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Developmental Biology Oct 2008Processing bodies (P-bodies) have emerged as important subcellular structures that are involved in mRNA metabolism. To date, a detailed description of P-bodies in...
Processing bodies (P-bodies) have emerged as important subcellular structures that are involved in mRNA metabolism. To date, a detailed description of P-bodies in Drosophila oogenesis is lacking. To this end, we first demonstrate that Drosophila decapping protein 2 (dDcp2) contains intrinsic decapping activity and its enzymatic activity was not detectably enhanced by Drosophila decapping protein 1 (dDcp1). dDcp1-containing bodies in the nurse cell cytoplasm can associate with the 5' to 3' exoribonuclease, Pacman in addition to dDcp2 and Me31B. The size and number of dDcp1 bodies are dynamic and dramatically increased in dDcp2 and pacman mutant backgrounds supporting the conclusion that dDcp1 bodies in nurse cell cytoplasm are Drosophila P-bodies. In stage 2-6 oocytes, dDcp1 bodies appear to be distinct from previously characterized P-bodies since they are insensitive to cycloheximide and RNase A treatments. Curiously, dDcp2 and Pacman do not colocalize with dDcp1 at the posterior end of the oocyte in stage 9-10 oocytes. This suggests that dDcp1 bodies are in a developmentally distinct state separate from the 5' end mRNA degradation enzymes at later stages in the oocyte. Interestingly, re-formation of maternally expressed dDcp1 with dDcp2 and Pacman was observed in early embryogenesis. With respect to developmental switching, the maternal dDcp1 is proposed to serve as a marker for the re-formation of P-bodies in early embryos. This also suggests that a regulated conversion occurs between maternal RNA granules and P-bodies from oogenesis to embryogenesis.
Topics: Animals; Animals, Genetically Modified; Caspases; Cycloheximide; Cytoplasm; DEAD-box RNA Helicases; Drosophila; Drosophila Proteins; Embryo, Nonmammalian; Exoribonucleases; Female; Heat-Shock Response; Mutation; Oogenesis; RNA Stability; RNA, Messenger, Stored; Ribonuclease, Pancreatic; Ribonucleases; Transcription Factors
PubMed: 18708044
DOI: 10.1016/j.ydbio.2008.07.033 -
RNA (New York, N.Y.) Apr 2005Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), wherein mRNA decay factors are concentrated and where mRNA decay can...
Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), wherein mRNA decay factors are concentrated and where mRNA decay can occur. However, the physical nature of P-bodies, their relationship to translation, and possible roles of P-bodies in cellular responses remain unclear. We describe four properties of yeast P-bodies that indicate that P-bodies are dynamic structures that contain nontranslating mRNAs and function during cellular responses to stress. First, in vivo and in vitro analysis indicates that P-bodies are dependent on RNA for their formation. Second, the number and size of P-bodies vary in response to glucose deprivation, osmotic stress, exposure to ultraviolet light, and the stage of cell growth. Third, P-bodies vary with the status of the cellular translation machinery. Inhibition of translation initiation by mutations, or cellular stress, results in increased P-bodies. In contrast, inhibition of translation elongation, thereby trapping the mRNA in polysomes, leads to dissociation of P-bodies. Fourth, multiple translation factors and ribosomal proteins are lacking from P-bodies. These results suggest additional biological roles of P-bodies in addition to being sites of mRNA degradation.
Topics: Cytoplasmic Granules; DEAD-box RNA Helicases; Endoribonucleases; Genotype; Glucose; Green Fluorescent Proteins; Microscopy, Confocal; Osmotic Pressure; Protein Biosynthesis; RNA Helicases; RNA Stability; RNA, Messenger; RNA-Binding Proteins; Saccharomyces cerevisiae Proteins; Yeasts
PubMed: 15703442
DOI: 10.1261/rna.7258505 -
Cell Biochemistry and Function Apr 2012P-bodies (processing bodies) are observed in different organisms such as yeast, Caenorhabditis elegans and mammals. A typical eukaryotic cell contains several types of... (Review)
Review
P-bodies (processing bodies) are observed in different organisms such as yeast, Caenorhabditis elegans and mammals. A typical eukaryotic cell contains several types of spatially formed granules, such as P-bodies, stress granules and a variety of ribonucleoprotein bodies. These microdomains play important role in mRNA processing, including RNA interference, repression of translation and mRNA decay. The P-bodies components as well as stress granules may play an important role in host defense against viral infection. The complete set of P-bodies protein elements is still poor known. They contain conserved protein core limited to different organisms or to stress status of the cell. P-bodies are related also to some neuronal mRNA granules as well as to maternal RNA granules or male germ cell granules. In this mini-review, we focus on the structure of P-bodies and their function in the mRNA utilization and processing because of the high mRNA's dynamics between different cellular compartments and its key role in modulation of gene expression.
