Genomes and Genes
small nucleolar ribonucleoproteins
Summary: Nucleolar RNA-protein complexes that function in pre-ribosomal RNA processing.
- Manival X, Charron C, Fourmann J, Godard F, Charpentier B, Branlant C. Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Nucleic Acids Res. 2006;34:826-39 pubmed publisher..By gel filtration assay, we showed that aNOP10 can dimerize in solution. As both residues Y41 and L48 were needed for dimerization, the dimerization likely takes place by interaction of parallel alpha-helices...
- Lafontaine D, Tollervey D. Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA. 1999;5:455-67 pubmed..Nop58p is the second common component of the box C+D snoRNPs to be identified and the first to be shown to be required for the stability and for the synthesis of these snoRNAs. ..
- Dragon F, Pogacic V, Filipowicz W. In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs. Mol Cell Biol. 2000;20:3037-48 pubmed..Moreover, we show that in vitro-reconstituted RNPs contain hGAR1 and that binding of hGAR1 does not appear to be a prerequisite for the assembly of the other H/ACA proteins. ..
- Watkins N, Ségault V, Charpentier B, Nottrott S, Fabrizio P, Bachi A, et al. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell. 2000;103:457-66 pubmed..5 kD in vitro. The similarities in structure and function observed between the U4 snRNP (chaperone for U6) and the box C/D snoRNPs raises the interesting possibility that these particles may have evolved from a common ancestral RNP. ..
- Yu Y. The most complex pseudouridylase. Structure. 2006;14:167-8 pubmed
- Rashid R, Aittaleb M, Chen Q, Spiegel K, Demeler B, Li H. Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J Mol Biol. 2003;333:295-306 pubmed..These findings underscore the importance of functional assembly in methyl transfer reactions. ..
- Matic I, Schimmel J, Hendriks I, van Santen M, van de Rijke F, van Dam H, et al. Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif. Mol Cell. 2010;39:641-52 pubmed publisher..In 16 proteins we identified a hydrophobic cluster SUMOylation motif (HCSM). SUMO conjugation of RanGAP1 and ZBTB1 via HCSMs is remarkably efficient. ..
- Meier U. The many facets of H/ACA ribonucleoproteins. Chromosoma. 2005;114:1-14 pubmed..The multiple functions of H/ACA RNPs appear to be reflected in the complex phenotype of dyskeratosis congenita. ..
- Girard J, Lehtonen H, Caizergues Ferrer M, Amalric F, Tollervey D, Lapeyre B. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 1992;11:673-82 pubmed..GAR1 is thus the fifth member of a family of nucleolar proteins containing GAR domains, and is involved in rRNA metabolism. ..
- Khanna M, Wu H, Johansson C, Caizergues Ferrer M, Feigon J. Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA. RNA. 2006;12:40-52 pubmed..Chemical shift mapping of the interaction of RNA constructs of U65 box H/ACA 3' hairpin with Nop10p shows that the beta-hairpin binds weakly but specifically to RNA. The unstructured region of Nop10p likely interacts with Cbf5p. ..
- Schultz A, Nottrott S, Watkins N, Luhrmann R. Protein-protein and protein-RNA contacts both contribute to the 15.5K-mediated assembly of the U4/U6 snRNP and the box C/D snoRNPs. Mol Cell Biol. 2006;26:5146-54 pubmed..5K. In conclusion, our data suggest that the formation of each RNP involves the direct recognition of specific elements in both 15.5K protein and the specific RNA. ..
- Bagni C, Lapeyre B. Gar1p binds to the small nucleolar RNAs snR10 and snR30 in vitro through a nontypical RNA binding element. J Biol Chem. 1998;273:10868-73 pubmed..The accessory domain can be either one of the glycine/arginine-rich domains or a second element of the core of the protein that is highly conserved between different species. ..
- Lafontaine D, Tollervey D. Synthesis and assembly of the box C+D small nucleolar RNPs. Mol Cell Biol. 2000;20:2650-9 pubmed..Unexpectedly, we found that Nop1p was specifically required for the synthesis and accumulation of box C+D snoRNAs processed from pre-mRNA introns and polycistronic transcripts. ..
- Rashid R, Liang B, Baker D, Youssef O, He Y, Phipps K, et al. Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol Cell. 2006;21:249-60 pubmed publisher..We have also identified a dyskeratosis congenita mutation cluster site within a modeled dyskerin structure...
