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Nucleic Acids Research Advance Access originally published online on July 14, 2008
Nucleic Acids Research 2008 36(14):4653-4666; doi:10.1093/nar/gkn447
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Nucleic Acids Research, 2008, Vol. 36, No. 14 4653-4666
© 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

RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region

Laurie James and Bruno Sargueil*

CNRS UPR2167 – Centre de Génétique Moléculaire, Avenue de la Terrasse, 91190 Gif sur yvette, France

*To whom correspondence should be addressed. Tel: +00 33 1 53 73 15 68; Fax: +00 33 1 53 73 99 25; Email: bruno.sargueil{at}univ-paris5.fr

Received May 14, 2008. Revised June 26, 2008. Accepted June 27, 2008.

The 5' untranslated region (5'UTR) of lentiviral genomic RNA is highly structured, and is the site of multiple RNA–RNA and RNA–protein interactions throughout the viral life cycle. The 5'UTR plays a critical role during transcription, translational regulation, genome dimerization, reverse transcription priming and encapsidation. The 5'UTR structures of human lentiviruses have been extensively studied, yet the respective role and conformation of each domain is still controversial. To gain insight into the structure-function relationship of lentiviral 5'UTRs, we modelled the RNA structure of the feline immunodeficiency virus (FIV), a virus that is evolutionarily distant from the primate viruses. Through combined chemical and enzymatic structure probing and a thorough phylogenetic study, we establish a model for the secondary structure of the 5'UTR and Gag coding region. This work highlights properties common to all lentiviruses, like the primer binding site structure and the presence of a stable stem-loop at the 5' extremity. We find that FIV has also evolved specific features, including a long stem loop overlapping the end of the 5'UTR and the beginning of the coding region. In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation.

Present address: Laurie James and Bruno Sargueil, CNRS UMR8015, Laboratoire de cristallographie et RMN biologique, Faculté de Pharmacie 4 avenue de l'o;bservatoire 75270, Cedex 06, Paris.


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The secondary structure of the 5' end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop
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[Abstract] [Full Text] [PDF]


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