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Cell Reports Jan 2023Membraneless condensates, such as stress granules (SGs) and processing bodies (P-bodies), have attracted wide attention due to their unique feature of rapid response to...
Membraneless condensates, such as stress granules (SGs) and processing bodies (P-bodies), have attracted wide attention due to their unique feature of rapid response to stress without first requiring nuclear feedback. In this study, we identify diaphanous-related formin 3 (DIAPH3), an actin nucleator, as a scaffold protein to initiate liquid-liquid phase separation (LLPS) and form abundant cytosolic phase-separated DIAPH3 granules (D-granules) in mammalian cells such as HeLa, HEK293, and fibroblasts under various stress conditions. Neither mRNAs nor known stress-associated condensate markers, such as G3BP1, G3BP2, and TIA1 for SGs and DCP1A for P-bodies, are detected in D-granules. Using overexpression and knockout of DIAPH3, pharmacological interventions, and optogenetics, we further demonstrate that stress-induced D-granules spatially sequester DIAPH3 within the condensation to inhibit the assembly of actin filaments in filopodia. This study reveals that D-granules formed by LLPS act as a regulatory hub for actin cytoskeletal remodeling in response to stress.
Topics: Animals; Humans; DNA Helicases; Actins; HEK293 Cells; Poly-ADP-Ribose Binding Proteins; RNA Helicases; RNA Recognition Motif Proteins; Actin Cytoskeleton; Mammals; Formins
PubMed: 36640348
DOI: 10.1016/j.celrep.2022.111986 -
Sensors (Basel, Switzerland) Dec 2023The Celestial Object Rendering TOol (CORTO) offers a powerful solution for generating synthetic images of celestial bodies, catering to the needs of space mission...
The Celestial Object Rendering TOol (CORTO) offers a powerful solution for generating synthetic images of celestial bodies, catering to the needs of space mission design, algorithm development, and validation. Through rendering, noise modeling, hardware-in-the-loop testing, and post-processing functionalities, CORTO creates realistic scenarios. It offers a versatile and comprehensive solution for generating synthetic images of celestial bodies, aiding the development and validation of image processing and navigation algorithms for space missions. This work illustrates its functionalities in detail for the first time. The importance of a robust validation pipeline to test the tool's accuracy against real mission images using metrics like normalized cross-correlation and structural similarity is also illustrated. CORTO is a valuable asset for advancing space exploration and navigation algorithm development and has already proven effective in various projects, including CubeSat design, lunar missions, and deep learning applications. While the tool currently covers a range of celestial body simulations, mainly focused on minor bodies and the Moon, future enhancements could broaden its capabilities to encompass additional planetary phenomena and environments.
PubMed: 38067968
DOI: 10.3390/s23239595 -
Trends in Plant Science Jul 2023The SERRATE (SE) protein is involved in the processing of RNA polymerase II (RNAPII) transcripts. It is associated with different complexes engaged in different aspects... (Review)
Review
The SERRATE (SE) protein is involved in the processing of RNA polymerase II (RNAPII) transcripts. It is associated with different complexes engaged in different aspects of plant RNA metabolism, including assemblies involved in transcription, splicing, polyadenylation, miRNA biogenesis, and RNA degradation. SE stability and interactome properties can be influenced by phosphorylation. SE exhibits an intriguing liquid-liquid phase separation property that may be important in the assembly of different RNA-processing bodies. Therefore, we propose that SE seems to participate in the coordination of different RNA-processing steps and can direct the fate of transcripts, targeting them for processing or degradation when they cannot be properly processed or are synthesized in excess.
Topics: Arabidopsis Proteins; Arabidopsis; Calcium-Binding Proteins; RNA Processing, Post-Transcriptional; Serrate-Jagged Proteins; RNA; MicroRNAs; RNA, Plant; Gene Expression Regulation, Plant
PubMed: 37019716
DOI: 10.1016/j.tplants.2023.03.009 -
DNA and Cell Biology Jun 2013The processing bodies (PBs) are a form of cytoplasmic aggregates that house the cellular RNA decay machinery as well as many RNA-binding proteins and mRNAs. The PBs are...
The processing bodies (PBs) are a form of cytoplasmic aggregates that house the cellular RNA decay machinery as well as many RNA-binding proteins and mRNAs. The PBs are constitutively present in eukaryotic cells and are involved in maintaining cellular homeostasis by regulating RNA metabolism, cell signaling, and survival. Virus infections result in modification of the PBs and their constituents. Many viruses induce compositionally altered PBs, while many others use specific components of the PBs for their replication. PB constituents are also known to restrict virus replication by a variety of mechanisms. Further, continuing studies in this rapidly emerging field of PB-virus interactions will undoubtedly provide important clues to the understanding of the role of PBs in cellular homeostasis as well as their role in virus infections and innate immune signaling.
