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A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA.
RNA. 2003 Jul; 9(7):821-38.RNA

Abstract

The 15.5-kD protein and its yeast homolog Snu13p bind U4 snRNA, U3 snoRNA, and the C/D box snoRNAs. In U4 snRNA, they associate with a helix-bulge-helix (K-turn) structure. U3 snoRNA contains two conserved pairs of boxes, C'/D and B/C, which were both expected to bind the 15.5-kD/Snu13 protein. Only binding to the B/C motif was experimentally demonstrated. Here, by chemical probing of in vitro reconstituted RNA/protein complexes, we demonstrate the independent binding of the 15.5-kD/Snu13 protein to each of the two motifs. Due to a highly reduced stem I (1 bp), the K-turn structure is not formed in the naked B/C motif. However, gel-shift experiments revealed a higher affinity of Snu13p for the B/C motif, compared to the C'/D motif. A phylogenetic analysis of U3 snoRNA, coupled with an analysis of Snu13p affinity for variant yeast C'/D and B/C motifs, and a study of the functionality of a truncated yeast U3 snoRNA carrying base substitutions in the C'/D and B/C motifs, revealed that conservation of the identities of residues 2 and 3 in the B/C K-turn is more important for Snu13p binding and U3 snoRNA function, than conservation of the identities of corresponding residues in the C'/D K-turn. This suggests that binding of Snu13p to K-turns with a very short helix I imposes sequence constraints in the bulge. Altogether, the data demonstrate the strong importance of the binding of the 15.5-kD/Snu13 protein to the C'/D and B/C motifs for both U3 snoRNP assembly and activity.

Authors+Show Affiliations

Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 UHP-CNRS, Université Henri Poincaré Nancy 1, 54506 Vandoeuvre-Lès-Nancy cedex, France.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

12810916

Citation

Marmier-Gourrier, Nathalie, et al. "A Structural, Phylogenetic, and Functional Study of 15.5-kD/Snu13 Protein Binding On U3 Small Nucleolar RNA." RNA (New York, N.Y.), vol. 9, no. 7, 2003, pp. 821-38.
Marmier-Gourrier N, Cléry A, Senty-Ségault V, et al. A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA. RNA. 2003;9(7):821-38.
Marmier-Gourrier, N., Cléry, A., Senty-Ségault, V., Charpentier, B., Schlotter, F., Leclerc, F., Fournier, R., & Branlant, C. (2003). A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA. RNA (New York, N.Y.), 9(7), 821-38.
Marmier-Gourrier N, et al. A Structural, Phylogenetic, and Functional Study of 15.5-kD/Snu13 Protein Binding On U3 Small Nucleolar RNA. RNA. 2003;9(7):821-38. PubMed PMID: 12810916.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA. AU - Marmier-Gourrier,Nathalie, AU - Cléry,Antoine, AU - Senty-Ségault,Veronique, AU - Charpentier,Bruno, AU - Schlotter,Florence, AU - Leclerc,Fabrice, AU - Fournier,Régis, AU - Branlant,Christaine, PY - 2003/6/18/pubmed PY - 2003/8/28/medline PY - 2003/6/18/entrez SP - 821 EP - 38 JF - RNA (New York, N.Y.) JO - RNA VL - 9 IS - 7 N2 - The 15.5-kD protein and its yeast homolog Snu13p bind U4 snRNA, U3 snoRNA, and the C/D box snoRNAs. In U4 snRNA, they associate with a helix-bulge-helix (K-turn) structure. U3 snoRNA contains two conserved pairs of boxes, C'/D and B/C, which were both expected to bind the 15.5-kD/Snu13 protein. Only binding to the B/C motif was experimentally demonstrated. Here, by chemical probing of in vitro reconstituted RNA/protein complexes, we demonstrate the independent binding of the 15.5-kD/Snu13 protein to each of the two motifs. Due to a highly reduced stem I (1 bp), the K-turn structure is not formed in the naked B/C motif. However, gel-shift experiments revealed a higher affinity of Snu13p for the B/C motif, compared to the C'/D motif. A phylogenetic analysis of U3 snoRNA, coupled with an analysis of Snu13p affinity for variant yeast C'/D and B/C motifs, and a study of the functionality of a truncated yeast U3 snoRNA carrying base substitutions in the C'/D and B/C motifs, revealed that conservation of the identities of residues 2 and 3 in the B/C K-turn is more important for Snu13p binding and U3 snoRNA function, than conservation of the identities of corresponding residues in the C'/D K-turn. This suggests that binding of Snu13p to K-turns with a very short helix I imposes sequence constraints in the bulge. Altogether, the data demonstrate the strong importance of the binding of the 15.5-kD/Snu13 protein to the C'/D and B/C motifs for both U3 snoRNP assembly and activity. SN - 1355-8382 UR - https://www.unboundmedicine.com/medline/citation/12810916/A_structural_phylogenetic_and_functional_study_of_15_5_kD/Snu13_protein_binding_on_U3_small_nucleolar_RNA_ DB - PRIME DP - Unbound Medicine ER -