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The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

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Abstract Box C/D and H/ACA RNPs are essential ribonucleoprotein particles that are found throughout both eukaryotes [small nucleolar RNPs (snoRNPs)] and archaea [snoRNP‐like complexes (sRNPs)]. These complexes catalyze the site‐specific pseudouridylation and most of the methylation of ribosomal RNA (rRNA). The numerous modifications, which are clustered in functionally important regions of the rRNA, are important for rRNA folding and ribosome function. The RNA component of the complexes [small nucleolar RNA (snoRNA) or small RNA (sRNA)] functions in substrate binding by base pairing with the target site and as a scaffold coordinating the organization of the complex. In eukaryotes, a subset of snoRNPs do not catalyze modification but, through base pairing to the rRNA or flanking precursor sequences, direct pre‐rRNA folding and are essential for rRNA processing. In the last few years there have been significant advances in our understanding of the structure of archaeal sRNPs. High resolution structures of the archaeal C/D and H/ACA sRNPs have not only provided a detailed understanding of the molecular architecture of these complexes but also produced key insights into substrate binding and product release. In both cases, this is mediated by significant movement in the complexes. Advances have also been made in our knowledge of snoRNP recruitment and release from pre‐ribosome complexes in eukaryotes. New snoRNA–rRNA interactions have been documented, and the roles of RNA helicases in releasing snoRNP complexes from the rRNA have been described. WIREs RNA 2012, 3:397–414. doi: 10.1002/wrna.117 This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes Translation > Ribosome Biogenesis RNA Processing > rRNA Processing

Small nucleolar RNA (snoRNA) structure and function. The schematic structure of H/ACA (a) and box C/D (b) snoRNAs is shown. The conserved box sequences are shown in gray and the rRNA target RNAs in red. The pseudouridylated or methylated residue is indicated by a Ψ (a) or a red circle (b), respectively.

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Three dimensional (3D) structure of the yeast 25S rRNA (ribosomal RNA) showing the binding sites for Prp43 (green) and the binding (red) and modification (white) sites of the small nucleolar RNAs (snoRNAs) linked to this helicase. The view shown is that of the subunit interface.

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Small nucleolar RNA (snoRNA) base‐pairing sites in the human 18S ribosomal RNA (rRNA). The secondary structure of the human 18S rRNA is shown142 (http://www.rna.ccbb.utexas.edu/). The canonical box C/D snoRNA methylation guide interactions and extra base‐pairing interactions (where determined) are indicated in red and light blue, respectively, with a gray line linking those regions belonging to a single snoRNA. Interactions linked to pre‐rRNA processing and/or rRNA folding are shown in purple. U?? indicates methylation sites where the snoRNA has yet to be identified.

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Small nucleolar RNA (snoRNA) structures and snoRNA–rRNA base‐pairing (small nucleolar–ribosomal RNA) interactions. The secondary structures of human (U3, U8, U13, U14, U16, and U17) and yeast (snR10) snoRNAs are shown. The conserved box regions are shown in white on a black background. Pre‐rRNA sequences are shown in gray. The methylation/pseudouridylation target region of the rRNA are shown in red, with the target nucleotide black and the region involved in extra base pairing in light blue. The rRNA regions targeted in interactions important for rRNA processing and/or folding are shown in purple. An alternative structure and rRNA base‐pairing scheme is presented for the 5′ end of the U8 snoRNA.

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The structure of the box C/D RNP. (a) Schematic representation of the two models of box C/D snoRNP‐like complex (sRNP) architecture. The sRNA is shown in black and the ribosomal RNA (rRNA) in red. The methylation target site is shown in yellow. The positions of the proteins in the two complexes are indicated. (b) Structural model of the Sulfolobus solfataricus C/D sRNP complex (REF: PDB ID: 3PLA and 3ID5). A surface view is shown for the proteins with Nop5 (blue and light blue), fibrillarin (orange), and L7Ae (gray). The S‐adenosylmethionine (SAM) cofactor analog, S‐adenosylhomocysteine (SAH), is shown in magenta. The sRNA and the rRNA substrate are shown in white and red, respectively, with the target nucleotides shown in yellow and marked by an arrow. The catalytic modules (fibrillarin/Nop5 N‐terminal domain) are shown in the inactive (lower) and active (upper) positions. The positions of the C/D and C′/D′ motifs and the Nop5 protrusion are indicated.

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The structure of the H/ACA RNP. (a) Schematic representation of the archaeal H/ACA snoRNP‐like complex (sRNP). The sequence of the K‐loop and ACA motif are indicated. The sRNA and ribosomal RNA (rRNA) substrate are represented as black and red lines, respectively, with the nucleotide converted to pseudouridine (Ψ) indicated. The relative binding sites of the proteins are shown. (b) Structural model of the Pyrococcus furiosus H/ACA sRNP complex (REF: protein data bank (PDB) ID: 3HAY). A surface view is shown for the proteins with the same color scheme as (a). The sRNA and rRNA substrates are shown in white and red, respectively. (c) Close‐up view of the interaction of the thumb loop of Cbf5 with the substrate RNA. A cartoon view of the proteins, using the same color scheme as (a), is shown. The target nucleotide and thumb loop are indicated. The arrow indicates the predicted movement of the thumb loop upon substrate binding and release. (d) Schematic representation of the eukaryotic H/ACA small nucleolar RNP (snoRNP). Organization and color scheme as in (a).

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RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
RNA Processing > rRNA Processing
Translation > Ribosome Biogenesis

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