Stress granules are condensates of non-translating mRNAs and proteins involved in the stress response and neurodegenerative diseases. Stress granules form in part through intermolecular RNA-RNA interactions, and to better understand how RNA-based condensation occurs, we demonstrate that RNA is effectively recruited to the surfaces of RNA or RNP condensates in vitro. We demonstrate that, through ATP-dependent RNA binding, the DEADbox protein eIF4A reduces RNA condensation in vitro and limits stress granule formation in cells. This defines a function for eIF4A to limit intermolecular RNA-RNA interactions in cells. These results establish an important role for eIF4A, and potentially other DEAD-box proteins, as ATP-dependent RNA chaperones that limit the condensation of RNA, analogous to the function of proteins like HSP70 in combatting protein aggregates.

Introduction

Eukaryotic cells contain ribonucleoprotein (RNP) granules in the nucleus and cytosol, including P-bodies (PBs) and stress granules (SGs) (Anderson and Kedersha, 2006; Banani et al., 2017). SGs are cytosolic condensates composed of non-translating RNPs that are involved in the stress response, neurodegeneration, and viral infection (Protter and Parker, 2016; Ivanov et al., 2019). SGs typically form in response to translation shutoff induced by noxious stimuli such as arsenite, heat shock, and endogenous inflammatory molecules like prostaglandins, which all lead to phosphorylation of eIF2a and the activation of the integrated stress response (Aulas et al., 2017; Tauber and Parker, 2019). SGs can also form independently of eIF2a phosphorylation in response to inhibition of the eIF4F complex or osmotic stress (Aulas et al., 2017). SGs and other RNP condensates are thought to form in part through multimeric RNA binding proteins crosslinking RNPs into larger networks (Banani et al., 2017; Shin and Brangwynne, 2017). Recent evidence suggests that intermolecular RNA-RNA interactions are involved in SG formation. SGs require a substantial pool of non-translating RNA to form (Protter and Parker, 2016). Thus, elevating the non-translating RNA concentration by injecting exogenous RNA induces SGs (Mahadevan et al., 2013). Furthermore, certain RNAs can seed foci in human cell lysates that recruit many SG proteins (Fay et al., 2017). Strikingly, modest concentrations of yeast total RNA readily condense in physiological salt and polyamine conditions, recapitulating the SG transcriptome in a protein-free context (Khong et al., 2017; Van Treeck et al., 2018), arguing that trans RNA-RNA interactions contribute to SG formation. Messenger RNPs (mRNPs) are recruited to SGs in a biphasic manner, first engaging in transient docking interactions with the SG surface, which then transition into stable locking interactions that leave the RNA immobile within the granule (Moon et al., 2019), implying that surface recruitment of RNAs to SGs is a precursor to a more stable RNP assembly.