Context-dependent deposition and regulation of mRNAs in P-bodies

AbstractCells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent pathway. Yet, P-bodies may facilitate not only decay but also act as storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies. mRNAs targeted for degradation to P-bodies, decayed with different kinetics. Moreover, the localization of a specific set of mRNAs to P-bodies under glucose deprivation was obligatory to prevent decay. Depending on its client mRNA, the RNA binding protein Puf5p either promoted or inhibited decay. The Puf5p-dependent storage of a subset of mRNAs in P-bodies under glucose starvation may be beneficial with respect to chronological lifespan.

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Context-dependent deposition and regulation of mRNAs in P-bodies

eLife ◽

10.7554/elife.29815 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 19

Author(s):

Congwei Wang ◽

Fabian Schmich ◽

Sumana Srivatsa ◽

Julie Weidner ◽

Niko Beerenwinkel ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Glucose Deprivation ◽

New Method ◽

Degradation Pathways ◽

Glucose Starvation ◽

P Bodies ◽

Storage Compartment ◽

Specific Mrna

Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies. mRNAs targeted for degradation to P-bodies, decayed with different kinetics. Moreover, the localization of a specific set of mRNAs to P-bodies under glucose deprivation was obligatory to prevent decay. Depending on its client mRNA, the RNA-binding protein Puf5p either promoted or inhibited decay. Furthermore, the Puf5p-dependent storage of a subset of mRNAs in P-bodies under glucose starvation may be beneficial with respect to chronological lifespan.

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Programmable RNA methylation and demethylation using PUF RNA binding proteins

Chemical Communications ◽

10.1039/c9cc09298f ◽

2020 ◽

Vol 56 (9) ◽

pp. 1365-1368 ◽

Cited By ~ 1

Author(s):

Kouki Shinoda ◽

Akiyo Suda ◽

Kenko Otonari ◽

Shiroh Futaki ◽

Miki Imanishi

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Rna Binding Protein ◽

New Method ◽

Rna Methylation

A new method manipulating local RNA methylation was developed by fusing the programmable RNA binding protein and the m6A demethylase or methyltransferase.

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KSHV RNA-binding protein ORF57 inhibits P-body formation to promote viral multiplication by interaction with Ago2 and GW182

Nucleic Acids Research ◽

10.1093/nar/gkz683 ◽

2019 ◽

Vol 47 (17) ◽

pp. 9368-9385 ◽

Cited By ~ 5

Author(s):

Nishi R Sharma ◽

Vladimir Majerciak ◽

Michael J Kruhlak ◽

Lulu Yu ◽

Jeong Gu Kang ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Time Lapse ◽

Processing Bodies ◽

P Bodies ◽

Rna Granules ◽

Inhibitory Function ◽

Invasion Mechanisms ◽

Initial Stage

Abstract Cellular non-membranous RNA-granules, P-bodies (RNA processing bodies, PB) and stress granules (SG), are important components of the innate immune response to virus invasion. Mechanisms governing how a virus modulates PB formation remain elusive. Here, we report the important roles of GW182 and DDX6, but not Dicer, Ago2 and DCP1A, in PB formation, and that Kaposi’s sarcoma-associated herpesvirus (KSHV) lytic infection reduces PB formation through several specific interactions with viral RNA-binding protein ORF57. The wild-type ORF57, but not its N-terminal dysfunctional mutant, inhibits PB formation by interacting with the N-terminal GW-domain of GW182 and the N-terminal domain of Ago2, two major components of PB. KSHV ORF57 also induces nuclear Ago2 speckles. Homologous HSV-1 ICP27, but not EBV EB2, shares this conserved inhibitory function with KSHV ORF57. By using time-lapse confocal microscopy of HeLa cells co-expressing GFP-tagged GW182, we demonstrated that viral ORF57 inhibits primarily the scaffolding of GW182 at the initial stage of PB formation. Consistently, KSHV-infected iSLK/Bac16 cells with reduced GW182 expression produced far fewer PB and SG, but 100-fold higher titer of infectious KSHV virions when compared to cells with normal GW182 expression. Altogether, our data provide the first evidence that a DNA virus evades host innate immunity by encoding an RNA-binding protein that promotes its replication by blocking PB formation.

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

10.21203/rs.3.rs-437201/v1 ◽

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.

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Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1

Molecular Biology of the Cell ◽

10.1091/mbc.e17-02-0100 ◽

2017 ◽

Vol 28 (22) ◽

pp. 3057-3069 ◽

Cited By ~ 4

Author(s):

Cornelia Kurischko ◽

James R. Broach

Keyword(s):

Rna Polymerase Ii ◽

Nuclear Export ◽

Rna Binding ◽

Binding Protein ◽

Neurological Diseases ◽

Rna Binding Protein ◽

Normal Function ◽

Nuclear Localization Sequence ◽

P Bodies ◽

Localization Sequence

Yeast Ssd1 is an RNA-binding protein that shuttles between the nucleus and cytoplasm. Ssd1 interacts with its target mRNAs initially during transcription by binding through its N-terminal prion-like domain (PLD) to the C-terminal domain of RNA polymerase II. Ssd1 subsequently targets mRNAs acquired in the nucleus either to daughter cells for translation or to stress granules (SGs) and P-bodies (PBs) for mRNA storage or decay. Here we show that PB components assist in the nuclear export of Ssd1and subsequent targeting of Ssd1 to PB sites in the cytoplasm. In the absence of import into the nucleus, Ssd1 fails to associate with PBs in the cytoplasm but rather is targeted to cytosolic insoluble protein deposits (IPODs). The association of Ssd1 either with IPOD sites or with PB/SG requires the PLD, whose activity is differentially regulated by the Ndr/LATS family kinase, Cbk1: phosphorylation suppresses PB/SG association but enhances IPOD formation. This regulation likely accrues from a phosphorylation-sensitive nuclear localization sequence located in the PLD. The results presented here may inform our understanding of aggregate formation by RBP in certain neurological diseases.

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