Nucleic Acids Research Advance Access originally published online on September 12, 2007
Nucleic Acids Research 2007 35(18):6196-6206; doi:10.1093/nar/gkm673
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Nucleic Acids Research, 2007, Vol. 35, No. 18 6196-6206
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
Dynamic interactions within sub-complexes of the H/ACA pseudouridylation guide RNP
Departments of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
*To whom correspondence should be addressed. Tel: +1 706 542 1703; Fax: +1 706 542 1752; Email: rterns{at}bmb.uga.edu Correspondence may also be addressed to Michael Terns. Tel: +1 706 542 1896; Fax: +1 706 542 1752; Email: mterns{at}bmb.uga.edu
Received June 27, 2007. Revised August 13, 2007. Accepted August 16, 2007.
H/ACA RNP complexes change uridines to pseudouridines in target non-coding RNAs in eukaryotes and archaea. H/ACA RNPs are comprised of a guide RNA and four essential proteins: Cbf5 (pseudouridine synthase), L7Ae, Gar1 and Nop10 in archaea. The guide RNA captures the target RNA via two antisense elements brought together to form a contiguous binding site within the pseudouridylation pocket (internal loop) of the guide RNA. Cbf5 and L7Ae interact independently with the guide RNA, and here we have examined the impacts of these proteins on the RNA in nucleotide protection assays. The results indicate that the interactions observed in a fully assembled H/ACA RNP are established in the sub-complexes, but also reveal a unique Cbf5–guide RNA interaction that is displaced by L7Ae. In addition, the results indicate that L7Ae binding at the kink (k)-turn of the guide RNA induces the formation of the upper stem, and thus also the pseudouridylation pocket. Our findings indicate that L7Ae is essential for formation of the substrate RNA binding site in the archaeal H/ACA RNP, and suggest that k-turn-binding proteins may remodel partner RNAs with important effects distant from the protein-binding site.