A pan-arboviral ATLAS of capsid-interacting proteins in mosquito cells identifies unique host factor specificities
In recent years, arbovirus cases have surged dramatically due to the expanding distribution of the main arbovirus-vectors Aedes and Culex mosquitoes. Despite significant efforts to uncover Orthoflavivirus-specific host adaptation mechanisms of humans, systematic studies aiming to characterize virus–host interactions in arthropods are largely missing. The capsid protein is highly versatile, with multiple functions and subcellular localizations, making it an attractive target for studying host susceptibility, vector competence, and virus–vector adaptation. Here, we employed affinity purification coupled to mass spectrometry to systematically evaluate the ability of capsid proteins of 12 different pathogenic arboviruses spanning three genera to interact with the Ae. aegypti proteome. This extensive protein-protein interaction atlas uncovered novel host targets, implicated in diverse cellular pathways i.e. translation, apoptosis and RNA processing. To functionally characterize prioritized interacting host proteins, we systematically silenced 110 host genes in Ae. aegypti-derived cells and characterized their impact on the replication of three representative arboviruses: La Crosse virus, dengue virus and West Nile virus. This approach identified 37 novel host-dependency factors, including a new role for two components of the chromatin-remodeling Brahma complex. Interestingly, systematic silencing of individual Brahma BAP subunits revealed a conserved pan-orthoflavivirus role for both BAP and PBAP subcomplexes, when compared to prototypic alphaviruses. Furthermore, using a combination of biochemical and sequencing approaches, we characterized the cellular determinants of these interactions and profiled their functional consequences on the chromatin landscape. Altogether, this study provides an evidence-based repository to categorize and characterize novel arboviral capsid targets and explore arbovirus-vector interactions.