The secondary structure of the 52 end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop

Julia C. Kenyon, Akela Ghazawi, Winsome K.S. Cheung, Pretty S. Phillip, Tahir A. Rizvi, Andrew M.L. Lever

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)

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. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish
Pages (from-to)2597-2608
Number of pages12
JournalRNA
Volume14
Issue number12
DOIs
Publication statusPublished - Dec 2008

Keywords

  • Dimerization
  • FIV
  • Lentivirus
  • Packaging signal
  • RNA

ASJC Scopus subject areas

  • Molecular Biology

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