Topics: APOBEC Deaminases; Cytidine Deaminase; Cytoplasmic Granules; Cytosine Deaminase; RNA Stability; RNA, Messenger; Viral Proteins; Virus Diseases; Virus Replication
PubMed: 23617258
DOI: 10.1089/dna.2013.2054 -
Frontiers in Molecular Neuroscience 2023Liquid-liquid phase separation results in the formation of dynamic biomolecular condensates, also known as membrane-less organelles, that allow for the assembly of... (Review)
Review
Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders.
Liquid-liquid phase separation results in the formation of dynamic biomolecular condensates, also known as membrane-less organelles, that allow for the assembly of functional compartments and higher order structures within cells. Multivalent, reversible interactions between RNA-binding proteins (RBPs), including FUS, TDP-43, and hnRNPA1, and/or RNA (e.g., RBP-RBP, RBP-RNA, RNA-RNA), result in the formation of ribonucleoprotein (RNP) condensates, which are critical for RNA processing, mRNA transport, stability, stress granule assembly, and translation. Stress granules, neuronal transport granules, and processing bodies are examples of cytoplasmic RNP condensates, while the nucleolus and Cajal bodies are representative nuclear RNP condensates. In neurons, RNP condensates promote long-range mRNA transport and local translation in the dendrites and axon, and are essential for spatiotemporal regulation of gene expression, axonal integrity and synaptic function. Mutations of RBPs and/or pathologic mislocalization and aggregation of RBPs are hallmarks of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. ALS/FTD-linked mutations of RBPs alter the strength and reversibility of multivalent interactions with other RBPs and RNAs, resulting in aberrant phase transitions. These aberrant RNP condensates have detrimental functional consequences on mRNA stability, localization, and translation, and ultimately lead to compromised axonal integrity and synaptic function in disease. Pathogenic protein aggregation is dependent on various factors, and aberrant dynamically arrested RNP condensates may serve as an initial nucleation step for pathologic aggregate formation. Recent studies have focused on identifying mechanisms by which neurons resolve phase transitioned condensates to prevent the formation of pathogenic inclusions/aggregates. The present review focuses on the phase separation of neurodegenerative disease-linked RBPs, physiological functions of RNP condensates, and the pathologic role of aberrant phase transitions in neurodegenerative disease, particularly ALS/FTD. We also examine cellular mechanisms that contribute to the resolution of aberrant condensates in neurons, and potential therapeutic approaches to resolve aberrantly phase transitioned condensates at a molecular level.
PubMed: 37720552
DOI: 10.3389/fnmol.2023.1242925 -
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 -
Viruses Jul 2022Most cytoplasmic-replicating negative-strand RNA viruses (NSVs) initiate genome transcription by cap snatching. The source of host mRNAs from which the cytoplasmic NSVs...
Most cytoplasmic-replicating negative-strand RNA viruses (NSVs) initiate genome transcription by cap snatching. The source of host mRNAs from which the cytoplasmic NSVs snatch capped-RNA leader sequences has remained elusive. Earlier reports have pointed towards cytoplasmic-RNA processing bodies (P body, PB), although several questions have remained unsolved. Here, the nucleocapsid (N) protein of plant- and animal-infecting members of the order , in casu Tomato spotted wilt virus (TSWV), Rice stripe virus (RSV), Sin nombre virus (SNV), Crimean-Congo hemorrhagic fever virus (CCHFV) and Schmallenberg virus (SBV) have been expressed and localized in cells of their respective plant and animal hosts. All N proteins localized to PBs as well as stress granules (SGs), but extensively to docking stages of PB and SG. TSWV and RSV N proteins also co-localized with Ran GTPase-activating protein 2 (RanGAP2), a nucleo-cytoplasmic shuttling factor, in the perinuclear region, and partly in the nucleus when co-expressed with its WPP domain containing a nuclear-localization signal. Upon silencing of PB and SG components individually or concomitantly, replication levels of a TSWV minireplicon, as measured by the expression of a GFP reporter gene, ranged from a 30% reduction to a four-fold increase. Upon the silencing of RanGAP homologs , replication of the TSWV minireplicon was reduced by 75%. During in vivo cap-donor competition experiments, TSWV used transcripts destined to PB and SG, but also functional transcripts engaged in translation. Altogether, the results implicate a more complex situation in which, besides PB, additional cytoplasmic sources are used during transcription/cap snatching of cytoplasmic-replicating and segmented NSVs.
