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G3BP2B stress granules regulate mRNA expression under ER stress [Riboseq_Exp2]

ABSTRACT: Stress granules (SGs) are macromolecular assemblies that form under cellular stress. Formation of these condensates is driven by the nucleation of proteins such as G3BPs. G3BPs are RNA-binding proteins that condense into SGs following translation shutoff during the integrated stress response (ISR). Three G3BP paralogs (G3BP1, G3BP2A, and G3BP2B) have been identified in vertebrates. However, the contribution of the different G3BP paralogs to stress granule formation and stress-induced gene expression changes are incompletely understood. Here, we identify a molecular tool to study G3BP condensation into SGs by mutating residue V11 of G3BPs. This conserved amino acid potentiates the G3BP-Caprin-1 complex, hence promoting SG assembly. Ribosome profiling revealed that disruption of G3BP condensation impacts mRNA levels and ribosome engagement during the ISR. Moreover, we found that G3BP2B preferentially condenses and promotes changes in mRNA expression under endoplasmic reticulum (ER) stress. Together, this work suggests that stress granule assembly promotes changes in gene expression under cellular stress, which is differentially regulated by G3BP paralogs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE254632 | GEO | 2024/10/07

REPOSITORIES: GEO

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G3BP2B stress granules regulate mRNA expression under ER stress [Riboseq_Exp3]

Project description:Stress granules (SGs) are macromolecular assemblies that form under cellular stress. Formation of these condensates is driven by the nucleation of proteins such as G3BPs. G3BPs are RNA-binding proteins that condense into SGs following translation shutoff during the integrated stress response (ISR). Three G3BP paralogs (G3BP1, G3BP2A, and G3BP2B) have been identified in vertebrates. However, the contribution of the different G3BP paralogs to stress granule formation and stress-induced gene expression changes are incompletely understood. Here, we identify a molecular tool to study G3BP condensation into SGs by mutating residue V11 of G3BPs. This conserved amino acid potentiates the G3BP-Caprin-1 complex, hence promoting SG assembly. Ribosome profiling revealed that disruption of G3BP condensation impacts mRNA levels and ribosome engagement during the ISR. Moreover, we found that G3BP2B preferentially condenses and promotes changes in mRNA expression under endoplasmic reticulum (ER) stress. Together, this work suggests that stress granule assembly promotes changes in gene expression under cellular stress, which is differentially regulated by G3BP paralogs.

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G3BP2B stress granules regulate mRNA expression under ER stress [RNAseq_Exp1]

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G3BP2B stress granules regulate mRNA expression under ER stress [Riboseq_Exp1]

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G3BP2B stress granules regulate mRNA expression under ER stress [RNAseq_Exp3]

Project description:Stress granules (SGs) are macromolecular assemblies that form under cellular stress. Their function is not completely understood. Formation of these organelles is driven by the nucleation of proteins such as G3BPs. G3BPs are RNA-binding proteins that condense into SGs following translation shutoff during the integrated stress response (ISR). Three G3BP paralogs (G3BP1, G3BP2A, and G3BP2B) have been identified in vertebrates. Here, we found a molecular tool to study G3BP condensation into SGs by mutating residue V11 of G3BPs. This conserved amino acid potentiates the G3BP-Caprin-1 complex, hence promoting SG assembly. Ribosome profiling revealed that disruption of G3BP condensation impacts mRNA expression during the ISR. Moreover, we found that G3BP2B robustly condenses and promotes changes in mRNA expression under endoplasmic reticulum (ER) stress. This indicates that G3BP paralogs differentially regulate SG assembly and gene expression programs. Together, this work suggests that stress granule assembly promotes changes in gene expression to mediate stress-response during the ISR.

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G3BP2B stress granules regulate mRNA expression under ER stress [RNAseq_Exp2]

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Proximity-dependent biotinylation detects association between stress granule associated proteins and SARS coronavirus nonstructural protein 1

Project description:Severe acute respiratory syndrome coronavirus (SARS-CoV and SARS-CoV-2) nonstructural protein 1 (nsp1) is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host messenger RNAs (mRNA). Using proximity-dependent biotinylation assay followed by proteomic analyses of biotinylated proteins, we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we have identified several mRNA processing proteins, including splicing factors and transcription termination proteins, exosomes- and stress granule (SG) associated proteins. The interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of K164 and H165 amino acids. We further show that nsp1 associates with SG protein G3BP and colocalizes with G3BP in SGs under sodium arsenite-induced stress for a short period of time. However, the presence of nsp1 disrupts the maturation of SGs over a long period.