Topics: Animals; Cell Cycle; Cytoplasmic Granules; Eukaryotic Cells; Humans; RNA Stability; RNA, Messenger
PubMed: 22249943
DOI: 10.1002/cbf.2804 -
PloS One 2023Messenger RNA processing bodies (P-bodies) are cytoplasmic membrane-free organelles that contain proteins involved in mRNA silencing, storage and decay. The mechanism by...
Messenger RNA processing bodies (P-bodies) are cytoplasmic membrane-free organelles that contain proteins involved in mRNA silencing, storage and decay. The mechanism by which P-body components interact and the factors that regulate the stability of these structures are incompletely understood. In this study, we used a fluorescence-based, two-hybrid assay to investigate interactions between P-body components that occur inside the cell. LSm14a, PATL1, XRN1, and NBDY were found to interact with the N-terminal, WD40-domain-containing portion of EDC4. The N-terminus of full-length PATL1 was required to mediate the interaction between EDC4 and DDX6. The C-terminal, alpha helix-domain- containing portion of EDC4 was sufficient to mediate interaction with DCP1a and CCHCR1. In the absence of endogenous P-bodies, caused by depletion of LSm14a or DDX6, expression of the portion of EDC4 that lacked the N-terminus retained the ability to form cytoplasmic dots that were indistinguishable from P-bodies at the level of UV light microscopy. Despite the absence of endogenous P-bodies, this portion of EDC4 was able to recruit DCP1a, CCHCR1 and EDC3 to cytoplasmic dots. The results of this study permit the development of a new model of P-body formation and suggest that the N-terminus of EDC4 regulates the stability of these structures.
Topics: Animals; Processing Bodies; Cell Membrane; Cytoplasm; Cytosol; Mammals; RNA, Messenger
PubMed: 36877681
DOI: 10.1371/journal.pone.0282496 -
RNA Biology Jul 2006Cytoplasmic processing bodies, or P-bodies, contain a high concentration of enzymes and factors required for mRNA turnover and translational repression. Recent studies... (Review)
Review
Cytoplasmic processing bodies, or P-bodies, contain a high concentration of enzymes and factors required for mRNA turnover and translational repression. Recent studies provide evidence that the mRNAs silenced by miRNAs are localized to P-bodies for storage or degradation, perhaps in adjacent subcompartments. mRNP remodeling, potentially induced by miRISC or RNA helicase activity, may cause the modification of the translation initiation complex at the 5' end of mRNA, following translational repression and localization to P-bodies. Further remodeling in P-bodies may facilitate access of the decapping complex to the cap structure, thus inducing mRNA degradation. However, with appropriate signals, stored mRNAs in P-bodies could be released and returned to the translational machinery through mechanisms requiring binding of regulatory proteins to the 3' UTR of mRNAs. Here a model is proposed to explain the repression and degradation stages of the mRNAs within PBs. This model includes preservation or disruption of a stable closed loop structure of the mRNAs, compartmentalization in PBs and mRNA escape triggered by additional binding proteins.
Topics: Cell Compartmentation; Cytoplasmic Structures; Gene Silencing; MicroRNAs; Models, Biological; RNA Helicases; RNA, Messenger; RNA-Binding Proteins
PubMed: 17179742
DOI: 10.4161/rna.3.3.3499 -
Frontiers in Cell and Developmental... 2022The African trypanosome is a parasite of the mammalian bloodstream and tissues, where an antigenically variable Variant Surface Glycoprotein (VSG) coat protects it from... (Review)
Review
The African trypanosome is a parasite of the mammalian bloodstream and tissues, where an antigenically variable Variant Surface Glycoprotein (VSG) coat protects it from immune attack. This dense layer comprised of ∼10 VSG proteins, makes VSG by far the most abundant mRNA (7-10% total) and protein (∼10% total) in the bloodstream form trypanosome. How can such prodigious amounts of VSG be produced from a single VSG gene? Extremely high levels of RNA polymerase I (Pol I) transcription of the active VSG provide part of the explanation. However, recent discoveries highlight the role of pre-mRNA processing, both in maintaining high levels of VSG transcription, as well as its monoallelic expression. Trypanosome mRNAs are matured through trans-splicing a spliced leader (SL) RNA to the 5' end of precursor transcripts, meaning abundant SL RNA is required throughout the nucleus. However, requirement for SL RNA in the vicinity of the active VSG gene is so intense, that the cell reconfigures its chromatin architecture to facilitate interaction between the SL RNA genes and the active VSG. This presumably ensures that sufficient localised SL RNA is available, and not limiting for VSG mRNA expression. Recently, novel nuclear splicing bodies which appear to provide essential trans-splicing components, have been identified associating with the active VSG. These observations highlight the underappreciated role of pre-mRNA processing in modulating gene expression in trypanosomes. Dissecting the function of these nuclear RNA processing bodies should help us elucidate the mechanisms of both VSG expression and monoallelic exclusion in .
