Dataset Information

Protein and metabolite composition of Arabidopsis stress granules

ABSTRACT: • Stress granules (SGs) are evolutionary conserved aggregates of proteins and untranslated mRNAs formed in response to stress. Despite their importance for stress adaptation, no complete proteome composition has been reported for plant SGs. Herein, we addressed the existing gap. Importantly, we also provide evidence for metabolite sequestration within the SGs. • To isolate SGs we used Arabidopsis seedlings expressing GFP fusion of the SGs marker protein, Rbp47b, and an experimental protocol combining differential centrifugation with affinity purification. SGs isolates were analyzed using mass spectrometry-based proteomics and metabolomics. • A quarter of the identified proteins constituted known or predicted SG components. Intriguingly, the remaining proteins were enriched in key enzymes and regulators, such as cyclin dependent kinase A (CDKA), that mediate plant responses to stress. In addition to proteins, also nucleotides, amino acids and phospholipids accumulated in SGs. • Taken together, our results indicate (i) the presence of a pre-existing SG protein interaction network, (ii) an evolutionary conservation of the proteins involved in SG assembly and dynamics, (iii) an important role for SGs in moderation of stress responses by selective storage of proteins and metabolites.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Michal Gorka

LAB HEAD: Aleksandra Skirycz

PROVIDER: PXD011716 | Pride | 2019-01-07

REPOSITORIES: Pride

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Publications

Protein and metabolite composition of Arabidopsis stress granules.

Kosmacz Monika M Gorka Michał M Schmidt Stephan S Luzarowski Marcin M Moreno Juan C JC Szlachetko Jagoda J Leniak Ewa E Sokolowska Ewelina M EM Sofroni Kostika K Schnittger Arp A Skirycz Aleksandra A

The New phytologist 20190217 3

Stress granules (SGs) are evolutionary conserved aggregates of proteins and untranslated mRNAs formed in response to stress. Despite their importance for stress adaptation, no complete proteome composition has been reported for plant SGs. In this study, we addressed the existing gap. Importantly, we also provide evidence for metabolite sequestration within the SGs. To isolate SGs we used Arabidopsis seedlings expressing green fluorescent protein (GFP) fusion of the SGs marker protein, Rbp47b, an ...[more]

PMID: 30664249

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Project description:The cellular stress response plays a vital role in regulating homeostasis by modulating cell survival and death. Stress granules (referred to as SGs) are cytoplasmic compartments that allow cells to survive various stressors. Defects in SG assembly and disassembly have been found to play important roles in neurodegenerative diseases, antiviral responses and cancer1–5. Inflammasomes are multi-protein heteromeric complexes that sense intracellular pathogen- and damage-associated molecular patterns and assemble into cytosolic compartments called ASC specks to facilitate caspase-1 (CASP1) activation. This activation of inflammasomes induces secretion of the leaderless proinflammatory cytokines IL-1β and IL-18 and also drives cell fate towards pyroptosis, a form of programmed inflammatory cell death that plays major role in health and disease6–12. Cellular stress sensing can trigger both SGs and inflammasomes; however, they drive contrasting cell fate decisions during stress conditions. Crosstalk between SGs and inflammasomes to decide cell fate has not been well studied. Here we show that the induction of SGs specifically inhibits NLRP3 inflammasome activation, ASC speck formation and pyroptosis. The SG protein DDX3X interacts with NLRP3 to drive inflammasome activation in the absence of SGs. Assembly of SGs leads to the sequestration of DDX3X to inhibit NLRP3 inflammasome function. SGs and the NLRP3 inflammasome compete for DDX3X molecules to coordinate the activation of innate responses and subsequent cell fate decisions under stress conditions. Induction of SGs or loss of DDX3X in the myeloid compartment leads to decreased production of inflammasome-dependent cytokines in vivo. Our findings suggest that macrophages utilize DDX3X availability to interpret stress signals and choose between pro-survival SGs and pyroptotic ASC specks. Together, our data show the role of DDX3X in driving NLRP3 inflammasome and SG assembly, informing a new rheostat-like mechanistic paradigm for regulating live or die cell fate decisions under stress conditions.

Dataset Information

Protein and metabolite composition of Arabidopsis stress granules

Publications

Protein and metabolite composition of Arabidopsis stress granules.

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