Structural model of the complete poly(A) region of HIV-1 pre-mRNA

In the HIV-1 retrovirus, identical sequences encompassing the AAUAAA hexamer and the U/GU-rich downstream sequence element (DSE) that compose the core poly(A) site are present at both the 5' and 3' ends of the HIV-1 pre-mRNA. The AAUAAA hexamer is partly occluded by base pairing in the upper part of a semi-stable polyA hairpin. This sets the stage for regulation of HIV-1 polyadenylation, which involves reaction suppression at the 5' end and its stimulation at the 3' end. Efficient utilization of the 3' core poly(A) site is promoted by major and minor upstream sequence elements (USEs) which are uniquely present at the 3' end of the HIV-1 transcript. The structures of the HIV-1 5' and 3' poly(A) sites are defined by overall architecture of complete 5' and 3' untranslated terminal regions (UTRs). To our knowledge, there is still no structural model of a complete 3' UTR of the HIV-1 pre-mRNA and complete 3' poly(A) region including the USEs except the fact that the polyA and transactivation response (TAR) hairpins are present at both ends of the HIV-1 pre-mRNA. In this work, we predicted a secondary structure of the 3' UTR of HIV-1 pre-mRNA based on our observation that the minor USEs are located in a region with a high potential to form G-quadruplex structures. We first present structural models for the major USE, complete 3' poly(A) region, and almost entire 3' UTR of HIV-1 pre-mRNA. Our models are built based on the mfold and UNAFold secondary structure prediction of these regions for about 1500 HIV-1 isolates of different subtypes and recombinant forms. We have demonstrated that these models are valid for most of the HIV-1 isolates studied. The proposed models include the known TAR and polyA hairpins and new structural elements containing the U-rich tract of the major USE and U/GU-rich DSE which are fully exposed and accessible to the polyadenylation machinery, which confirms the functional competence of our models.