Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene.

RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 2'-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.