scholarly journals Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Sonja Kroschwald ◽  
Shovamayee Maharana ◽  
Daniel Mateju ◽  
Liliana Malinovska ◽  
Elisabeth Nüske ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Extreme Environments ◽  
Stress Granules ◽  
Protein Aggregates ◽  
Living Cells ◽  
Granule Formation ◽  
P Bodies ◽  
State Of Stress ◽  
Material State ◽  
Rnp Granules

RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine.

scholarly journals P bodies promote stress granule assembly in Saccharomyces cerevisiae

2008 ◽  
Vol 183 (3) ◽  
pp. 441-455 ◽  
Author(s):  
J. Ross Buchan ◽  
Denise Muhlrad ◽  
Roy Parker
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mammalian Cells ◽  
Protein Composition ◽  
Stress Granules ◽  
Glucose Deprivation ◽  
Stress Granule ◽  
Granule Formation ◽  
P Bodies ◽  
Rna Granules ◽  
Kinetics Of

Recent results indicate that nontranslating mRNAs in eukaryotic cells exist in distinct biochemical states that accumulate in P bodies and stress granules, although the nature of interactions between these particles is unknown. We demonstrate in Saccharomyces cerevisiae that RNA granules with similar protein composition and assembly mechanisms as mammalian stress granules form during glucose deprivation. Stress granule assembly is dependent on P-body formation, whereas P-body assembly is independent of stress granule formation. This suggests that stress granules primarily form from mRNPs in preexisting P bodies, which is also supported by the kinetics of P-body and stress granule formation both in yeast and mammalian cells. These observations argue that P bodies are important sites for decisions of mRNA fate and that stress granules, at least in yeast, primarily represent pools of mRNAs stalled in the process of reentry into translation from P bodies.

scholarly journals Transcriptome-Wide Comparison of Stress Granules and P-Bodies Reveals that Translation Plays a Major Role in RNA Partitioning

2019 ◽  
Vol 39 (24) ◽  
Author(s):  
Tyler Matheny ◽  
Bhalchandra S. Rao ◽  
Roy Parker
Keyword(s):  
Stress Granules ◽  
Stress Granule ◽  
Dominant Factor ◽  
Differential Centrifugation ◽  
P Bodies ◽  
Translation Repression ◽  
First Approximation ◽  
Rnp Granules ◽  
Interpretation Of Results

ABSTRACT The eukaryotic cytosol contains multiple RNP granules, including P-bodies and stress granules. Three different methods have been used to describe the transcriptome of stress granules or P-bodies, but how these methods compare and how RNA partitioning occurs between P-bodies and stress granules have not been addressed. Here, we compare the analysis of the stress granule transcriptome based on differential centrifugation with and without subsequent stress granule immunopurification. We find that while differential centrifugation alone gives a first approximation of the stress granule transcriptome, this methodology contains nonspecific transcripts that play a confounding role in the interpretation of results. We also immunopurify and compare the RNAs in stress granules and P-bodies under arsenite stress and compare those results to those for the P-body transcriptome described under nonstress conditions. We find that the P-body transcriptome is dominated by poorly translated mRNAs under nonstress conditions, but during arsenite stress, when translation is globally repressed, the P-body transcriptome is very similar to the stress granule transcriptome. This suggests that translation is a dominant factor in targeting mRNAs into both P-bodies and stress granules, and during stress, when most mRNAs are untranslated, the composition of P-bodies reflects this broader translation repression.

scholarly journals Are stress granules the RNA analogs of misfolded protein aggregates?

RNA ◽  
2021 ◽  
pp. rna.079000.121
Author(s):  
Nina Ripin ◽  
Roy Parker
Keyword(s):  
Protein Aggregates ◽  
Eukaryotic Cells ◽  
Misfolded Protein ◽  
Granule Formation ◽  
Unfolded Protein ◽  
Rna Chaperones ◽  
Rnp Granules ◽  
Disease Understanding ◽  
Insight Into

RNP 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 allows insight into their composition and how cells have evolved functions for RNP granules.

scholarly journals Poly(A) binding protein is required for mRNP remodeling to form P-bodies in mammalian cells

2021 ◽  
Author(s):  
Jingwei Xie ◽  
Yu Chen ◽  
Xiaoyu Wei ◽  
Guennadi Kozlov
Keyword(s):  
Mammalian Cells ◽  
Binding Protein ◽  
Stress Granules ◽  
Body Formation ◽  
P Bodies ◽  
Rna Granules ◽  
Cellular Processes ◽  
Early Stages ◽  
Summary Statement

AbstractCompartmentalization of mRNA through formation of RNA granules is involved in many cellular processes, yet it is not well understood. mRNP complexes undergo dramatic changes in protein compositions, reflected by markers of P-bodies and stress granules. Here, we show that PABPC1, albeit absent in P-bodies, plays important role in P-body formation. Depletion of PABPC1 decreases P-body population in unstressed cells. Upon stress in PABPC1 depleted cells, individual P-bodies fail to form and instead P-body proteins assemble on PABPC1-containing stress granules. We hypothesize that mRNP recruit proteins via PABPC1 to assemble P-bodies, before PABPC1 is displaced from mRNP. Further, we demonstrate that GW182 can mediate P-body assembly. These findings help us understand the early stages of mRNP remodeling and P-body formation.Summary statementA novel role of poly(A) binding protein is reported in P-body formation

scholarly journals Author response: Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

