RNA granules and cytoskeletal links

2014 ◽  
Vol 42 (4) ◽  
pp. 1206-1210 ◽  
Author(s):  
Dipen Rajgor ◽  
Catherine M. Shanahan
Keyword(s):  
Mammalian Cells ◽  
Dynamic Properties ◽  
Translational Repression ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Messenger Ribonucleoprotein ◽  
Cytoskeletal Networks ◽  
And Control ◽  
Lower Eukaryote

In eukaryotic cells, non-translating mRNAs can accumulate into cytoplasmic mRNP (messenger ribonucleoprotein) granules such as P-bodies (processing bodies) and SGs (stress granules). P-bodies contain the mRNA decay and translational repression machineries and are ubiquitously expressed in mammalian cells and lower eukaryote species including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. In contrast, SGs are only detected during cellular stress when translation is inhibited and form from aggregates of stalled pre-initiation complexes. SGs and P-bodies are related to NGs (neuronal granules), which are essential in the localization and control of mRNAs in neurons. Importantly, RNA granules are linked to the cytoskeleton, which plays an important role in mediating many of their dynamic properties. In the present review, we discuss how P-bodies, SGs and NGs are linked to cytoskeletal networks and the importance of these linkages in maintaining localization of their RNA cargoes.

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

2019 ◽  
Vol 47 (17) ◽  
pp. 9368-9385 ◽  
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.

scholarly journals Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae

2007 ◽  
Vol 179 (3) ◽  
pp. 437-449 ◽  
Author(s):  
Carolyn J. Decker ◽  
Daniela Teixeira ◽  
Roy Parker
Keyword(s):  
Protein Interactions ◽  
Messenger Rna ◽  
Mrna Decay ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Rich Domain ◽  
Cytoplasmic Rna ◽  
Processing Body ◽  
The Individual

Processing bodies (P-bodies) are cytoplasmic RNA granules that contain translationally repressed messenger ribonucleoproteins (mRNPs) and messenger RNA (mRNA) decay factors. The physical interactions that form the individual mRNPs within P-bodies and how those mRNPs assemble into larger P-bodies are unresolved. We identify direct protein interactions that could contribute to the formation of an mRNP complex that consists of core P-body components. Additionally, we demonstrate that the formation of P-bodies that are visible by light microscopy occurs either through Edc3p, which acts as a scaffold and cross-bridging protein, or via the “prionlike” domain in Lsm4p. Analysis of cells defective in P-body formation indicates that the concentration of translationally repressed mRNPs and decay factors into microscopically visible P-bodies is not necessary for basal control of translation repression and mRNA decay. These results suggest a stepwise model for P-body assembly with the initial formation of a core mRNA–protein complex that then aggregates through multiple specific mechanisms.

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.

Acidic stress induces the formation of P-bodies, but not stress granules, with mild attenuation of bulk translation in Saccharomyces cerevisiae

2012 ◽  
Vol 446 (2) ◽  
pp. 225-233 ◽  
Author(s):  
Aya Iwaki ◽  
Shingo Izawa
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lactic Acid ◽  
Stress Granules ◽  
Glucose Deprivation ◽  
Acidic Stress ◽  
Processing Bodies ◽  
Body Formation ◽  
P Bodies ◽  
Glucose Depletion ◽  
Messenger Ribonucleoprotein

The stress response of eukaryotic cells often causes an attenuation of bulk translation activity and the accumulation of non-translating mRNAs into cytoplasmic mRNP (messenger ribonucleoprotein) granules termed cytoplasmic P-bodies (processing bodies) and SGs (stress granules). We examined effects of acidic stress on the formation of mRNP granules compared with other forms of stress such as glucose deprivation and a high Ca2+ level in Saccharomyces cerevisiae. Treatment with lactic acid clearly caused the formation of P-bodies, but not SGs, and also caused an attenuation of translation initiation, albeit to a lesser extent than glucose depletion. P-body formation was also induced by hydrochloric acid and sulfuric acid. However, lactic acid in SD (synthetic dextrose) medium with a pH greater than 3.0, propionic acid and acetic acid did not induce P-body formation. The results of the present study suggest that the assembly of yeast P-bodies can be induced by external conditions with a low pH and the threshold was around pH 2.5. The P-body formation upon acidic stress required Scd6 (suppressor of clathrin deficiency 6), a component of P-bodies, indicating that P-bodies induced by acidic stress have rules of assembly different from those induced by glucose deprivation or high Ca2+ levels.

