Efficiency of a programmed −1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M

Abstract

The synthesis of the Gag-Pol polyprotein, the precursor of the enzymes of the human immunodeficiency virus type 1 (HIV-1), requires a programmed −1 ribosomal frameshift. This frameshift has been investigated so far only for subtype B of HIV-1 group M. In this subtype, the frameshift stimulatory signal was found to be a two-stem helix, in which a three-purine bulge interrupts the two stems. In this study, using a luciferase reporter system, we compare, for the first time, the frameshift efficiency of all the subtypes of group M. Mutants of subtype B, including a natural variant were also investigated. Our results with mutants of subtype B confirm that the bulge and the lower stem of the frameshift stimulatory signal contribute to the frameshift in addition to the upper stem-loop considered previously as the sole participant. Our results also show that the frameshift stimulatory signal of all of the other subtypes of group M can be folded into the same structure as in subtype B, despite sequence variations. Moreover, the frameshift efficiency of these subtypes, when assessed in cultured cells, falls within a narrow window (the maximal deviation from the mean value calculated from the experimental values of all the subtypes being ∼35%), although the predicted thermodynamic stability of the frameshift stimulatory signal differs between the subtypes (from −17.2 kcal/mole to −26.2 kcal/mole). The fact that the frameshift efficiencies fall within a narrow range for all of the subtypes of HIV-1 group M stresses the potential of the frameshift event as an antiviral target.

Gag Mutations Can Impact Virological Response to Dual-Boosted Protease Inhibitor Combinations in Antiretroviral-Naïve HIV-Infected Patients

“…HIV-1 non-B subtypes generally have higher numbers of gag cleavage site and gag-pol frameshift mutations. The similarity of the gag-pol frameshift signal structures of different HIV-1 group M viruses has been demonstrated (3,6). HIV-1 A, F, and CRF_01AE subtypes had lower levels of thermodynamic stability than B, C, and D subtypes (6).…”

Identification of a Cellular Factor That Modulates HIV-1 Programmed Ribosomal Frameshifting

“…Ϫ1 PRF occurs in all viruses via a similar mechanism (17, 18). Two basic RNA elements have been identified which are absolutely required to generate and regulate PRF: a slippery site and a segment of RNA secondary structure called the frameshift stimulatory signal (11,17,19,20) (Fig. 1).…”

“…The slippery sequence of HIV-1 is U UUU UUA. The PRF-stimulatory signal of HIV-1 is contained within a 69-base segment (11) which forms an extended stem-loop and helps regulate the probability of the PRF event (9,11,19,20,(25)(26)(27)(28)(29). This contrasts with most other viral systems containing Ϫ1 frameshift signals as they have been reported to form pseudoknots 3Ј to the slippery site.…”

CD8 + T Cell Recognition of Cryptic Epitopes Is a Ubiquitous Feature of AIDS Virus Infection

“…Not all of the predicted translation products contain translation initiation codons. In such cases, alternate start codons, such as CUG (encoding leucine) (14), or ribosomal frameshifts (3,11,19), might account for translation.…”