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SARS-CoV-2 nsp14 induces the m7G methylation and the sequestration of host RNAs in stress granules Twin-Strep Streptactin pull-down LC-MSMS

ABSTRACT: Viruses grab the host translation machinery to facilitate their replication by disturbing the host translation. SARS-CoV-2 nsp14 was known to inhibit host translation, yet the mechanistic details are still obscure. In this study, we report that nsp14 can elevate stress granules (SG) formation in a N7 methyltransferase activity-dependent manner. ER/Golgi localized nsp14 promotes m7G methylation of host RNAs, which are delivered into stress granules (SG), leading to elevated SG formation. Except for a few methylation-associated proteins, most components of SGs induced by nsp14 can be identified in SGs induced by other stress inducers, like sodium arsenite. nsp14-induced SG formation relies on methyl donors, because altering the amount of methyl donors, like decreasing SAM level with overexpression of Glycine N-methyltransferase (GNMT) or increasing SAM level with the supplement of folic acid, can alter SG formation and affect viral replication. Collectively, we characterized nsp14 as an SG formation regulator involved in viral hijacking of the host translation machinery.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Weiyi Huang

LAB HEAD: Xiaoxue Peng

PROVIDER: PXD060757 | Pride | 2026-02-06

REPOSITORIES: Pride

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			Action	DRS
	20241024_OE480_FAIMS_LY_huangweiyi_GDY_IP_1.raw	Raw
	20241024_OE480_FAIMS_LY_huangweiyi_GDY_IP_2.raw	Raw
	20241024_OE480_FAIMS_LY_huangweiyi_GDY_IP_2vs1.msf	Msf
	20241024_OE480_FAIMS_LY_huangweiyi_GDY_IP_3.raw	Raw
	20241024_OE480_FAIMS_LY_huangweiyi_GDY_IP_3vs1.msf	Msf

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SARS-CoV-2 nsp14 induces the m7G methylation and the sequestration of host RNAs in stress granules TurboID Biotin-Streptavidin pull-down LC-MSMS

Project description:Viruses grab the host translation machinery to facilitate their replication by disturbing the host translation. SARS-CoV-2 nsp14 was known to inhibit host translation, yet the mechanistic details are still obscure. In this study, we report that nsp14 can elevate stress granules (SG) formation in a N7 methyltransferase activity-dependent manner. ER/Golgi localized nsp14 promotes m7G methylation of host RNAs, which are delivered into stress granules (SG), leading to elevated SG formation. Except for a few methylation-associated proteins, most components of SGs induced by nsp14 can be identified in SGs induced by other stress inducers, like sodium arsenite. nsp14-induced SG formation relies on methyl donors, because altering the amount of methyl donors, like decreasing SAM level with overexpression of Glycine N-methyltransferase (GNMT) or increasing SAM level with the supplement of folic acid, can alter SG formation and affect viral replication. Collectively, we characterized nsp14 as an SG formation regulator involved in viral hijacking of the host translation machinery.

2026-02-06 | PXD060759 | Pride

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

2015-02-27 | E-GEOD-65778 | biostudies-arrayexpress

Stress granule-mediated sequestration of EGR1 mRNAs correlates with lomustine-induced cell death prevention

Project description:Some chemotherapy drugs influence the formation of stress granules (SGs), cytoplasmic RNA foci involved in stress response pathways. The exact role of SGs in promoting cell survival or apoptosis needs further clarification. The chemotherapy drug lomustine induces SG formation by activating the eIF2α kinase HRI (EIF2AK1). We performed a DNA microarray transcriptome analysis to identify genes affected by lomustine-induced stress and to explore the role of SGs. Our findings show that lomustine specifically regulates the expression of the pro-apoptotic EGR1 gene. The presence of EGR1 mRNA in SGs correlates with reduced translation of EGR1 mRNA. Lomustine likely sequesters EGR1 mRNA into SGs, preventing its ribosomal translation and thereby limiting apoptosis. This supports a model where SGs selectively sequester specific mRNAs in response to stress, modulate their translation, and thus determine the fate of stressed cells.

2024-06-20 | GSE269691 | GEO

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

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Spatially resolved multi-bait mapping of stress granule and processing body transcriptome

Project description:Stress granules (SGs) are dynamic, membrane-less organelles containing complex RNA-protein networks. The RNA components of SGs have been profiled through various approaches, characterized as long, translation-repressed, and highly epigenetically modified. However, it remains unclear whether these RNAs are uniformly distributed within SGs. In this study, we used multiple SG core proteins to genetically target the photocatalyst protein miniSOG, which allows for comprehensive CAP-seq profiling of RNA components within SGs. We discovered that RNAs associated with different SG core proteins exhibit heterogeneous distribution and distinct intrinsic features. Furthermore, we applied CAP-seq to map the RNA components in processing bodies (PBs) under both unstressed conditions and arsenite stimulation. By comparing the SG and PB transcriptomes, our data revealed that m6A modification may promote the localization of RNAs to SGs, while higher AU content may facilitate the targeting of mRNAs to PBs. This suggests potential regulatory roles in determining the subcellular localization of mRNAs within membrane-less organelles.

2024-09-29 | GSE271045 | GEO

Stress granule assembly impairs macrophage efferocytosis [SG RNA-seq]

Project description:Stress granules (SGs) assembly in response to various stress, has been demonstrated in the regulation of anti-viral immune response and tumor progression. However, lack of evidence to illustrate the relation between SGs formation and allergic diseases. Applying RNA-seq in total RNA and SGs of primary macrophages, SG-specific expressed genes were defined.

2024-05-01 | GSE263848 | GEO

The 19S RP-associated deubiquitylation downstream of AP-3β disassembles heat-induced stress granules in plants

Project description:To survive under adverse conditions, plants form stress granules (SGs) to temporally store mRNA and halt translation as a primary response. Dysregulation in SG disassembly can have detrimental effects on plant survival after stress release, yet the underlying mechanism remains poorly understood in plants. Using Arabidopsis as a model system, we demonstrated that the AP-3 subunit AP-3β participates in heat response independently of its conventional role in vacuolar transport. We also discovered that AP-3β serves as an adaptor to recruit the 19S regulatory particle (RP) of the proteasome to SGs upon heat induction. Notably, the 19S RP promotes SG disassembly through RP-associated deubiquitylation, independent of its proteolytic activity. This deubiquitylation process of SG components is crucial for translation reinitiation and growth recovery after heat release. Our findings shed light on the non-proteolytic function of the 19S RP in regulating SGs dynamics and provide insights into a non-degradation mechanism for cellular adaptation to environmental stresses

2025-01-24 | PXD054299 | Pride

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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Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

Project description:Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. At different stages of assembly, various RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Despite recent efforts of fluorescence microscopy and biochemical fractionation analysis, there still lacks a complete description of the dynamic changes in the molecular inventory of SG components during different stages of assembly and disassembly. In this study, we applied a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of local transcriptome in SGs, in the context of live mammalian cells. CAP-seq captures 457 and 822 RNAs in arsenite- and sorbitol-induced SGs in HEK293T cells, respectively, revealing that SG enrichment is positively correlated with RNA length and AU content, but negatively correlated with translation efficiency. The high spatial specificity of CAP-seq dataset is validated by single-molecule FISH imaging. We further applied CAP-seq profile RNA components in microscopically invisible SG cores, both before stress and after recovery from stress, thus mapping the dynamic changes in SG-proximal transcriptome along the time course of granule assembly/disassembly processes. Our data portray a model of AU-rich and translationally repressed SG nanostructure that are memorized long after the removal of stress.

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