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Identification of mRNAs enriched in G3BP immunoprecipitation

Project description:A phosphorylation-dependent endoribonuclease G3BP localizes in cytoplasmic stress granules (SGs). G3BP promotes SG assembly, oligomerizes, binds mRNA, and regulates levels of certain mRNAs. Transcripts bound to G3BP were identified through expression profiling of a total of 12,135 genes by immunoprecipitation (IP) with anti-G3BP or control IgG from S2-013 cells, converting the immunoprecipitated transcripts to cDNA by reverse transcription, and hybridizing these products to cDNA microarrays. Five G3BP-associated transcripts were identified.

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The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly

Project description:We recently identified ISRIB as a potent inhibitor of the integrated stress response (ISR). ISRIB renders cells resistant to the effects of eIF2α phosphorylation and enhances long-term memory in rodents (10.7554/eLife.00498). Here we show by genome-wide in vivo ribosome profiling that translation of a restricted subset of mRNAs is induced upon ISR activation. ISRIB substantially reversed the translational effects elicited by phosphorylation of eIF2α and induced no major changes in translation or mRNA levels in unstressed cells. eIF2α phosphorylation-induced stress granule (SG) formation was blocked by ISRIB. Strikingly, ISRIB addition to stressed cells with pre-formed SGs induced their rapid disassembly, liberating mRNAs into the actively translating pool. Restoration of mRNA translation and modulation of SG dynamics may be an effective treatment of neurodegenerative diseases characterized by eIF2α phosphorylation, SG formation and cognitive loss. Ribosome profiling with paired RNA-seq

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Intracellular Energy Controls Dynamics of Stress-induced Ribonucleoprotein Granules Implicated in ALS/FTD

Project description:Energy metabolism and membraneless organelles have been implicated in human diseases including neurodegeneration. How energy deficiency regulates ribonucleoprotein particles such as stress granules (SGs) is still unclear. Here we identified a unique type of granules formed under energy deficiency and uncovered the mechanisms by which the dynamics of diverse stressinduced granules are regulated. Severe energy deficiency induced the rapid formation of energy deficiency-induced stress granule (eSGs), whereas moderate energy deficiency delayed the clearance of conventional SGs. The formation of eSGs or the clearance of SGs was regulated by the mTOR-4EBP1-eIF4E pathway or eIF4A1, involving eIF4F complex assembly or RNA condensation, respectively. In ALS patients’ neurons or cortical organoids, the eSG formation was enhanced, and conventional SG clearance was impaired. These results reveal a critical role for intracellular energy in the regulation of diverse granules and suggest that disruptions in energycontrolled granule dynamics may contribute to the pathogenesis of relevant diseases.

2022-10-15 | PXD035747 | Pride

RNA partitioning into stress granules is independent of G3BP

Project description:Stress granules (SGs) are stress induced RNA-protein assemblies formed from untranslating mRNPs. Mammalian SGs are non-uniform and contain “cores”, which are stable in lysates and heterogenous in protein composition. The interactions defining RNA recruitment into SGs, and whether the RNA composition varies between different cores remains unclear. Herein, we determine the SG transcriptome through purification of both PABPC1 and G3BP SG cores during both arsenite and sorbitol stress. We observe that similar RNAs are recruited to SGs independent of the protein used for core purification, suggesting individual RNA-binding proteins (RBPs) may play a limited role in defining the SG transcriptome. Analysis of the sorbitol-induced SG transcriptome reveals G3BP1/2 has little effect on RNAs recruited to SGs suggesting RNAs localize to SGs independent of individual RBPs. Taken together, we suggest that partitioning of RNAs to SGs is independent of at least some proteins, consistent with SGs forming through intermolecular RNA-RNA interactions.

2019-01-30 | GSE119977 | GEO

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