research · 2015Article
- Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and -independent pseudouridine synthase Cbf5.RNA (New York, N.Y.) · 2015Article
- Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10.RNA (New York, N.Y.) · 2013Article
- RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.RNA biology · 2013Article
- Article
- Ribonucleoproteins in archaeal pre-rRNA processing and modification.Archaea (Vancouver, B.C.) · 2013Review
- Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features.RNA (New York, N.Y.) · 2012Article
- Comparative analysis of RNA families reveals distinct repertoires for each domain of life.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How far do H/ACA sRNPs contribute to rRNA pseudouridylation in Archaea was still an open question. Hence here, by computational search in three Pyrococcus genomes, we identified seven H/ACA sRNAs and predicted their target sites in rRNAs. In parallel, we experimentally identified 17 Psi residues in P. abyssi rRNAs. By in vitro reconstitution of H/ACA sRNPs, we assigned 15 out of the 17 Psi residues to the 7 identified H/ACA sRNAs: one H/ACA motif can guide up to three distinct pseudouridylations. Interestingly, by using a 23S rRNA fragment as the substrate, one of the two remaining Psi residues could be formed in vitro by the aCBF5/aNOP10/aGAR1 complex without guide sRNA. Our results shed light on structural constraints in archaeal H/ACA sRNPs: the length of helix H2 is of 5 or 6 bps, the distance between the ANA motif and the targeted U residue is of 14 or 15 nts, and the stability of the interaction formed by the substrate rRNA and the 3'-guide sequence is more important than that formed with the 5'-guide sequence. Surprisingly, we showed that a sRNA-rRNA interaction with the targeted uridine in a single-stranded 5'-UNN-3' trinucleotide instead of the canonical 5'-UN-3' dinucleotide is functional.
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