Poster abstracts
Poster number 118 submitted by Vidusha Kothwela
Orthogonal Organic Phase Separation (OOPS) Reveals Virus-Specific RNA binding of Non-Canonical RNA-Binding Proteins During ZIKV and HCV Infections
Vidusha Kothwela (Case Western Reserve University, School of Medicine, Biochemistry Department, Cleveland, OH), Joseph Luna (Case Western Reserve University, School of Medicine, Biochemistry Department, Cleveland, OH)
Abstract:
RNA-binding proteins (RBPs) play critical roles in viral pathogenesis by regulating host and viral RNA metabolism. While canonical RBPs are well-characterized, emerging evidence suggests that many proteins exhibit context-dependent RNA-binding activity during cellular stress, including viral infection. Here, we applied Orthogonal Organic Phase Separation (OOPS) to profile RNA-protein interactions in ZIKV- and HCV-infected cells to systematically identify the complete RBP landscape during viral infection. Our analysis revealed extensive virus-specific alterations in the cellular RBPome during both infections. We identified 319 and 339 Gene Ontology-annotated RBPs in ZIKV- and HCV-infected cells, respectively, with 218 proteins common to both infections, indicating both shared and virus-specific RNA regulatory mechanisms. Notably, we discovered a substantial population of putative non-canonical RBPs (ncRBPs), with 557 proteins identified in HCV-infected cells and 504 in ZIKV-infected cells, where 272 were shared between conditions. Domain architecture analysis revealed that most identified proteins lack classical RNA-binding domains. This distribution underscores the non-canonical nature of the ncRBPs and suggests novel mechanisms of RNA interaction beyond traditional domain-mediated binding. Functional enrichment analysis revealed that ncRBPs are predominantly involved in chromosome segregation, Golgi vesicle transport, and cytokinesis. Protein-protein interaction network analysis showed virus-specific patterns, with ZIKV ncRBPs enriched in transcription elongation and DNA repair pathways, while HCV ncRBPs were associated with mitotic nuclear division and chromatin remodeling complexes. These findings suggest that viral infections dramatically alter the cellular RBPome, revealing substantial non-canonical RNA-binding activities within the proteome. Our comprehensive characterization provides new insights into host-pathogen interactions and reveals potential therapeutic targets for antiviral intervention.
Keywords: RNA binding proteins, Flavivirus, Non-canonical RNA-RBP interactions