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Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing.
RNA. 2013 Oct; 19(10):1372-83.RNA

Abstract

Eukaryotic ribosome biogenesis requires rapid hybridization between the U3 snoRNA and the pre-rRNA to direct cleavages at the A0, A1, and A2 sites in pre-rRNA that liberate the small subunit precursor. The bases involved in hybridization of one of the three duplexes that U3 makes with pre-rRNA, designated the U3-18S duplex, are buried in conserved structures: box A/A' stem-loop in U3 snoRNA and helix 1 (H1) in the 18S region of the pre-rRNA. These conserved structures must be unfolded to permit the necessary hybridization. Previously, we reported that Imp3 and Imp4 promote U3-18S hybridization in vitro, but the mechanism by which these proteins facilitate U3-18S duplex formation remained unclear. Here, we directly addressed this question by probing base accessibility with chemical modification and backbone accessibility with ribonuclease activity of U3 and pre-rRNA fragments that mimic the secondary structure observed in vivo. Our results demonstrate that U3-18S hybridization requires only Imp3. Binding to each RNA by Imp3 provides sufficient energy to unfold both the 18S H1 and the U3 box A/A' stem structures. The Imp3 unfolding activity also increases accessibility at the U3-dependent A0 and A1 sites, perhaps signaling cleavage at these sites to generate the 5' mature end of 18S. Imp4 destabilizes the U3-18S duplex to aid U3 release, thus differentiating the roles of these proteins. Protein-dependent unfolding of these structures may serve as a switch to block U3-pre-rRNA interactions until recruitment of Imp3, thereby preventing premature and inaccurate U3-dependent pre-rRNA cleavage and folding events in eukaryotic ribosome biogenesis.

Authors

No 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

23980203

Citation

Shah, Binal N., et al. "Imp3 Unfolds Stem Structures in pre-rRNA and U3 snoRNA to Form a Duplex Essential for Small Subunit Processing." RNA (New York, N.Y.), vol. 19, no. 10, 2013, pp. 1372-83.
Shah BN, Liu X, Correll CC. Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing. RNA. 2013;19(10):1372-83.
Shah, B. N., Liu, X., & Correll, C. C. (2013). Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing. RNA (New York, N.Y.), 19(10), 1372-83. https://doi.org/10.1261/rna.039511.113
Shah BN, Liu X, Correll CC. Imp3 Unfolds Stem Structures in pre-rRNA and U3 snoRNA to Form a Duplex Essential for Small Subunit Processing. RNA. 2013;19(10):1372-83. PubMed PMID: 23980203.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing. AU - Shah,Binal N, AU - Liu,Xin, AU - Correll,Carl C, Y1 - 2013/08/26/ PY - 2013/8/28/entrez PY - 2013/8/28/pubmed PY - 2013/11/8/medline KW - RNA conformational switch KW - ribonucleoprotein KW - ribosome synthesis KW - yeast SP - 1372 EP - 83 JF - RNA (New York, N.Y.) JO - RNA VL - 19 IS - 10 N2 - Eukaryotic ribosome biogenesis requires rapid hybridization between the U3 snoRNA and the pre-rRNA to direct cleavages at the A0, A1, and A2 sites in pre-rRNA that liberate the small subunit precursor. The bases involved in hybridization of one of the three duplexes that U3 makes with pre-rRNA, designated the U3-18S duplex, are buried in conserved structures: box A/A' stem-loop in U3 snoRNA and helix 1 (H1) in the 18S region of the pre-rRNA. These conserved structures must be unfolded to permit the necessary hybridization. Previously, we reported that Imp3 and Imp4 promote U3-18S hybridization in vitro, but the mechanism by which these proteins facilitate U3-18S duplex formation remained unclear. Here, we directly addressed this question by probing base accessibility with chemical modification and backbone accessibility with ribonuclease activity of U3 and pre-rRNA fragments that mimic the secondary structure observed in vivo. Our results demonstrate that U3-18S hybridization requires only Imp3. Binding to each RNA by Imp3 provides sufficient energy to unfold both the 18S H1 and the U3 box A/A' stem structures. The Imp3 unfolding activity also increases accessibility at the U3-dependent A0 and A1 sites, perhaps signaling cleavage at these sites to generate the 5' mature end of 18S. Imp4 destabilizes the U3-18S duplex to aid U3 release, thus differentiating the roles of these proteins. Protein-dependent unfolding of these structures may serve as a switch to block U3-pre-rRNA interactions until recruitment of Imp3, thereby preventing premature and inaccurate U3-dependent pre-rRNA cleavage and folding events in eukaryotic ribosome biogenesis. SN - 1469-9001 UR - https://www.unboundmedicine.com/medline/citation/23980203/Imp3_unfolds_stem_structures_in_pre_rRNA_and_U3_snoRNA_to_form_a_duplex_essential_for_small_subunit_processing_ L2 - http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=23980203 DB - PRIME DP - Unbound Medicine ER -