Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

• DOI: 10.1371/journal.ppat.1003294
• Publication Date: 2013-04-04T22:17:52Z
• Authors: Elizabeth Pollom; Kristen K. Dang; E. Lake Potter; Robert J. Gorelick; Christina L. Burch; Kevin M. Weeks; Ronald Swanstrom
• Keywords: Conserved sequence; Sequence (biology)

RNA secondary structure plays a central role in the replication and metabolism of all viruses, including retroviruses like HIV-1. However, structures with known function represent only fraction reported for HIV-1NL4-3. One tool to assess importance is examine their conservation over evolutionary time. To this end, we used SHAPE model second primate lentiviral genome, SIVmac239, which shares 50% sequence identity at nucleotide level Only about half paired nucleotides are both genomic RNAs and, across just 71 base pairs form same pairing partner genomes. On average thus evolving much faster rate than sequence. Structure Gag-Pro-Pol frameshift site maintained but significantly altered form, while impact selection maintaining protein binding interaction can be seen partners small RRE stems where Rev binds. Structures that conserved between SIVmac239 HIV-1NL4-3 also occur 5′ polyadenylation sequence, plus strand primer sites, PPT cPPT, stem-loop includes first splice acceptor site. The two genomes adenosine-rich cytidine-poor. structured regions enriched guanosines, unpaired adenosines, functionaly important have stronger nonconserved structures. We conclude result fortuitous metastable state reforms during evolution. elements stabilized by higher guanosine content allows persist as evolution proceeds, within confines selective pressure, evolve.