Topics: Animals; Cytoplasmic Granules; Processing Bodies; RNA Caps; RNA Viruses; RNA, Viral; Stress Granules; Tenuivirus; Tospovirus
PubMed: 36016301
DOI: 10.3390/v14081679 -
International Review of Cell and... 2012In a variety of cell types in plants, animals, and fungi, ribonucleoprotein (RNP) complexes play critical roles in regulating RNA metabolism. These RNP granules include... (Review)
Review
In a variety of cell types in plants, animals, and fungi, ribonucleoprotein (RNP) complexes play critical roles in regulating RNA metabolism. These RNP granules include processing bodies and stress granules that are found broadly across cell types, as well as RNP granules unique to the germline, such as P granules, polar granules, sponge bodies, and germinal granules. This review focuses on RNP granules localized in oocytes of the major model systems, Caenorhabditis elegans, Drosophila, Xenopus, mouse, and zebrafish. The signature families of proteins within oocyte RNPs include Vasa and other RNA-binding proteins, decapping activators and enzymes, Argonaute family proteins, and translation initiation complex proteins. This review describes the many recent insights into the dynamics and functions of RNP granules, including their roles in mRNA degradation, mRNA localization, translational regulation, and fertility. The roles of the cytoskeleton and cell organelles in regulating RNP granule assembly are also discussed.
Topics: Animals; Cytoplasmic Granules; Cytoskeleton; Humans; Oocytes; Organelles; Ribonucleoproteins; Stress, Physiological
PubMed: 22449492
DOI: 10.1016/B978-0-12-394306-4.00013-7 -
Frontiers in Plant Science 2022Phytochromes are red- and far-red light receptors that control the growth and development of plants, enabling them to respond adequately to changing light conditions. It...
Phytochromes are red- and far-red light receptors that control the growth and development of plants, enabling them to respond adequately to changing light conditions. It has been shown that halted mRNAs stored in RNA granules called processing bodies are released upon light perception and contribute to the adaptation to the light environment. However, the photophysiological background of this process is largely unknown. We found that light of different wavelengths can trigger the disassembly of processing bodies in a dose- and time-dependent manner. We show that phytochromes control this process in red- and far-red light and that cytoplasmic phytochrome A is sufficient and necessary for the far-red light-induced disassembly of processing bodies. This adds a novel, unexpected cytoplasmic function to the processes controlled by phytochrome A. Overall, our findings suggest a role of phytochromes in the control of translationally halted mRNAs that are stored in processing bodies. We expect our findings to facilitate understanding of how light and environmental cues control the assembly and disassembly of processing bodies, which could have broader implications for the regulation of non-membranous organelles in general.
PubMed: 35283917
DOI: 10.3389/fpls.2022.828529 -
Developmental Biology Nov 2008In somatic cells, untranslated mRNAs accumulate in cytoplasmic foci called processing bodies or P-bodies. P-bodies contain complexes that inhibit translation and...
In somatic cells, untranslated mRNAs accumulate in cytoplasmic foci called processing bodies or P-bodies. P-bodies contain complexes that inhibit translation and stimulate mRNA deadenylation, decapping, and decay. Recently, certain P-body proteins have been found in germ granules, RNA granules specific to germ cells. We have investigated a possible connection between P-bodies and germ granules in Caenorhabditis elegans. We identify PATR-1, the C. elegans homolog of the yeast decapping activator Pat1p, as a unique marker for P-bodies in C. elegans embryos. We find that P-bodies are inherited maternally as core granules that mature differently in somatic and germline blastomeres. In somatic blastomeres, P-bodies recruit the decapping activators LSM-1 and LSM-3. This recruitment requires the LET-711/Not1 subunit of the CCR4-NOT deadenylase and correlates spatially and temporally with the onset of maternal mRNA degradation. In germline blastomeres, P-bodies are maintained as core granules lacking LSM-1 and LSM-3. P-bodies interact with germ granules, but maintain distinct dynamics and components. The maternal mRNA nos-2 is maintained in germ granules, but not in P-bodies. We conclude that P-bodies are distinct from germ granules, and represent a second class of RNA granules that behaves differently in somatic and germline cells.
Topics: Animals; Caenorhabditis elegans; Cytoplasmic Granules; Embryo, Nonmammalian; Fluorescent Antibody Technique, Indirect; Germ Cells; Green Fluorescent Proteins; In Situ Hybridization; In Situ Hybridization, Fluorescence; Inclusion Bodies; Models, Biological; RNA; RNA Interference; RNA Processing, Post-Transcriptional; Recombinant Fusion Proteins; Transgenes
PubMed: 18692039
DOI: 10.1016/j.ydbio.2008.07.008