Atomic resolution map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates.

Biomolecules can be sequestered into membrane-less compartments, referred to as biomolecular condensates. Experimental and computational methods have helped define the physical-chemical properties of condensates. Less is known about how the high macromolecule concentrations in condensed phases contribute "solvent" interactions that can remodel the free-energy landscape of other condensate-resident proteins, altering thermally accessible conformations and, in turn, modulating function. Here, we use solution NMR spectroscopy to obtain atomic resolution insights into the interactions between the immature form of superoxide dismutase 1 (SOD1), which can mislocalize and aggregate in stress granules, and the RNA-binding protein CAPRIN1, a component of stress granules. NMR studies of CAPRIN1:SOD1 interactions, focused on both unfolded and folded SOD1 states in mixed phase and demixed CAPRIN1-based condensates, establish that CAPRIN1 shifts the SOD1 folding equilibrium toward the unfolded state through preferential interactions with the unfolded ensemble, with little change to the structure of the folded conformation. Key contacts between CAPRIN1 and the H80-H120 region of unfolded SOD1 are identified, as well as SOD1 interaction sites near both the arginine-rich and aromatic-rich regions of CAPRIN1. Unfolding of immature SOD1 in the CAPRIN1 condensed phase is shown to be coupled to aggregation, while a more stable zinc-bound, dimeric form of SOD1 is less susceptible to unfolding when solvated by CAPRIN1. Our work underscores the impact of the condensate solvent environment on the conformational states of resident proteins and supports the hypothesis that ALS mutations that decrease metal binding or dimerization function as drivers of aggregation in condensates.

DDX6 modulates P-body and stress granule assembly, composition, and docking.

Stress granules and P-bodies are ribonucleoprotein (RNP) granules that accumulate during the stress response due to the condensation of untranslating mRNPs. Stress granules form in part by intermolecular RNA-RNA interactions and can be limited by components of the RNA chaperone network, which inhibits RNA-driven aggregation. Herein, we demonstrate that the DEAD-box helicase DDX6, a P-body component, can also limit the formation of stress granules, independent of the formation of P-bodies. In an ATPase, RNA-binding dependent manner, DDX6 limits the partitioning of itself and other RNPs into stress granules. When P-bodies are limited, proteins that normally partition between stress granules and P-bodies show increased accumulation within stress granules. Moreover, we show that loss of DDX6, 4E-T, and DCP1A increases P-body docking with stress granules, which depends on CNOT1 and PAT1B. Taken together, these observations identify a new role for DDX6 in limiting stress granules and demonstrate that P-body components can influence stress granule composition and docking with P-bodies.

Condensation Goes Viral: A Polymer Physics Perspective.

The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state.

The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome-containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified a potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion.

GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents.

Phase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates' constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins' localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.

What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?

Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.

Using quantitative reconstitution to investigate multicomponent condensates.

Many biomolecular condensates are thought to form via liquid-liquid phase separation (LLPS) of multivalent macromolecules. For those that form through this mechanism, our understanding has benefitted significantly from biochemical reconstitutions of key components and activities. Reconstitutions of RNA-based condensates to date have mostly been based on relatively simple collections of molecules. However, proteomics and sequencing data indicate that natural RNA-based condensates are enriched in hundreds to thousands of different components, and genetic data suggest multiple interactions can contribute to condensate formation to varying degrees. In this Perspective, we describe recent progress in understanding RNA-based condensates through different levels of biochemical reconstitutions as a means to bridge the gap between simple in vitro reconstitution and cellular analyses. Complex reconstitutions provide insight into the formation, regulation, and functions of multicomponent condensates. We focus on two RNA-protein condensate case studies: stress granules and RNA processing bodies (P bodies), and examine the evidence for cooperative interactions among multiple components promoting LLPS. An important concept emerging from these studies is that composition and stoichiometry regulate biochemical activities within condensates. Based on the lessons learned from stress granules and P bodies, we discuss forward-looking approaches to understand the thermodynamic relationships between condensate components, with the goal of developing predictive models of composition and material properties, and their effects on biochemical activities. We anticipate that quantitative reconstitutions will facilitate understanding of the complex thermodynamics and functions of diverse RNA-protein condensates.

Are stress granules the RNA analogs of misfolded protein aggregates?

