Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India

HIV-1 displays very high genetic diversity and has been classified into various subtypes and recombinant forms. While subtype B predominates in US and UK, it is subtype C that is predominant in India, China and South Africa. Most of the changes are observed in the Envelope region but other region like p24-Gag is relatively conserved among subtypes and has been exploited to develop ELISA for diagnostic purposes. HIV-1 exploits the splicing machinery very efficiently by using the Rev protein which binds with high affinity and specificity to highly structured cis-acting RNA element present within the coding region of HIV-1 Envelope gene [1] called Rev Responsive Element (RRE). This RRE element folds into 4 well defined stem-loop structures (A to D) and stem-loop B (stem-bulge-stem structure) is critically important for efficient binding with Rev Protein [2]. Natural variations in the RRE sequences can potentially impact on the secondary structure which might modulate the efficiency of Rev binding. Several studies have earlier suggested that the major Rev protein binding site resides in the predicted second branched stem-loop region [1,3] and other regions of the full-length RRE may influence the binding of Rev protein [4]. Rev - RRE interaction is crucial for efficient late gene expression and replication and efforts are being made to develop novel antiviral approaches that interfere with this interaction. RevM10, a transdominant negative Rev protein, was earlier shown to interfere with HIV-1 replication in T-cell lines and also in primary T-cells [5]. RRE element has been exploited as decoy for specific targeting of HIV-1 gene expression and replication [6].RRE variants are produced when cells are treated with this protein [7]. Very recently resistant mutants were identified due to altered RRE structures in presence of RevM10 protein [8]. These two studies strongly suggest that sequences in RRE can change under pressure that can have great functional implications. Ear