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Nucleic Acids Research Advance Access originally published online on August 27, 2008
Nucleic Acids Research 2008 36(17):5530-5539; doi:10.1093/nar/gkn530
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Nucleic Acids Research, 2008, Vol. 36, No. 17 5530-5539
© 2008 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.

RNA

A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA

Nikolay G. Kolev, Emilia I. Hartland and Paul W. Huber*

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA

*To whom correspondence should be addressed. Tel: +1 574 631 6042; Fax: +1 574 631 6652; Email: huber.l{at}nd.edu

Received June 2, 2008. Revised July 8, 2008. Accepted August 1, 2008.

The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and β-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs only in the presence of manganese or cadmium ions and proceeds optimally near 30°C and physiological pH. The time course of cleavage in Vg1 mRNA best fits a two-step process in which both steps are first-order. In Vg1 mRNA, the ribozyme is positioned adjacent to a polyadenylation signal, but has no influence on translation of the mRNA in Xenopus oocytes. Putative GAAA ribozyme structures are also near polyadenylation sites in yeast and rat actin mRNAs. Analysis of sequences in the PolyA Cleavage Site and 3'-UTR Database (PACdb) revealed no particular bias in the frequency or distribution of the GAAA motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts. Nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mRNAs.

Present address: Nikolay G. Kolev, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06519, USA


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