- Henras A, Dez C, Noaillac Depeyre J, Henry Y, Caizergues Ferrer M. Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p. Nucleic Acids Res. 2001;29:2733-46 pubmed
- Lyman S, Gerace L, Baserga S. Human Nop5/Nop58 is a component common to the box C/D small nucleolar ribonucleoproteins. RNA. 1999;5:1597-604 pubmed..Thus, hNop5/Nop58 is a common component of the box C/D snoRNPs, and joins fibrillarin as the second such component identified and characterized in metazoans. ..
- Henras A, Dez C, Henry Y. RNA structure and function in C/D and H/ACA s(no)RNPs. Curr Opin Struct Biol. 2004;14:335-43 pubmed
- Hardin J, Batey R. The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity. Nucleic Acids Res. 2006;34:5039-51 pubmed
- Aittaleb M, Rashid R, Chen Q, Palmer J, Daniels C, Li H. Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol. 2003;10:256-63 pubmed publisher..A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data...
- Pellizzoni L, Baccon J, Charroux B, Dreyfuss G. The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1. Curr Biol. 2001;11:1079-88 pubmed..We propose that the SMN complex performs functions necessary for the biogenesis and function of diverse ribonucleoprotein complexes. ..
- Ganot P, Caizergues Ferrer M, Kiss T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 1997;11:941-56 pubmed..The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., GAR1) suggests that these RNAs possess closely related nucleolar functions. ..
- Watkins N, Gottschalk A, Neubauer G, Kastner B, Fabrizio P, Mann M, et al. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA. 1998;4:1549-68 pubmed..Electron microscopy of purified snR42 and snR30 particles revealed that these two snoRNPs possess a similar bipartite structure that we propose to be a major structural determining principle for all H/ACA snoRNPs. ..
- Cahill N, Friend K, Speckmann W, Li Z, Terns R, Terns M, et al. Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J. 2002;21:3816-28 pubmed..Box C/D small nucleolar ribonucleoproteins (snoRNPs) contain four core proteins: fibrillarin, Nop56, Nop58 and 15.5 kDa...
- Nelson S, Santora K, LaRochelle W. Isolation and characterization of a novel PDGF-induced human gene. Gene. 2000;253:87-93 pubmed..The presence of potential regulatory elements, together with growth factor induction and widespread expression is consistent with the hypothesis that the NOP5 gene product may play a role in fundamental cellular growth processes. ..
- Charpentier B, Muller S, Branlant C. Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res. 2005;33:3133-44 pubmed..However, particles more efficient in targeted pseudouridylation can be formed with the addition of proteins L7Ae and/or aGAR1. Although necessary for optimal activity, the conserved ACA motif in the sRNA was found to be not essential...
- Verheggen C, Mouaikel J, Thiry M, Blanchard J, Tollervey D, Bordonne R, et al. Box C/D small nucleolar RNA trafficking involves small nucleolar RNP proteins, nucleolar factors and a novel nuclear domain. EMBO J. 2001;20:5480-90 pubmed..We conclude that snoRNP assembly occurs either in the nucleoplasm, or during transit of snoRNAs through the NB, followed by routing of the complete snoRNP to functional sites of ribosome synthesis...
- King T, Liu B, McCully R, Fournier M. Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol Cell. 2003;11:425-35 pubmed..The possibility that modifying snoRNPs might affect ribosome structure in other ways is also discussed. ..
- Morlando M, Ballarino M, Greco P, Caffarelli E, Dichtl B, Bozzoni I. Coupling between snoRNP assembly and 3' processing controls box C/D snoRNA biosynthesis in yeast. EMBO J. 2004;23:2392-401 pubmed..These data suggest a mechanism of quality control in which efficient transcription and 3'-end formation occur only when nascent snoRNAs are successfully assembled into functional particles. ..
- Henras A, Henry Y, Bousquet Antonelli C, Noaillac Depeyre J, Gelugne J, Caizergues Ferrer M. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J. 1998;17:7078-90 pubmed..Our results suggest that Nhp2p and Nop10p, together with Cbf5p, constitute the core of H/ACA snoRNPs. ..
- Gautier T, Berges T, Tollervey D, Hurt E. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol. 1997;17:7088-98 pubmed..Well-conserved homologs are present in a range of organisms, including humans (52% identity between human hNop56p and yeast Nop56p), suggesting that these complexes have been conserved in evolution. ..
