Stress granule

Stress granules are dense aggregations in the cytosol composed of proteins & RNAs that appear when the cell is under stress. The RNA molecules stored are stalled translation pre-initiation complexes: failed attempts to make protein from mRNA. Stress granules are 100–200 nm in size (when biochemically purified), not surrounded by membrane, and associated with the endoplasmatic reticulum. Note that there are also nuclear stress granules. This article is about the cytosolic variety. Stress granules are dense aggregations in the cytosol composed of proteins & RNAs that appear when the cell is under stress. The RNA molecules stored are stalled translation pre-initiation complexes: failed attempts to make protein from mRNA. Stress granules are 100–200 nm in size (when biochemically purified), not surrounded by membrane, and associated with the endoplasmatic reticulum. Note that there are also nuclear stress granules. This article is about the cytosolic variety. The function of stress granules remains largely unknown. Stress granules have long been proposed to have a function to protect RNAs from harmful conditions, thus their appearance under stress. The accumulation of RNAs into dense globules could keep them from reacting with harmful chemicals and safeguard the information coded in their RNA sequence. Stress granules might also function as a decision point for untranslated mRNAs. Molecules can go down one of three paths: further storage, degradation, or re-initiation of translation. Conversely, it has also been argued that stress granules are not important sites for mRNA storage nor do they serve as an intermediate location for mRNAs in transit between a state of storage and a state of degradation. Efforts to identify all RNAs within stress granules (the stress granule transcriptome) in an unbiased way by sequencing RNA from biochemically purified stress granule 'cores' have shown that RNAs are not recruited to stress granules in a sequence-specific manner, but rather generically, with longer and/or less-optimally translated transcripts being enriched. These data imply that the stress granule transcriptome is influenced the valency of RNA (for proteins or other RNAs) and by the rates of RNA run-off from polysomes. The latter is further supported by recent single molecule imaging studies. Furthermore, it was estimated that only about 15% of the total mRNA in the cell is localized to stress granules, suggesting that stress granules only influence a minority of mRNAs in the cell and may not be as important for mRNA processing as previously thought. That said, these studies represent only a snapshot in time, and it is likely that a larger fraction of mRNAs are at one point stored in stress granules due to those RNAs transiting in and out. The stress proteins that are the main component of stress granules in plant cells are molecular chaperones that sequester, protect, and possibly repair proteins that unfold during heat and other types of stress. Therefore, any association of mRNAs with stress granules may simply be a side effect of the association of partially unfolded RNA-binding proteins with stress granules, similar to the association of mRNAs with proteasomes. Environmental stressors trigger cellular signaling which eventually leads to the formation of stress granules. In vitro, these stressors can include heat, cold, oxidative stress (sodium arsenite), endoplasmic reticulum stress (thapsigargin), proteasome inhibition (MG132), hyperosmotic stress, ultraviolet radiation, inhibition of eIF4A (pateamine A, hippuristanol, or RocA), nitric oxide accumulation after treatment with 3-morpholinosydnonimine (SIN-1), perturbation of pre-mRNA splicing, and other stressors like puromycin that result in disassembled polysomes. Many of these stressors result in the activation of particular stress-associated kinases (HRI, PERK, PKR, and GCN2), translational inhibition and stress granule formation. Stress granule formation is often downstream of the stress-activated phosphorylation of eukaryotic translation initiation factor eIF2α, but this isn't true for all types of stressors that induce stress granules, for instance, eIF4A inhibition. Further downstream, prion-like aggregation of the protein TIA-1 promotes the formation of stress granules. The term prion-like is used because aggregation of TIA-1 is concentration dependent, inhibited by chaperones, and because the aggregates are resistant to proteases. It has also been proposed that microtubules play a role in the formation of stress granules, maybe by transporting granule components. This hypothesis is based on the fact that disruption of microtubules with the chemical nocodazole blocks the appearance of the granules. Furthermore, many signaling molecules were shown to regulate the formation or dynamics of stress granules; these include the master energy sensor AMP-activated protein kinase (AMPK), the O-GlcNAc transferase enzyme (OGT), and the pro-apoptotic kinase ROCK1. RNA aggregation from intermolecular RNA-RNA interactions may play a role in stress granule formation. Similar to intrinsically disordered protein aggregation, total RNA extracts are capable of self-assembling in physiological conditions in vitro. RNA-seq analyses demonstrate that these assemblies share a largely overlapping transcriptome with stress granules, with RNA enrichment in both being predominately based on the length of the RNA. Furthermore, stress granules contain many RNA helicases, including the DEAD/H-box helicases Ded1p/DDX3, eIF4A1, and RHAU. In yeast, catalytic ded1 mutant alleles give rise to constitutive stress granules ATPase-deficient DDX3X (the mammalian homolog of Ded1) mutant alleles are found in pediatric medulloblastoma, and these coincide with constitutive granular assemblies in patient cells. These mutant DDX3 proteins promote stress granule assembly in HeLa cells. In mammalian cells, RHAU mutants lead to reduced stress granule dynamics. Thus, some hypothesize that RNA aggregation facilitated by intermolecular RNA-RNA interactions plays a role in stress granule formation and that this role may be regulated by RNA helicases. There is also evidence that RNA within stress granules is more compacted compared to RNA in the cytoplasm and that the RNA is preferentially post-translationally modified by N6-methyladenosine (m6A) on its 5' ends. Stress granules and processing bodies share RNA and protein components, both appear under stress, and can physically associate with one another. As of 2018, of the ~660 proteins identified as localizing to stress granules, ~11% also have been identified as processing body-localized proteins (see below). The protein G3BP1 is necessary for the proper docking of processing bodies and stress granules to each other, which may be important for the preservation of polyadenylated mRNAs.