RNA and RNP Structures that Contribute to Viral Pathogenesis

Abstract

RNA viruses persist to pose serious threats to human health and global economies. Disease progression mediated by viral pathogenesis requires numerous intersections between host proteins and viral RNA (vRNA) elements. Host‐vRNA complexes drive essential processes in the replication cycles of viruses; as such, they represent novel targets for therapeutic intervention. Members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family are cellular proteins often usurped by RNA viruses. My lab studies the molecular mechanisms by which HIV and Enterovirus 71 redirects hnRNPs to control viral gene expression. To that end, we have designed an integrated biophysical framework to elucidate the structures of vRNAs and protein‐vRNA complexes. Here, we describe 3D structures of conserved HIV and EV71 RNA elements that regulate splicing and translation. We further show that conformational adaptation and slow protein motions are fundamental properties by which hnRNP A1 and hnRNP H achieve cognate RNA recognition. To globally identify determinants of specificity, we used High Throughput Sequencing Equilibrium (HTS‐EQ) binding experiments to characterize the complete affinity distribution of human hnRNP A1 bound to the HIV ESS3 stem loop. HTS‐EQ involves competitive binding of hnRNP A1 to a completely randomized pool of ESS3 apical loop variants (n=16,384). Quantitative analysis of the resulting affinity distribution reveals RNA sequence; motif copy number; motif spacing; and secondary structure determine specificity by modulating the rates of productive hnRNP A1‐RNA encounters. Collectively, our work is offering mechanistic insights into the strategies by which viruses coopt cellular RNA binding proteins.Support or Funding InformationNIH R01 GM101979NIH U54 GM103297This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.