scholarly journals RGG-motif protein Sbp1 is required for Processing body (P-body) disassembly

2021 ◽  
Author(s):  
Raju Roy ◽  
Ishwarya Achappa Kuttanda ◽  
Nupur Bhatter ◽  
Purusharth I Rajyaguru
Keyword(s):  
Mrna Decay ◽  
Glucose Deprivation ◽  
Low Complexity ◽  
Wild Type ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Processing Body ◽  
Mrna Fate

AbstractRNA granules are conserved mRNP complexes that play an important role in determining mRNA fate by affecting translation repression and mRNA decay. Processing bodies (P-bodies) harbor enzymes responsible for mRNA decay and proteins involved in modulating translation. Although many proteins have been identified to play a role in P-body assembly, a bonafide disassembly factor remains unknown. In this report, we identify RGG-motif translation repressor protein Sbp1 as a disassembly factor of P-bodies. Disassembly of Edc3 granules but not the Pab1 granules (a conserved stress granule marker) that arise upon sodium azide and glucose deprivation stress are defective in Δsbp1. Disassembly of other P-body proteins such as Dhh1 and Scd6 is also defective in Δsbp1. Complementation experiments suggest that the wild type Sbp1 but not an RGG-motif deletion mutant rescues the Edc3 granule disassembly defect in Δsbp1. We observe that purified Edc3 forms assemblies, which is promoted by the presence of RNA and NADH. Strikingly, addition of purified Sbp1 leads to significantly decreased Edc3 assemblies. Although low complexity sequences have been in general implicated in assembly, our results reveal the role of RGG-motif (a low-complexity sequence) in the disassembly of P-bodies.

Yeast mRNA localization: protein asymmetry, organelle localization and response to stress

2014 ◽  
Vol 42 (4) ◽  
pp. 1256-1260 ◽  
Author(s):  
Mariavittoria Pizzinga ◽  
Mark P. Ashe
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Mrna Localization ◽  
Translational Repression ◽  
Yeast Saccharomyces Cerevisiae ◽  
Processing Bodies ◽  
Control Of Gene Expression ◽  
P Bodies ◽  
Response To Stress ◽  
Kinetics Of

The localization of mRNA forms a key facet of the post-transcriptional control of gene expression and recent evidence suggests that it may be considerably more widespread than previously anticipated. For example, defined mRNA-containing granules can be associated with translational repression or activation. Furthermore, mRNA P-bodies (processing bodies) harbour much of the mRNA decay machinery and stress granules are thought to play a role in mRNA storage. In the present review, we explore the process of mRNA localization in the yeast Saccharomyces cerevisiae, examining connections between organellar mRNA localization and the response to stress. We also review recent data suggesting that even where there is a global relocalization of mRNA, the specificity and kinetics of this process can be regulated.

Pat1 proteins: a life in translation, translation repression and mRNA decay

2010 ◽  
Vol 38 (6) ◽  
pp. 1602-1607 ◽  
Author(s):  
Aline Marnef ◽  
Nancy Standart
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Mrna Decay ◽  
Current Knowledge ◽  
Translational Repression ◽  
Processing Bodies ◽  
P Bodies ◽  
Expression Control ◽  
Gene Expression Control ◽  
Sequential Binding

Pat1 proteins are conserved across eukaryotes. Vertebrates have evolved two Pat1 proteins paralogues, whereas invertebrates and yeast only possess one such protein. Despite their lack of known domains or motifs, Pat1 proteins are involved in several key post-transcriptional mechanisms of gene expression control. In yeast, Pat1p interacts with translating mRNPs (messenger ribonucleoproteins), and is responsible for translational repression and decapping activation, ultimately leading to mRNP degradation. Drosophila HPat and human Pat1b (PatL1) proteins also have conserved roles in the 5′→3′ mRNA decay pathway. Consistent with their functions in silencing gene expression, Pat1 proteins localize to P-bodies (processing bodies) in yeast, Drosophila, Caenorhabditis elegans and human cells. Altogether, Pat1 proteins may act as scaffold proteins allowing the sequential binding of repression and decay factors on mRNPs, eventually leading to their degradation. In the present mini-review, we present the current knowledge on Pat1 proteins in the context of their multiple functions in post-transcriptional control.

