Functional analysis of the SRV-1 RNA frameshifting pseudoknot.

Nucleic Acids Research
René C L OlsthoornHans A Heus

Abstract

Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109-1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for -1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is di...Continue Reading

References

Jan 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·M ChamorroH E Varmus
Nov 1, 1993·Molecular and Cellular Biology·P SomogyiS C Inglis
Dec 10, 1999·Proceedings of the National Academy of Sciences of the United States of America·Y G KimA Rich
Jan 29, 2000·Molecular and Cellular Biology·J D LopinskiJ A Bruenn
Feb 12, 2000·Journal of Molecular Biology·P L Nixon, D P Giedroc
Apr 17, 2002·Journal of Molecular Biology·Durga M ChadalavadaPhilip C Bevilacqua
Sep 13, 2002·Journal of Molecular Biology·Paul L NixonDavid P Giedroc
May 24, 2003·Cold Spring Harbor Symposia on Quantitative Biology·I Brierley, S Pennell
Aug 6, 2003·Journal of Molecular Biology·Martin BarilLéa Brakier-Gingras
Oct 22, 2004·RNA·R C L OlsthoornC W A Pleij
Apr 1, 2005·Nucleic Acids Research·Ewan P Plant, Jonathan D Dinman
Aug 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Peter V CornishDavid P Giedroc
Feb 3, 2006·Chembiochem : a European Journal of Chemical Biology·Philipp WenterStefan Pitsch
Feb 8, 2006·Trends in Genetics : TIG·Pavel V BaranovJohn F Atkins
Mar 29, 2007·Proceedings of the National Academy of Sciences of the United States of America·Thomas M HansenMichael A Sørensen
Nov 21, 2007·Journal of Molecular Biology·Lisa GreenIgnacio Tinoco
Mar 11, 2008·Nature·Jin-Der WenIgnacio Tinoco
Jul 16, 2008·Virus Research·David P Giedroc, Peter V Cornish
Jul 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Gang ChenIgnacio Tinoco

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Citations

Aug 2, 2011·Nucleic Acids Research·Chien-Hung YuRené C L Olsthoorn
Jan 23, 2014·Journal of the American Chemical Society·Dustin B RitchieMichael T Woodside
Sep 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Dustin B RitchieMichael T Woodside
Jan 21, 2012·Angewandte Chemie·Kaihang WangJason W Chin
Aug 26, 2014·Wiley Interdisciplinary Reviews. RNA·Gitali DeviGang Chen
Mar 16, 2012·RNA Biology·Aditi GuptaMichael Gribskov
Jan 19, 2013·ACS Chemical Biology·Chien-Hung YuRené C L Olsthoorn
Dec 25, 2015·PLoS Genetics·Albino BacollaKaren M Vasquez

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Methods Mentioned

BETA
NMR
PCR
column filtration
transfection
optical tweezers

Software Mentioned

Quantity One

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