Compositional analysis of Sindbis virus ribonucleoproteins reveals an extensive co-opting of key nuclear RNA-binding proteins

Kamel, Wael; Ruscica, Vincenzo; Garcia-Moreno, Manuel; Palmalux, Natasha; Iselin, Louisa; Hannan, Maximilian; Järvelin, Aino; Noerenberg, Marko; Moore, Samantha; Merits, Andres; Davis, Ilan; Martinez, Javier; Mohammed, Shabaz; Castello, Alfredo

The expansion of tropical mosquito habitats and associated arboviruses is a risk for human health, and it thus becomes fundamental to identify new antiviral strategies. In this study we employ a new approach to elucidate the composition of the ribonucleoproteins (RNPs) of a prototypical arbovirus called Sindbis (SINV). SINV RNPs contain 453 cellular and 6 viral proteins, many of these proteins are nuclear in uninfected cells and redistribute to the cytoplasm upon infection. These findings suggest that SINV RNAs act as ’spiderwebs’, capturing host factors required for viral replication and gene expression in the cytoplasm. Functional perturbation of several of these host proteins causes profound effects in virus infection, as illustrated here with the tRNA ligase complex. Moreover, inhibition of viral RNP components with available drugs hampers the infection of a wide range of viruses, opening new avenues for the development of broad-spectrum therapies. Research highlights SINV RNA interactome includes 453 cellular and 6 viral proteins. Nuclear RBPs that interact with SINV RNA are selectively redistributed to the cytoplasm upon infection The tRNA ligase complex plays major regulatory roles in SINV and SARS-CoV- 2 replication The SINV RNA interactome is enriched in pan-viral regulators with therapeutic potential.