Ribonucleoprotein granules are ubiquitous features of eukaryotic cells. Several observations argue that the formation of at least some RNP granules can be considered analogous to the formation of unfolded protein aggregates. First, unfolded protein aggregates form from the exposure of promiscuous protein interaction surfaces, while some mRNP granules form, at least in part, by promiscuous intermolecular RNA-RNA interactions due to exposed RNA surfaces when mRNAs are not engaged with ribosomes. Second, analogous to the role of protein chaperones in preventing misfolded protein aggregation, cells contain abundant "RNA chaperones" to limit inappropriate RNA-RNA interactions and prevent mRNP granule formation. Third, analogous to the role of protein aggregates in diseases, situations where RNA aggregation exceeds the capacity of RNA chaperones to disaggregate RNAs may contribute to human disease. Understanding that RNP granules can be considered as promiscuous, reversible RNA aggregation events allow insight into their composition and how cells have evolved functions for RNP granules.

SARS-CoV-2 nucleocapsid protein interacts with immunoregulators and stress granules and phase separates to form liquid droplets.

The current work investigated SARS-CoV-2 Nucleocapsid (NCAP or N protein) interactors in A549 human lung cancer cells using a SILAC-based mass spectrometry approach. NCAP interactors included proteins of the stress granule (SG) machinery and immunoregulators. NCAP showed specific interaction with the SG proteins G3BP1, G3BP2, YTHDF3, USP10 and PKR, and translocated to SGs following oxidative stress and heat shock. Treatment of recombinant NCAP with RNA isolated from A549 cells exposed to oxidative stress-stimulated NCAP to undergo liquid-liquid phase separation (LLPS). RNA degradation using RNase A treatment completely blocked the LLPS property of NCAP as well as its SG association. The RNA intercalator mitoxantrone also disrupted NCAP assembly in vitro and in cells. This study provides insight into the biological processes and biophysical properties of the SARS-CoV-2 NCAP.

Thioredoxin 1 is required for stress granule assembly upon arsenite-induced oxidative stress.

Arsenic is a major water pollutant and health hazard, leading to acute intoxication and, upon chronic exposure, several diseases including cancer development. Arsenic exerts its pronounced cellular toxicity through its trivalent oxide arsenite (ASN), which directly inhibits numerous proteins including Thioredoxin 1 (Trx1), and causes severe oxidative stress. Cells respond to arsenic by inhibition of protein synthesis and subsequent assembly of stress granules (SGs), cytoplasmic condensates of stalled mRNAs, translation factors and RNA-binding proteins. The biological role of SGs is diverse and not completely understood; they are important for regulation of cell signaling and survival under stress conditions, and for adapting de novo protein synthesis to the protein folding capacity during the recovery from stress. In this study, we identified Trx1 as a novel component of SGs. Trx1 is required for the assembly of ASN-induced SGs, but not for SGs induced by energy deprivation or heat shock. Importantly, our results show that Trx1 is essential for cell survival upon acute exposure to ASN, through a mechanism that is independent of translation inhibition.

Assembly of Cytoplasmic Stress Granules in Placentas in Women with Preeclampsia.

Inflammation is a well-recognized factor associated with preeclampsia (PE). Stress granules (SGs) have been shown to play an important role in regulating inflammation and immune responses. However, whether SGs are involved in the pathogenesis of PE has not been studied. Here, we evaluated the expression of SG components in placenta of pregnancies with PE. Placental samples or serum were collected from PE patients (n = 31) or healthy age-matched pregnancy (n = 17). mRNA expressions of SG-associated genes in placenta from PE or normal pregnancies were detected by real-time quantitative PCR, and protein expressions of HuR and G3BP were detected using western blot. Immunofluorescence staining was performed to evaluate SG components expression in placentas or 10% serum treated HTR-8/Svneo cells using antibodies against HuR and G3BP. Our study showed higher levels of elavl1, lsm2, lsm4, and ago1 mRNA expression and SG marker proteins expression in placental homogenates of PE patients. HuR/G3BP-positive SG structure was further observed in placental villi of PE by immunofluorescence assay. Besides, serum from PE patients could induce SG aggregation in human trophoblast cell line HTR-8/Svneo cells, suggesting the involvement of SGs in the development of PE.