- Bachellerie J, Cavaille J, Huttenhofer A. The expanding snoRNA world. Biochimie. 2002;84:775-90 pubmed..Recent characterization of homologs of eukaryotic modification guide snoRNAs in Archaea reveals the ancient origin of these non-coding RNA families and offers new perspectives as to their range of function. ..
- Kittur N, Darzacq X, Roy S, Singer R, Meier U. Dynamic association and localization of human H/ACA RNP proteins. RNA. 2006;12:2057-62 pubmed
- Balakin A, Smith L, Fournier M. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell. 1996;86:823-34 pubmed..Binding of this or another common small nucleolar ribonucleoprotein particle protein is predicted to be a critical entry point to snoRNA posttranscriptional life, including precise formation of the snoRNA 3' end. ..
- Whitehead S, Jones K, Zhang X, Cheng X, Terns R, Terns M. Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. J Biol Chem. 2002;277:48087-93 pubmed..Our results argue against post-translational arginine dimethylation as a general requirement for SMN recognition of proteins bearing arginine/glycine-rich domains. ..
- Schimmang T, Tollervey D, Kern H, Frank R, Hurt E. A yeast nucleolar protein related to mammalian fibrillarin is associated with small nucleolar RNA and is essential for viability. EMBO J. 1989;8:4015-24 pubmed..This suggests that NOP1 is in association with small nucleolar RNAs, required for rRNA processing and likely to be the homologue of the mammalian fibrillarin. ..
- Wu P, Brockenbrough J, Metcalfe A, Chen S, Aris J. Nop5p is a small nucleolar ribonucleoprotein component required for pre-18 S rRNA processing in yeast. J Biol Chem. 1998;273:16453-63 pubmed..Also, 37C12 co-immunoprecipitated Nop1p. These results suggest that Nop5p functions with Nop1p in the execution of early pre-rRNA processing steps that lead to formation of 18 S rRNA. ..
- Mitchell J, Wood E, Collins K. A telomerase component is defective in the human disease dyskeratosis congenita. Nature. 1999;402:551-5 pubmed..The pathology of DKC is consistent with compromised telomerase function leading to a defect in telomere maintenance, which may limit the proliferative capacity of human somatic cells in epithelia and blood. ..
- Wang H, Boisvert D, Kim K, Kim R, Kim S. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J. 2000;19:317-23 pubmed..Mapping temperature-sensitive mutations found in yeast fibrillarin Nop1 to the Methanococcus homologue structure reveals that many of the mutations cluster in the core of the methyltransferase-like domain. ..
- Yang Y, Isaac C, Wang C, Dragon F, Pogacic V, Meier U. Conserved composition of mammalian box H/ACA and box C/D small nucleolar ribonucleoprotein particles and their interaction with the common factor Nopp140. Mol Biol Cell. 2000;11:567-77 pubmed..We propose that Nopp140 functions as a chaperone of snoRNPs in yeast and vertebrate cells. ..
- Ballarino M, Morlando M, Pagano F, Fatica A, Bozzoni I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol Cell Biol. 2005;25:5396-403 pubmed..All these data suggest that proper cotranscriptional snoRNP assembly controls 3'-end formation of snoRNAs and, consequently, the release of a functional particle. ..
- Verheggen C, Lafontaine D, Samarsky D, Mouaikel J, Blanchard J, Bordonné R, et al. Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. EMBO J. 2002;21:2736-45 pubmed..These are likely places for snoRNP assembly, 3' end maturation and cap modification...
- Decatur W, Fournier M. RNA-guided nucleotide modification of ribosomal and other RNAs. J Biol Chem. 2003;278:695-8 pubmed
- Romanova L, Kellner S, Katoku Kikyo N, Kikyo N. Novel role of nucleostemin in the maintenance of nucleolar architecture and integrity of small nucleolar ribonucleoproteins and the telomerase complex. J Biol Chem. 2009;284:26685-94 pubmed publisher..function of NS in the maintenance of the tripartite nucleolar structure as well as the integrity of small nucleolar ribonucleoproteins (snoRNPs)...
- Henras A, Capeyrou R, Henry Y, Caizergues Ferrer M. Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. RNA. 2004;10:1704-12 pubmed..We also show that the absence of any component necessary for assembly of box H/ACA snoRNPs inhibits accumulation of Cbf5p, Gar1p, or Nop10p, whereas Nhp2p levels are little affected. ..
