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Nucleic Acids Research 2005 33(15):4754-4761; doi:10.1093/nar/gki760
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Published online 22 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Specific roles of 5' RNA secondary structures in stabilizing transcripts in chloroplasts

Loreto Suay, Maria L. Salvador, Emnet Abesha1 and Uwe Klein1,*

Department of Biochemistry and Molecular Biology, University of Valencia Dr Moliner 50, Burjassot, Valencia 46100, Spain 1Department of Molecular Biosciences, University of Oslo PO Box 1041 Blindern, 0316 Oslo, Norway

*To whom correspondence should be addressed. Tel: +34 47 22854662; Fax +34 47 22854726; Email: uwe.klein{at}imbv.uio.no

Received June 1, 2005. Revised July 22, 2005. Accepted July 22, 2005.

RNA secondary structures, e.g. stem–loops that are often found at the 5' and 3' ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem–loop at the 5' end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem–loop has a formative function in that it mediates folding of a short sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevity of rbcL transcripts in chloroplasts. Disturbing this structure renders transcripts completely unstable, even if the sequence of this element is not altered. The requirement of a specific 5' sequence and structure for RNA longevity suggests an interaction of this element with a trans-acting factor that protects transcripts from rapid degradation in chloroplasts.


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