Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding.

Nucleic Acids Research
Ruud J W Schoemaker, Alexander P Gultyaev

Abstract

Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA-RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of...Continue Reading

References

Oct 10, 1981·Nucleic Acids Research·F R Kramer, D R Mills
Dec 8, 1995·Science·J A Steitz, K T Tycowski
Sep 27, 1994·Proceedings of the National Academy of Sciences of the United States of America·A E WalterM Zuker
Jun 30, 1995·Journal of Molecular Biology·A P GultyaevC W Pleij
Oct 1, 1995·Genes & Development·W Q Liang, M J Fournier
Jul 1, 1995·Trends in Biochemical Sciences·J P BachellerieM J Fournier
Nov 1, 1995·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·S A Gerbi
Apr 18, 1997·Journal of Molecular Biology·M HuynenD Konings
Jul 1, 1997·Trends in Biochemical Sciences·J P Bachellerie, J Cavaillé
Sep 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·R A PootJ van Duin
Nov 21, 1997·Journal of Molecular Biology·J PanS A Woodson
Dec 10, 1998·Nucleic Acids Research·D A Samarsky, M J Fournier
Jun 16, 1999·Journal of Molecular Evolution·E A SchultesT H LaBean
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·T PanT R Sosnick
Dec 3, 1999·Nature Structural Biology·X W FangT R Sosnick
Feb 26, 2000·Annual Review of Genetics·J Venema, D Tollervey
Apr 25, 2000·Science·A D OmerP P Dennis
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·H Isambert, E D Siggia
Jul 13, 2000·Cellular and Molecular Life Sciences : CMLS·S A Woodson
Oct 3, 2000·Nature·B T WimberlyV Ramakrishnan
May 22, 2001·Molecular Microbiology·P P DennisT Lowe
Sep 20, 2001·Journal of the American Chemical Society·D N DubinsT V Chalikian
Dec 6, 2001·Journal of Molecular Evolution·Alexander P GultyaevCornelis W A Pleij
Feb 13, 2002·Current Biology : CB·Wayne A SpeckmannMichael P Terns
May 7, 2002·RNA·Amanda SolemMark G Caprara
Sep 5, 2002·Genes & Development·Christina WaldsichRenée Schroeder
Nov 8, 2002·Journal of Molecular Biology·Amy Diegelman-Parente, Philip C Bevilacqua
May 21, 2003·RNA·Susan L Heilman-Miller, Sarah A Woodson
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Nov 7, 2003·Nucleic Acids Research·Patrice VitaliJérôme Cavaillé
Nov 26, 2003·Journal of Molecular Biology·Linhui Julie SuAnna Marie Pyle
Dec 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·A XayaphoummineH Isambert
Dec 19, 2003·Nucleic Acids Research·Jan WuytsYves Van De Peer

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Citations

Sep 25, 2009·Journal of Molecular Evolution·David PennyDaniel C Jeffares
Mar 1, 2012·Chemical Reviews·Emil Paleček, Martin Bartošík
Mar 21, 2013·Nucleic Acids Research·Jeff R Proctor, Irmtraud M Meyer
Oct 18, 2013·RNA·Daniel LaiIrmtraud M Meyer
Apr 5, 2013·Archaea : an International Microbiological Journal·W S Vincent YipSusan J Baserga

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Methods Mentioned

BETA
RNA folding

Software Mentioned

mfold
STAR

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