Yellow fever virus infection triggers the assembly of compositionally unique and specialised stress granules

The phase separation of biomolecules into stress granules (SGs) allows the cell to tightly regulate translation activity in response to different stimuli, such as oxidative stress, starvation, or the recognition of non-cellular RNA. Recent reports suggest SGs induced during viral infection may act as a crossroad between the cellular stress response and the activation of the innate immune response. Here, we aimed to dissect the role of SGs in the context of yellow fever virus (YFV) infection. We found that YFV infection with both 17D vaccine and Asibi pathogenic strains resulted in translational shut-off and the formation of SGs at 48 hours post infection (hpi), although viral infection was already apparent at 24 hpi. This delay may be coupled to the ability of the YFV capsid to inhibit SG formation through an interaction with the SG scaffolding protein G3BP1. To elucidate the role of YFV-induced SGs during infection, we inhibited SG assembly using a small-molecule inhibitor as well as siRNA-mediated knockdown of SGs and found that while SG formation does not impact viral replication, silencing of SG scaffolding proteins is associated with increased expression of interferon-stimulated genes (ISG). Uncovering the proteome of YFV-induced SGs, our compositional analysis revealed a unique composition, distinct from NaAs-induced SGs, which displayed enrichment in mitochondrial proteins. Further functional analysis revealed that YFV infection is associated with mitochondrial damage and dysfunction, which coincides with formation of virus-induced SGs. Together, we propose that YFV-induced SGs may be involved not only in the modulation of cellular homeostasis but also in influencing mitochondrial functions.Author summary: Viruses impose a major burden on the infected host, from structural rearrangements needed to assemble replication complexes, to exploiting cellular energy resources and genetic rewiring associated with antiviral responses. The assembly of membrane-less organelles such as stress granules (SGs) enable cells to rapidly tune cellular processes upon sensing of stresses such as viruses. Moreover, the cell’s innate immune response is proposed to be regulated by SGs and in turn many viruses disrupt or hijack their components. Yet, the molecular basis for SG functions during infection remains ambiguous. Here, we investigated the interplay between yellow fever virus (YFV) infection and SGs. We demonstrate that infection with attenuated or pathogenic strains result in the formation of SGs. Compositional analysis reveal that SGs sequester mitochondrial proteins, correlating with altered mitochondrial functions during infection. This highlights a novel complex interplay between membrane-bound and membrane-less organelles, which could present novel opportunities for antiviral therapies.