- Carneiro T, Carvalho C, Braga J, Rino J, Milligan L, Tollervey D, et al. Inactivation of cleavage factor I components Rna14p and Rna15p induces sequestration of small nucleolar ribonucleoproteins at discrete sites in the nucleus. Mol Biol Cell. 2008;19:1499-508 pubmed publisher..We propose that the foci detected after CFIA inactivation correspond to quality control centers in the nucleoplasm. ..
- Darzacq X, Kittur N, Roy S, Shav Tal Y, Singer R, Meier U. Stepwise RNP assembly at the site of H/ACA RNA transcription in human cells. J Cell Biol. 2006;173:207-18 pubmed..Our analyses indicate that NAF1 binds NAP57 and escorts it to the nascent H/ACA RNA and that GAR1 then replaces NAF1 to yield mature H/ACA RNPs in Cajal bodies and nucleoli. ..
- Wang C, Meier U. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. EMBO J. 2004;23:1857-67 pubmed..Nonetheless, functional H/ACA snoRNPs assembled in cytosolic extracts are stable and do not exchange their RNA components, suggesting that new particle formation requires de novo synthesis. ..
- Fatica A, Dlakic M, Tollervey D. Naf1 p is a box H/ACA snoRNP assembly factor. RNA. 2002;8:1502-14 pubmed..We propose that Naf1 p is recruited to the CTD of RNA polymerase II and binds to nascent box H/ACA snoRNAs promoting snoRNP assembly. ..
- Wang C, Query C, Meier U. Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140. Mol Cell Biol. 2002;22:8457-66 pubmed..These data suggest that substrate release takes place without RNA helicase activity but may be aided by the snoRNP core proteins. ..
- Hamma T, Ferré D Amaré A. Pseudouridine synthases. Chem Biol. 2006;13:1125-35 pubmed
- Wu H, Feigon J. H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc Natl Acad Sci U S A. 2007;104:6655-60 pubmed
- Dez C, Noaillac Depeyre J, Caizergues Ferrer M, Henry Y. Naf1p, an essential nucleoplasmic factor specifically required for accumulation of box H/ACA small nucleolar RNPs. Mol Cell Biol. 2002;22:7053-65 pubmed..Naf1p is unlikely to be directly required for the synthesis of H/ACA snoRNP components. Naf1p could participate in H/ACA snoRNP assembly and/or transport. ..
- Yang P, Hoareau C, Froment C, Monsarrat B, Henry Y, Chanfreau G. Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly. Mol Cell Biol. 2005;25:3295-304 pubmed
- Aftab M, He H, Skogerbø G, Chen R. Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins. BMC Genomics. 2008;9:278 pubmed publisher..Thereby, the study also demonstrates the feasibility of combining RNAi against candidate proteins with ncRNA microarray analysis to investigate ncRNA-protein interactions and hence ncRNA cellular functions. ..
- Watkins N, Dickmanns A, Luhrmann R. Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol Cell Biol. 2002;22:8342-52 pubmed..5K, to the snoRNA. Indeed, the sequence of stem II was essential for nucleolar localization of U14 snoRNA microinjected into HeLa cells. Thus, the conserved sequence of stem II determines the specific assembly of the box C/D snoRNP. ..
- Matera A, Terns R, Terns M. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8:209-20 pubmed publisher..The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs. ..
- Reichow S, Hamma T, Ferré D Amaré A, Varani G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 2007;35:1452-64 pubmed..Furthermore, the recent structure of an H/ACA complex has revealed the organization of a complete sRNP. Combined with current biochemical data, these structures offer insight into the highly homologous eukaryotic snoRNPs. ..
- Terns M, Terns R. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr. 2002;10:17-39 pubmed..The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications. ..
- Boulon S, Verheggen C, Jady B, Girard C, Pescia C, Paul C, et al. PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. Mol Cell. 2004;16:777-87 pubmed..Our data indicate that the role of PHAX in determining the identity of small RNAs extends to nonexported species, and this appears critical to promote their transport within the nucleus. ..
- Pogacic V, Dragon F, Filipowicz W. Human H/ACA small nucleolar RNPs and telomerase share evolutionarily conserved proteins NHP2 and NOP10. Mol Cell Biol. 2000;20:9028-40 pubmed
- Hamma T, Reichow S, Varani G, Ferr D Amar A. The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nat Struct Mol Biol. 2005;12:1101-7 pubmed publisher..Mutagenesis results implicate an adjacent basic patch in RNA binding. This tripartite RNA-binding surface may function as a molecular bracket that organizes the multihelical H/ACA and telomerase RNAs...