Differential stability of the mRNA secondary structures in the frameshift site of various HIV type 1 viruses.
For many retroviruses, one or more ribosomal frameshift events are required for translation of the Gag-Pol precursor protein, which is subsequently processed into the structural and enzymatic proteins found in mature virions. A specific nucleotide motif, the slippery sequence, as well as a downstream mRNA secondary structure are generally believed to have roles in the frameshift event. In HIV-1, a particular stem-loop mRNA secondary structure has been proposed for subtype B. On the basis of this model, HIV-1 subtypes A, E, and F were found in this study to share a similar stem-loop structure predicted to have a lower thermodynamic stability as compared with HIV-1 subtypes B, C, and D. The potential impact of this differential thermodynamic stability on HIV-1 replication remains to be determined.
Chang
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SY
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
Sutthent
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R
Auewarakul
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P
Apichartpiyakul
C
C
Essex
M
M
Lee
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TH
D001483:Base Sequence; D018965:Frameshifting, Ribosomal; D015750:Genes, gag / Q000235:genetics; D015751:Genes, pol / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D016415:Sequence Alignment; D013816:Thermodynamics
D012333:RNA, Messenger; D012367:RNA, Viral