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

7744–7761 Nucleic Acids Research, 2015, Vol. 43, No. 16 doi: 10.1093/nar/gkv756 Published online 3 August 2015 Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea Claire Toffano-Nioche, Daniel Gautheret and Fabrice Leclerc* I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France Received March 09, 2015; Revised July 07, 2015; Accepted July 09, 2015 ABSTRACT INTRODUCTION The H/ACA guide RNAs are part of a RNP machinery including several proteins (L7Ae, Cbf5, Nop10 and Gar1) which catalyzes the uridine-to-pseudouridine isomerization. Homologs of the eukaryotic snoRNA H/ACA, these guide RNAs are found in a widespread number of Archaea, in Euryarchaea (Archaeoglobus fulgidus (1), Haloferax volcanii (2), Pyrococcus abyssi (3–5)), in Crenarchaea (Sulfolobus solfataricus (6)) and in Nanoarchaea (Nanoarchaeum equitans (7)). Computational screens for H/ACA RNAs and their potential targets in the archaeal genomes suggest they are present in a variable number of copies among all the archaeal phyla (5,8). The natural targets are ribosomal RNAs but other RNAs might be targeted with functional implications (9,10). In eukaryotes, other targets include the U2 snRNA (11) which is modified in S. cerevisiae under particular conditions (12). De- * To whom correspondence should be addressed. Tel: +33 169 156214; Fax: +33 169 157296; Email:  C The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 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. signed mRNAs including a nonsense codon were shown to be fully expressed when modified by the H/ACA guide RNP machinery at the first position of stop codons (13). On the other hand, snoRNAs have also been involved in unusual roles: in alternative splicing in the case of the C/D box guide RNA HBII-52 (14) or as one of the RNA biomarkers for non-small-cell lung cancer in the case of the H/ACA guide RNA snoRA42 (15). Extensive structural and functional studies have focused on the H/ACA RNAs and RNPs from Pyrococcus: P. abyssi (4,5,20–25), P. horikoshii and P. furiosus (3,5,17–19,26–31) which is the only genus with so many genes for this class of sRNA (seven H/ACA genes corresponding to 11 H/ACA motifs). These studies describe the structure/function relationships for this RNA guide machinery regarding: the RNA fold, the RNA:RNA interactions between the guide and its target(s) and the RNA:protein contacts (between L7Ae and the K-turn or K-loop motif, between Cbf5 and the ACA box, etc.). The H/ACA motif is well described as a stem-loop-stem motif closed by an apical loop and terminated by an ACA box at the 3’ end (32) (Figure 1). In archaea, the L7Ae ribosomal protein is part of the H/ACA RNP particle and specifically binds to a K-turn motif which is embedded in the upper stem or merged within the apical loop as a K-loop. The lower stem includes between 7 and 9 base-pairs in the canonical H/ACA motifs and the distance between the ACA box and the base-pair closing the internal loop in the upper stem is reported to be between 14 and 16 nt (1) (3’ strands of the internal loop and lower stem); in the H/ACA motifs from P. abyssi, an empirical constraint between 14 and 15 nt was proposed (5) (Figure 1A). On the other hand, no well-defined constraint is proposed regarding the position of the K-turn or K-loop motif with respect to the internal loop. The distance from the base-pair closing the internal loop in the upper stem to the second G:A basepair of the K-turn or K-loop motif, defined as ‘GA stem’ (Figure 1), spans from 8 to 11 base-pairs (5). In Haloferax volcanii, the length of the GA stem ranges from 8 (2) to 9 (1,20,33) and 10 base-pairs (1,20). Nucleic Acids Research, 2015, Vol. 43, No. 16 7745 Pae_HACA Pab_HACA 3-20 nt R K-turn/K-loop U A G G A 17-18 nt Y R C G 0-3 nt 0-1 nt 17-19 nt Y A G 0-6 nt Pae_HACAlike G U G A A 0-1 nt A C R 8-11 bp GA stem U G Y 0-1 nt 0-1 nt G C G C G Y R 3-5 nt Y R C G 5-8 nt 3´ guide sequence 0-1 nt 5´ 5´ C R 3-4 nt B 0-2 nt 2-6 nt ACA A ACA 14-17 nt U 6 nt G C C 12-26 nt 5-6 nt AYA 5´ C Y G G G G 9 bp R C C C ACA D Figure 1. Structure/Function Models of H/ACA guide RNAs from structural and functional studies. (A) Consensus functional model of H/ACA motif in Pyrococcus abyssi (Supplementary Data: Figure S1 and Listing 1). (B) Consensus functional model of H/ACA motif in Pyrobaculum aerophilum (Supplementary Data: Figure S2 and Listing 2). (C) Consensus functional model of H/ACA-like motif in Pyrobaculum aerophilum (Supplementary Data: Figure S3 and Listing 3). (D) Consensus structural model of H/ACA motif for crystallized chimeric RNAs from Pyrococcus furiosus and Archaeaglobus fulgidus (Supplementary Data: Figure S4 and Listing 4). The consensus model for Pyrococcus abyssi was derived from the Stockholm alignment of all H/ACA motifs as previously folded (5) and represented using R2R (see Materials and Methods). The consensus models for Pyrobaculum aerophilum were derived from the Stockholm alignment of the two canonical H/ACA motifs (sR201 and sR202) or that of the other H/ACA-like motifs (sR203 to sR210) (16). The consensus structural model was derived from the alignment of the three guide RNAs included in the 3D structures of the full H/ACA RNP assemblies (L7Ae, Nop10, Cbf5 with or without Gar1) determined by X-ray crystallography (PDB IDs: 2HVY (17), 3HAX (18), 3LWO (19)). More recently, the discovery of ‘atypical’ H/ACA motifs in the Pyrobaculum genus has suggested an alternate way for this machinery to assemble and achieve its function (16). These non-canonical H/ACA motifs, further designated as H/ACA-like motifs, are detected specifically in this genus of Crenarchaea and differ from the canonical (...truncated)