2015 ◽  
Author(s):  
Sonja Kroschwald ◽  
Shovamayee Maharana ◽  
Daniel Mateju ◽  
Liliana Malinovska ◽  
Elisabeth Nüske ◽  
...  
Keyword(s):  
Author Response ◽  
State Of Stress ◽  
Material State ◽  
Rnp Granules

scholarly journals RNA Binding Protein TAF15 Suppresses Toxicity in a Yeast Model of FUS Proteinopathy

2021 ◽  
Author(s):  
Elliott Hayden ◽  
Aicha Kebe ◽  
Shuzhen Chen ◽  
Abagail Chumley ◽  
Chenyi Xia ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Stress Granules ◽  
Rna Recognition Motif ◽  
Body Formation ◽  
P Bodies ◽  
Associated Proteins ◽  
Rnp Granules ◽  
Yeast Model

Abstract Mutations in Fused in Sarcoma (FUS), an RNA binding protein that functions in multiple steps in gene expression regulation and RNA processing, are known to cause familial amyotrophic lateral sclerosis (ALS). Since this discovery, mutations in several other RNA binding proteins (RBPs) have also been linked to ALS. Some of these ALS-associated RBPs have been shown to colocalize with ribonucleoprotein (RNP) granules such as stress granules and processing bodies (p-bodies). Characterization of ALS-associated proteins, their mis-localization, aggregation and toxicity in cellular and animal models have provided critical insights in disease. More and more evidence has emerged supporting a hypothesis that impaired clearance, inappropriate assembly, and dysregulation of RNP granules play a role in ALS. Through genome-scale overexpression screening of a yeast model of FUS toxicity, we found that TAF15, a human RBP with a similar protein domain structure and belonging to the same FET protein family as FUS, suppresses FUS toxicity. The suppressor effect of TAF15 is specific to FUS and not found in other yeast models of neurodegenerative disease-associated proteins. We showed that the RNA recognition motif (RRM) of TAF15 is required for its rescue of FUS toxicity. Furthermore, FUS and TAF15 physically interact, and the C-terminus of TAF15 is required for both the physical protein-protein interaction and its protection against FUS toxicity. Finally, while FUS induces and colocalizes with both stress granules and p-bodies, TAF15 only induces and colocalizes with p-bodies. Importantly, co-expression of FUS and TAF15 induces more p-bodies than individually expressing each gene alone, and FUS toxicity is exacerbated in yeast that is deficient in p-body formation. Overall, our findings suggest a role of p-body formation in the suppression of FUS toxicity by TAF15.

scholarly journals Modulation of RNA condensation by the DEAD-box protein eIF4A

2019 ◽  
Author(s):  
Devin Tauber ◽  
Gabriel Tauber ◽  
Anthony Khong ◽  
Briana Van Treeck ◽  
Jerry Pelletier ◽  
...  
Keyword(s):  
Stress Granules ◽  
Protein Aggregates ◽  
Stress Granule ◽  
List Type ◽  
Dependent Manner ◽  
Granule Formation ◽  
Dead Box ◽  
The Dead ◽  
In Cells

SUMMARYStress granules are condensates of non-translating mRNAs and proteins involved in the stress response and neurodegenerative diseases. Stress granules form in part through intermolecular RNA-RNA interactions, although the process of RNA condensation is poorly understood. In vitro, we demonstrate that RNA is effectively recruited to the surfaces of RNA or RNP condensates. We demonstrate that the DEAD-box protein eIF4A reduces RNA condensation in vitro and limits stress granule formation in cells. This defines a purpose for eIF4A to limit intermolecular RNA-RNA interactions in cells, thereby allowing for proper RNP function. These results establish an important role for DEAD-box proteins as ATP-dependent RNA chaperones that can limit the intermolecular condensation and entanglement of RNA, analogous to the function of proteins like HSP70 in combatting protein aggregates.eTOC BlurbStress granules are formed in part by the process of RNA condensation, which is mediated by and promotes trans RNA-RNA interactions. The essential DEAD-box protein and translation initiation factor eIF4A limits stress granule formation by reducing RNA condensation through its function as an ATP-dependent RNA binding protein, behaving analogously to how protein chaperones like HSP70 combat protein aggregates.HighlightsRNA condensates promote intermolecular RNA-RNA interactions at their surfaceseIF4A limits the recruitment of RNAs to stress granules in cellseIF4A reduces the nucleation of stress granules in cellsRecombinant eIF4A1 inhibits the condensation of RNA in vitro in an ATP-dependent manner

scholarly journals Dcp2 phosphorylation by Ste20 modulates stress granule assembly and mRNA decay in Saccharomyces cerevisiae

