Novel GACG-hairpin pair motif in the 5' untranslated region of type C retroviruses related to murine leukemia virus

Abstract

We searched for the presence of common RNA structural motifs in mammalian type C retroviruses related to murine leukemia viruses and the closely related avian spleen necrosis virus. A novel motif consisting of a pair of hairpins, called hairpin pair motif, was detected in the 5' untranslated regions of the genomes of these retroviruses. A combination of computational analyses that included the assessment of phylogenetic sequence conservation by multiple alignment, the search for regions with unusual RNA folding properties, and the analysis of RNA secondary structure by suboptimal free-energy calculations highlighted the significance of this hairpin pair motif. The hairpin pair motif encompasses 70 to 80 nucleotides between the splice donor site and the gag translational initiation codon of these viruses. The motif is composed of two adjacent hairpins both with a perfectly conserved GACG tetraloop. We propose that the novel GACG-hairpin pair motif described here constitutes an essential component of the regulatory machinery in these type C retroviruses.

A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication

“…This observation seems to hold for other retroviruses. Avian spleen necrosis virus contains in the 5Ј leader region a double hairpin which is conserved in several type C retroviruses (36) and involved in RNA packaging (59). It should also be noted that several HIV-1 motifs involved in packaging have been implicated in the process of dimerization (13,40,47), a finding consistent with the idea that these processes are linked (21,22).…”

Secondary structure model of the Mason-Pfizer monkey virus 5' leader sequence: identification of a structural motif common to a variety of retroviruses

“…No similar structure was identified by free energy studies on the analogous regions of SMRV or mouse mammary tumor virus. There are two GACG sequences at positions 788 to 794 which will form the stem-loop structure represented in panel C. This bears some resemblance to the motif identified by Konings et al (34). The biochemical data support the existence of this structure, but it is not conserved in SRV-2 and the free energy prediction is lower than those for the structures shown in panels A and B.…”

“…The GACG-hairpin motifs identified by Konings et al (34) occur in type C murine leukemia viruses and SNV (63). In the latter, linker-scanning mutagenesis showed that mutation of the GACG motif impairs packaging.…”

“…Yang and Temin (63) showed that two hairpin structures are required for encapsidation of the spleen necrosis virus (SNV) genomic RNA and that a similar region in MoMuLV could substitute for these two hairpins in an SNV-based retroviral vector. Both stem loops in SNV contain the GACG sequence identified by Konings et al (34).…”

“…There is no sequence conservation between identified packaging signals; therefore, the specificity of packaging is likely to involve physical recognition of unique RNA structures, formed because of intramolecular base pairing and further tertiary folding. The only sequence which has previously been shown to be common to ⌿'s of different retroviruses is the GACG motif identified by Konings et al (34), which is on a stem structure. For human immunodeficiency virus type 1 (HIV-1), we have published an RNA secondary structure model based on biochemical analysis, free energy minimization, and sequence comparison in a region known to be important for packaging (24).…”