scholarly journals The DEAD-Box RNA Helicase Ded1p Affects and Accumulates inSaccharomyces cerevisiaeP-Bodies

2008 ◽  
Vol 19 (3) ◽  
pp. 984-993 ◽  
Author(s):  
Carla Beckham ◽  
Angela Hilliker ◽  
Anne-Marie Cziko ◽  
Amine Noueiry ◽  
Mani Ramaswami ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Processing Bodies ◽  
Body Formation ◽  
P Bodies ◽  
Dead Box ◽  
Inhibition Of Growth ◽  
Messenger Ribonucleoprotein ◽  
Positive Effect

Recent results suggest that cytoplasmic mRNAs can form translationally repressed messenger ribonucleoprotein particles (mRNPs) capable of decapping and degradation, or accumulation into cytoplasmic processing bodies (P-bodies), which can function as sites of mRNA storage. The proteins that function in transitions between the translationally repressed mRNPs that accumulate in P-bodies and mRNPs engaged in translation are largely unknown. Herein, we demonstrate that the yeast translation initiation factor Ded1p can localize to P-bodies. Moreover, depletion of Ded1p leads to defects in P-body formation. Overexpression of Ded1p results in increased size and number of P-bodies and inhibition of growth in a manner partially suppressed by loss of Pat1p, Dhh1p, or Lsm1p. Mutations that inactivate the ATPase activity of Ded1p increase the overexpression growth inhibition of Ded1p and prevent Ded1p from localizing in P-bodies. Combined with earlier work showing Ded1p can have a positive effect on translation, these results suggest that Ded1p is a bifunctional protein that can affect both translation initiation and P-body formation.

scholarly journals Processing bodies control the selective translation for optimal development of Arabidopsis young seedlings

2019 ◽  
Vol 116 (13) ◽  
pp. 6451-6456 ◽  
Author(s):  
Geng-Jen Jang ◽  
Jun-Yi Yang ◽  
Hsu-Liang Hsieh ◽  
Shu-Hsing Wu
Keyword(s):  
Translational Repression ◽  
Light Conditions ◽  
Wild Type ◽  
Translation Control ◽  
Processing Bodies ◽  
P Bodies ◽  
Plant Seeds ◽  
Before And After ◽  
Selective Translation ◽  
Specific Mrnas

Germinated plant seeds buried in soil undergo skotomorphogenic development before emergence to reach the light environment. Young seedlings transitioning from dark to light undergo photomorphogenic development. During photomorphogenesis, light alters the transcriptome and enhances the translation of thousands of mRNAs during the dark-to-light transition inArabidopsisyoung seedlings. About 1,500 of these mRNAs have comparable abundance before and after light treatment, which implies widespread translational repression in dark-grown seedlings. Processing bodies (p-bodies), the cytoplasmic granules found in diverse organisms, can balance the storage, degradation, and translation of mRNAs. However, the function of p-bodies in translation control remains largely unknown in plants. Here we found that anArabidopsismutant defective in p-body formation (Decapping 5;dcp5-1) showed reduced fitness under both dark and light conditions. Comparative transcriptome and translatome analyses of wild-type anddcp5-1seedlings revealed that p-bodies can attenuate the premature translation of specific mRNAs in the dark, including those encoding enzymes for protochlorophyllide synthesis and PIN-LIKES3 for auxin-dependent apical hook opening. When the seedlings protrude from soil, light perception by photoreceptors triggers a reduced accumulation of p-bodies to release the translationally stalled mRNAs for active translation of mRNAs encoding proteins needed for photomorphogenesis. Our data support a key role for p-bodies in translation repression, an essential mechanism for proper skotomorphogenesis and timely photomorphogenesis in seedlings.

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