Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

Nucleic Acids Res. 2015 Sep 18;43(16):7744-61. doi: 10.1093/nar/gkv756. Epub 2015 Aug 3.

Abstract

A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.

MeSH terms

  • Base Pairing
  • Euryarchaeota / genetics
  • Gene Expression Regulation, Archaeal
  • Models, Molecular
  • Nucleotide Motifs
  • Pyrobaculum / genetics*
  • Pyrococcus abyssi / genetics*
  • RNA Folding
  • RNA, Archaeal / chemistry*
  • RNA, Archaeal / metabolism
  • RNA, Guide, CRISPR-Cas Systems
  • RNA, Small Nucleolar / chemistry*
  • RNA, Small Nucleolar / metabolism
  • RNA, Transfer / metabolism
  • Structure-Activity Relationship

Substances

  • RNA, Archaeal
  • RNA, Small Nucleolar
  • RNA, Transfer