SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization.

Abstract

Feline immunodeficiency virus (FIV) infects many species of cat, and is related to HIV, causing a similar pathology. High-throughput selective 2' hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows structural interrogation at each nucleotide, was used to map the secondary structure of the FIV packaging signal RNA. Previous studies of this RNA showed four conserved stem-loops, extensive long-range interactions (LRIs) and a small, palindromic stem-loop (SL5) within the gag open reading frame (ORF) that may act as a dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Our analyses of wild-type (wt) and mutant RNAs suggest that although the four conserved stem-loops are static structures, the 5' and 3' regions previously shown to form LRI also adopt an alternative, yet similarly conserved conformation, in which the putative DIS is occluded, and which may thus favour translational and splicing functions over encapsidation. SHAPE and in vitro dimerization assays were used to examine SL5 mutants. Dimerization contacts appear to be made between palindromic loop sequences in SL5. As this stem-loop is located within the gag ORF, recognition of a dimeric RNA provides a possible mechanism for the specific packaging of genomic over spliced viral RNAs.

• Authors: Julia C Kenyon, Sian J Tanner, Michal Legiewicz, Pretty S Phillip, Tahir A Rizvi, Stuart F J Le Grice, Andrew M L Lever
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 39 Issue 15 Pg. 6692-704 (Aug 2011) ISSN: 1362-4962 [Electronic] England
• PMID: 21546549 (Publication Type: Journal Article, Research Support, N.I.H., Intramural, Research Support, Non-U.S. Gov't)

Chemical References

• 5' Untranslated Regions
• RNA, Viral
• Regulatory Sequences, Ribonucleic Acid

Topics

• 5' Untranslated Regions
• Base Sequence
• Dimerization
• Electrophoresis, Polyacrylamide Gel
• Genome, Viral
• Immunodeficiency Virus, Feline (genetics)
• Molecular Probe Techniques
• Molecular Sequence Data
• Nucleic Acid Conformation
• RNA, Viral (chemistry)
• Regulatory Sequences, Ribonucleic Acid
• Virus Assembly