2010 ◽  
Vol 189 (5) ◽  
pp. 813-827 ◽  
Author(s):  
Je-Hyun Yoon ◽  
Eui-Ju Choi ◽  
Roy Parker
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Messenger Rna ◽  
Mrna Decay ◽  
Control Point ◽  
Stress Granules ◽  
Mrna Degradation ◽  
Stress Granule ◽  
Granule Formation ◽  
P Bodies

Translation and messenger RNA (mRNA) degradation are important sites of gene regulation, particularly during stress where translation and mRNA degradation are reprogrammed to stabilize bulk mRNAs and to preferentially translate mRNAs required for the stress response. During stress, untranslating mRNAs accumulate both in processing bodies (P-bodies), which contain some translation repressors and the mRNA degradation machinery, and in stress granules, which contain mRNAs stalled in translation initiation. How signal transduction pathways impinge on proteins modulating P-body and stress granule formation and function is unknown. We show that during stress in Saccharomyces cerevisiae, Dcp2 is phosphorylated on serine 137 by the Ste20 kinase. Phosphorylation of Dcp2 affects the decay of some mRNAs and is required for Dcp2 accumulation in P-bodies and specific protein interactions of Dcp2 and for efficient formation of stress granules. These results demonstrate that Ste20 has an unexpected role in the modulation of mRNA decay and translation and that phosphorylation of Dcp2 is an important control point for mRNA decapping.

scholarly journals Stimulation of Gαq Promotes Stress Granule Formation

2019 ◽  
Author(s):  
Androniqi Qifti ◽  
Lela Jackson ◽  
Ashima Singla ◽  
Osama Garwain ◽  
Suzanne Scarlata
Keyword(s):  
Plasma Membrane ◽  
Mammalian Cells ◽  
Stress Granules ◽  
Stress Granule ◽  
Granule Formation ◽  
Adverse Conditions ◽  
Granule Proteins ◽  
Regulate Protein ◽  
As Stress ◽  
Number Of Particles

ABSTRACTDuring adverse conditions, mammalian cells regulate protein production by carefully sequestering the translation machinery in membraneless organelles referred to as stress granules. Here, we show that activation of Gαq promotes the formation of particles that contain stress granule proteins through a mechanism linked to the presence of phospholipase Cβ1 (PLCβ1). In cells, PLCβ1, the most prominent isoform of PLCβ in neuronal cells, localizes to both the cytoplasm and plasma membrane. We show that a major population of cytosolic PLCβ1 binds to stress granule proteins, such as PABPC1, eIF5A and Ago2. PLCβ1 is activated by Gαq in response to hormones and neurotransmitters and we find that activation of Gαq shifts the cytosolic population of PLCβ1 to the plasma membrane, reducing its association to stress granule proteins. The loss of cytosolic PLCβ1 is accompanied by an increase in the size and number of particles containing PABPC1, G3BP1 or Ago2, and a shift of cytosolic RNAs to larger sizes consistent with cessation of translation. Particles containing stress granule proteins are seen when the cytosolic level of PLCβ1 is lowered by siRNA or by osmotic stress but not cold, heat, oxidative or arsenite stress suggesting that their composition is distinct from those formed from other stresses. Our results fit a simple thermodynamic model in which cytosolic PLCβ1 solubilizes stress granule proteins and its movement to Gαq upon stimulation releases these particles to allow the formation of stress granules. Taken together, our studies show a link between Gαq-coupled signals and translation through stress granule formation.

scholarly journals Phase-separated stress granules and processing bodies are compromised in Myotonic Dystrophy Type 1

2021 ◽  
Author(s):  
Selma Gulyurtlu ◽  
Monika S Magon ◽  
Patrick Guest ◽  
Panagiotios P Papavasiliou ◽  
Alan R Prescott ◽  
...  
Keyword(s):  
Myotonic Dystrophy ◽  
Mammalian Cells ◽  
Trinucleotide Repeat ◽  
Stress Granules ◽  
Myotonic Dystrophy Type 1 ◽  
Myotonic Dystrophy Type ◽  
Kinase Gene ◽  
Processing Bodies ◽  
P Bodies

RNA regulation in mammalian cells requires complex physical compartmentalisation using structures thought to be formed by liquid-liquid phase separation. Disruption of these structures is implicated in numerous degenerative diseases. Myotonic Dystrophy Type 1 (DM1) is a multi-systemic trinucleotide repeat disorder resulting from a CTG expansion in the dystonia myotonica protein kinase gene (DMPK). The cellular hall-mark of DM1 is the formation of nuclear foci containing expanded DMPK RNA (CUGexp). We report here the deregulation of stress granules and processing bodies (P-bodies), two cytoplasmic structures key for mRNA regulation, in cell culture models of DM1. Alterations to the rates of formation and dispersal of stress granules suggest an altered ability to respond to stress associated with DM1, while changes to the structure and dynamics of stress granules and P- bodies suggest that a more widespread alteration to the biophysical properties of cellular structures may be a consequence of the presence of CUGexp RNA.

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