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
- 30 October 2008
- journal article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 14 (12), 2597-2608
- https://doi.org/10.1261/rna.1284908
Abstract
Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV). Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem–loops and a conserved long-range interaction between heptanucleotide sequences 5′-CCCUGUC-3′ in R/U5 and 5′-GACAGGG-3′ in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in species-specific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 5′ UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism.Keywords
This publication has 40 references indexed in Scilit:
- RNA secondary structure of the feline immunodeficiency virus 5′UTR and Gag coding regionNucleic Acids Research, 2008
- Molecular mechanisms of FIV infectionVeterinary Immunology and Immunopathology, 2008
- A Dormant Internal Ribosome Entry Site Controls Translation of Feline Immunodeficiency VirusJournal of Virology, 2008
- Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wildBMC Genomics, 2008
- Recombination in feline immunodeficiency virus genomes from naturally infected cougarsVirology, 2007
- Human Immunodeficiency Virus Type 1 Gag Polyprotein Modulates Its Own TranslationJournal of Virology, 2006
- Functional Interactions of Nucleocapsid Protein of Feline Immunodeficiency Virus and Cellular Prion Protein with the Viral RNAJournal of Molecular Biology, 2002
- The Major Human Immunodeficiency Virus Type 2 (HIV-2) Packaging Signal Is Present on All HIV-2 RNA Species: Cotranslational RNA Encapsidation and Limitation of Gag Protein Confer SpecificityJournal of Virology, 2001
- Identification of a high affinity nucleocapsid protein binding element within the moloney murine leukemia virus Ψ-RNA packaging signal: implications for genome recognitionJournal of Molecular Biology, 2001
- Cis elements and Trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1Journal of Molecular Biology, 1990