scholarly journals Imaging of single mRNA translation repression reveals diverse interactions with mRNP granules

2018 ◽  
Author(s):  
Stephanie L. Moon ◽  
Tatsuya Morisaki ◽  
Anthony Khong ◽  
Kenneth Lyon ◽  
Roy Parker ◽  
...  
Keyword(s):  
Mrna Translation ◽  
Stress Granules ◽  
Granule Size ◽  
Mrna Regulation ◽  
P Bodies ◽  
Stable Association ◽  
Mrna Length ◽  
Rnp Granules ◽  
Diverse Interactions ◽  
Ribosome Association

AbstractDuring cellular stress mRNAs exit translation and accumulate in stress granules and P-bodies, although the dynamics of these interactions remain unclear. We imaged in real-time single mRNAs, their translational output, and mRNA-granule interactions during stress. We observed single mRNAs interacting with stress granules and P-bodies, with mRNAs moving bidirectionality between them. While translating mRNAs only interact with RNP granules dynamically, non-translating mRNAs can form stable associations that rigidly immobilize the mRNA within the granule. Imaging thousands of individual mRNA-granule interactions showed the probability of stable association increases with both mRNA length and granule size. Therefore, the recruitment of mRNAs to RNP granules involves both highly dynamic and stable interactions, influenced by several parameters, demonstrating a new layer of complexity in mRNA regulation during stress.One Sentence SummarymRNAs interact with stress granules and P-bodies in stable and dynamic manners influenced by ribosome association, mRNA length, and granule size.

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 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 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.

Focusing on mRNA Granules and Stalled Polysomes Amidst Diverse Mechanisms Underlying mRNA Transport, mRNA Storage, and Local Translation

2020 ◽  
Author(s):  
Mina N. Anadolu ◽  
Wayne S. Sossin
Keyword(s):  
Protein Synthesis ◽  
Liquid Phase ◽  
Mrna Translation ◽  
Rna Transport ◽  
P Bodies ◽  
Rna Granules ◽  
Mrna Granules ◽  
Transport Particle ◽  
As Stress ◽  
The Individual

In neurons, mRNAs are transported to distal sites to allow for localized protein synthesis. There are many diverse mechanisms underlying this transport. For example, an individual mRNA can be transported in an RNA transport particle that is tailored to the individual mRNA and its associated binding proteins. In contrast, some mRNAs are transported in liquid-liquid phase separated structures called neuronal RNA granules that are made up of multiple stalled polysomes, allowing for rapid initiation-independent production of proteins required for synaptic plasticity. Moreover, neurons have additional types of liquid-liquid phase–separated structures containing mRNA, such as stress granules and P bodies. This chapter discusses the relationships between all of these structures, what proteins distinguish them, and the possible roles they play in the complex control of mRNA translation at distal sites that allow neurons to use protein synthesis to refine their local proteome in many different ways.

scholarly journals The catalytic activity of the Ubp3 deubiquitinating protease is required for efficient stress granule assembly inS. cerevisiae

2015 ◽  
pp. MCB.00609-15 ◽  
Author(s):  
Regina Nostramo ◽  
Sapna N. Varia ◽  
Bo Zhang ◽  
Megan M. Emerson ◽  
Paul K. Herman
Keyword(s):  
Catalytic Activity ◽  
Stress Granules ◽  
Eukaryotic Cell ◽  
Stress Granule ◽  
Resting Cells ◽  
Term Survival ◽  
General Role ◽  
Rnp Complex ◽  
Processing Body ◽  
Rnp Granules

The interior of the eukaryotic cell is a highly compartmentalized space containing both membrane-bound organelles and the recently-identified nonmembranous ribonucleoprotein (RNP) granules. This study examines inSaccharomyces cerevisiaethe assembly of one conserved type of the latter compartment, known as the stress granule. Stress granules form in response to particular environmental cues and have been linked to a variety of human diseases, including amyotrophic lateral sclerosis. To further our understanding of these structures, a candidate genetic screen was employed to identify regulators of stress granule assembly in quiescent cells. These studies identified a ubiquitin-specific protease, Ubp3, as having an essential role in the assembly of these RNP granules. This function was not shared by other members of the Ubp protease family and required Ubp3 catalytic activity as well as its interaction with the cofactor, Bre5. Interestingly, the loss of stress granules was correlated with a decrease in the long-term survival of stationary phase cells. This phenotype is similar to that observed in mutants defective for the formation of a related RNP complex, the Processing-body. Altogether, these observations raise the interesting possibility of a general role for these types of cytoplasmic RNP granules in the survival of G0-like resting cells.

scholarly journals The GNU subunit of PNG kinase, the developmental regulator of mRNA translation, binds BIC-C to localize to RNP granules

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Emir E Avilés-Pagán ◽  
Masatoshi Hara ◽  
Terry L Orr-Weaver
Keyword(s):  
Translational Regulation ◽  
Mrna Translation ◽  
Mature Oocyte ◽  
Early Embryogenesis ◽  
Egg Activation ◽  
Maternal Mrna ◽  
Rnp Granules

Control of mRNA translation is a key mechanism by which the differentiated oocyte transitions to a totipotent embryo. In Drosophila, the PNG kinase complex regulates maternal mRNA translation at the oocyte-to-embryo transition. We previously showed the GNU activating subunit is crucial in regulating PNG and timing its activity to the window between egg activation and early embryogenesis (Hara et al., 2017). In this study, we find associations between GNU and proteins of RNP granules and demonstrate that GNU localizes to cytoplasmic RNP granules in the mature oocyte, identifying GNU as a new component of a subset of RNP granules. Furthermore, we define roles for the domains of GNU. Interactions between GNU and the granule component BIC-C reveal potential conserved functions for translational regulation in metazoan development. We propose that by binding to BIC-C, upon egg activation GNU brings PNG to its initial targets, translational repressors in RNP granules.

scholarly journals mRNA with Mammalian Codon Bias Accumulates in Yeast Mutants with Constitutive Stress Granules

2020 ◽  
Vol 21 (4) ◽  
pp. 1234
Author(s):  
Natalia V. Kozlova ◽  
Chantal Pichon ◽  
A. Rachid Rahmouni
Keyword(s):  
Codon Bias ◽  
Gene Deletion ◽  
Stress Granules ◽  
Stress Factors ◽  
Yeast Gene ◽  
P Bodies ◽  
Mrna Surveillance ◽  
Steady State Levels ◽  
Cytoplasmic Structures ◽  
Yeast Mutants

Stress granules and P bodies are cytoplasmic structures assembled in response to various stress factors and represent sites of temporary storage or decay of mRNAs. Depending on the source of stress, the formation of these structures may be driven by distinct mechanisms, but several stresses have been shown to stabilize mRNAs via inhibition of deadenylation. A recent study identified yeast gene deletion mutants with constitutive stress granules and elevated P bodies; however, the mechanisms which trigger its formation remain poorly understood. Here, we investigate the possibility of accumulating mRNA with mammalian codon bias, which we termed the model RNA, in these mutants. We found that the model RNA accumulates in dcp2 and xrn1 mutants and in four mutants with constitutive stress granules overlapping with P bodies. However, in eight other mutants with constitutive stress granules, the model RNA is downregulated, or its steady state levels vary. We further suggest that the accumulation of the model RNA is linked to its protection from the main mRNA surveillance path. However, there is no obvious targeting of the model RNA to stress granules or P bodies. Thus, accumulation of the model RNA and formation of constitutive stress granules occur independently and only some paths inducing formation of constitutive stress granules will stabilize mRNA as well.

Sign in / Sign up

Export Citation Format

Share Document