Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element.
Expression of the HIV reverse transcriptase and other essential viral enzymes requires a -1 translational frameshift. The frameshift event is induced by two highly conserved RNA elements within the HIV-1 mRNA: a UUUUUUA heptamer known as the slippery sequence, and a downstream RNA structure. Here, we report structural and thermodynamic evidence that the HIV-1 frameshift site RNA forms a stem-loop and lower helix separated by a three-purine bulge. We have determined the structure of the 45 nucleotide frameshift site RNA using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The upper helix is highly thermostable (T(m)>90 degrees C), forming 11 Watson-Crick base-pairs capped by a stable ACAA tetraloop. The eight base-pair lower helix was found to be only moderately stable (T(m)=47 degrees C). A three-purine bulge separates the highly stable upper helix from the lower helix. Base stacking in the bulge forms a wedge, introducing a 60 degrees bend between the helices. Interestingly, this bend is similar to those seen in a number of frameshift inducing pseudoknots for which structures have been solved. The lower helix must denature to allow the ribosome access to the slippery site, but likely functions as a positioning element that enhances frameshift efficiency.
Staple
David W
DW
Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA.
Butcher
Samuel E
SE
D018965:Frameshifting, Ribosomal; D015967:Gene Expression Regulation, Viral; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D008670:Metals / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics; D012996:Solutions; D013816:Thermodynamics
D008670:Metals; D012367:RNA, Viral; D012996:Solutions