PubMed: 35517511
DOI: 10.3389/fcell.2022.876701 -
The Plant Cell Sep 2023Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular...
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
Topics: Biomolecular Condensates; Proteome
PubMed: 37162152
DOI: 10.1093/plcell/koad127 -
Stem Cells (Dayton, Ohio) Jan 2021Mesenchymal stromal cells (MSCs) are widely used in clinical trials because of their ability to modulate inflammation. The success of MSCs has been variable over...
Mesenchymal stromal cells (MSCs) are widely used in clinical trials because of their ability to modulate inflammation. The success of MSCs has been variable over 25 years, most likely due to an incomplete understanding of their mechanism. After MSCs are injected, they traffic to the lungs and other tissues where they are rapidly cleared. Despite being cleared, MSCs suppress the inflammatory response in the long term. Using human cord tissue-derived MSCs (hCT-MSCs), we demonstrated that hCT-MSCs directly interact and reprogram monocytes and macrophages. After engaging hCT-MSCs, monocytes and macrophages engulfed cytoplasmic components of live hCT-MSCs, then downregulated gene programs for antigen presentation and costimulation, and functionally suppressed the activation of helper T cells. We determined that low-density lipoprotein receptor-related proteins on monocytes and macrophages mediated the engulfment of hCT-MSCs. Since a large amount of cellular information can be packaged in cytoplasmic RNA processing bodies (p-bodies), we generated p-body deficient hCT-MSCs and confirmed that they failed to reprogram monocytes and macrophages in vitro and in vivo. hCT-MSCs suppressed an inflammatory response caused by a nasal lipopolysaccharide challenge. Although both control and p-body deficient hCT-MSCs were engulfed by infiltrating lung monocytes and macrophages, p-body deficient hCT-MSCs failed to suppress inflammation and downregulate MHC-II. Overall, we identified a novel mechanism by which hCT-MSCs indirectly suppressed a T-cell response by directly interacting and reprogramming monocytes and macrophages via p-bodies. The results of this study suggest a novel mechanism for how MSCs can reprogram the inflammatory response and have long-term effects to suppress inflammation.
Topics: Animals; Cellular Reprogramming; Heterografts; Humans; Macrophages; Mesenchymal Stem Cell Transplantation; Mesenchymal Stem Cells; Mice; Monocytes
PubMed: 33166420
DOI: 10.1002/stem.3292 -
The EMBO Journal May 2023Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological...
Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis thaliana through a proximity-biotinylation proteomics approach. Using in situ protein-protein interaction approaches, genetics and high-resolution dynamic imaging, we show that processing bodies comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can localize to unique plasma membrane subdomains including cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is regulated by DCP1, independently from its role in decapping, and the actin-nucleating SCAR-WAVE complex, whereby the DCP1-SCAR-WAVE interaction confines and enhances actin nucleation. This study reveals an unexpected function for a conserved condensate at unique membrane interfaces.
Topics: Actin-Related Protein 2-3 Complex; Actins; Arabidopsis; Arabidopsis Proteins; Processing Bodies
PubMed: 36741000
DOI: 10.15252/embj.2022111885 -
Seminars in Cell & Developmental Biology Apr 2024P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized... (Review)
Review
P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized in yeast and mammalian tissue culture cells. We describe here related condensates in the germline of animal models. Germline P-bodies have been reported at all stages of germline development from primordial germ cells to gametes. The activity of the universal germ cell fate regulator, Nanos, is linked to the mRNA decay function of P-bodies, and spatially-regulated condensation of P-body like condensates in embryos is required to localize mRNA regulators to primordial germ cells. In most cases, however, it is not known whether P-bodies represent functional compartments or non-functional condensation by-products that arise when ribonucleoprotein complexes saturate the cytoplasm. We speculate that the ubiquity of P-body-like condensates in germ cells reflects the strong reliance of the germline on cytoplasmic, rather than nuclear, mechanisms of gene regulation.
Topics: Animals; RNA-Binding Proteins; Processing Bodies; Germ Cells; RNA, Messenger; Gene Expression Regulation; Mammals
PubMed: 37407370
DOI: 10.1016/j.semcdb.2023.06.010