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

Abstract

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

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

“…1a). Different HIV-1 isolates and the related SIVmac239 can fold a similar 59ss structure (Mueller et al, 2014;Pollom et al, 2013). This evolutionary conservation supports the idea that this structure has an important role in viral replication.…”

Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure

“…We normalized the corrected reactivity by a multiplier based on the reactivity distribution of the full-length SERPINA1 transcript. To examine the broad, overall SHAPE reactivity, we averaged select data sets (defined in each section, available as Supplemental Files 1-4 and on http://snrnasm.web.unc.edu) and calculated the median reactivity for 40-50 nt sliding windows (Pollom et al 2013). We used this SHAPE reactivity to inform a minimum free energy structure using RNAstructure with a maximum pairing distance of 200/300 nts ( Fig.…”

Structural dynamics of a single-stranded RNA–helix junction using NMR

“…They can act as spacers between structured domains (Lodeiro et al 2009;Watts et al 2009), provide binding sites for protein or RNA recognition (Auweter et al 2006), act as checkpoints in RNA maturation (Spitzfaden et al 2000), serve as signaling elements that can be sequestered into helices to generate switching behavior (Schwalbe et al 2007), and form active sites to perform catalysis (Shi et al 2012) and are key components of structured motifs such as pseudoknots (Zhang et al 2011). Secondary structure analysis of RNA genomes and large structured RNAs reveals a pattern of adenine-enriched single-stranded regions (Gutell et al 1985;Pollom et al 2013).…”