-
The Journal of General Virology Oct 2019RNA processing bodies (P-bodies) are non-membranous cytoplasmic aggregates of mRNA and proteins involved in mRNA decay and translation repression. P-bodies actively...
RNA processing bodies (P-bodies) are non-membranous cytoplasmic aggregates of mRNA and proteins involved in mRNA decay and translation repression. P-bodies actively respond to environmental stresses, associated with another type of RNA granules, known as stress granules (SGs). Alphaviruses were previously shown to block SG induction at late stages of infection, which is important for efficient viral growth. In this study, we found that P-bodies were disassembled or reduced in number very early in infection with Semliki Forest virus (SFV) or chikungunya virus (CHIKV) in a panel of cell lines. Similar to SGs, reinduction of P-bodies by a second stress (sodium arsenite) was also blocked in infected cells. The disassembly of P-bodies still occurred in non-phosphorylatable eIF2α mouse embryonal fibroblasts (MEFs) that are impaired in SG assembly. Studies of translation status by ribopuromycylation showed that P-body disassembly is independent of host translation shutoff, which requires the phosphorylation of eIF2α in the SFV- or CHIKV-infected cells. Labelling of newly synthesized RNA with bromo-UTP showed that host transcription shutoff correlated with P-body disassembly at the same early stage (3-4 h) after infection. However, inhibition of global transcription with actinomycin D (ActD) failed to disassemble P-bodies as effectively as the viruses did. Interestingly, blocking nuclear import with importazole led to an efficient P-bodies loss. Our data reveal that P-bodies are disassembled independently from SG formation at early stages of Old World alphavirus infection and that nuclear import is involved in the dynamic of P-bodies.
Topics: Alphavirus Infections; Animals; Arenaviruses, Old World; Cell Line; Eukaryotic Initiation Factor-2; Humans; Mice; Protein Biosynthesis; RNA Processing, Post-Transcriptional; RNA, Messenger; Virus Replication
PubMed: 31418676
DOI: 10.1099/jgv.0.001310 -
Advances in Experimental Medicine and... 2013Deadenylation is the major step in triggering mRNA decay and results in mRNA translation inhibition in eukaryotic cells. Therefore, it is plausible that deadenylation... (Review)
Review
Deadenylation is the major step in triggering mRNA decay and results in mRNA translation inhibition in eukaryotic cells. Therefore, it is plausible that deadenylation also induces the mRNP remodeling required for formation of GW bodies or RNA processing bodies (P-bodies), which harbor translationally silenced mRNPs. In this chapter, we discuss several examples to illustrate the roles of deadenylation in regulating gene expression. We highlight several lines of evidence indicating that even though non-translatable mRNPs may be prepared and/or assembled into P-bodies in different ways, deadenylation is always a necessary, and perhaps the earliest, step in mRNA decay pathways that enable mRNP remodeling required for P-body formation. Thus, deadenylation and the participating deadenylases are not simply required for preparing mRNA substrates; they play an indispensable role both structurally and functionally in P-body formation and regulation.
Topics: Animals; Carrier Proteins; Drosophila Proteins; Exoribonucleases; Gene Expression Regulation; Humans; MicroRNAs; Microbodies; Protein Biosynthesis; RNA Interference; RNA Stability; RNA, Messenger; Ribonucleases; Ribonucleoproteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 23224971
DOI: 10.1007/978-1-4614-5107-5_11 -
Liver International : Official Journal... Mar 2018Over the last few years, many reports have defined several types of RNA cell granules composed of proteins and messenger RNA (mRNA) that regulate gene expression on a... (Review)
Review
Over the last few years, many reports have defined several types of RNA cell granules composed of proteins and messenger RNA (mRNA) that regulate gene expression on a post-transcriptional level. Processing bodies (P-bodies) and stress granules (SGs) are among the best-known RNA granules, only detectable when they accumulate into very dynamic cytosolic foci. Recently, a tight association has been found between positive-stranded RNA viruses, including hepatitis C virus (HCV), and these granules. The present article offers a comprehensive review on the complex and paradoxical relationship between HCV, P-bodies and SGs from a translational perspective. Despite the fact that components of P-bodies and SGs have assiduously controlled mRNA expression, either by sequestration or degradation, for thousands of years, HCV has learned how to dangerously exploit certain of them for its own benefit in an endless biological war. Thus, HCV has gained the ability to hack ancient host machineries inherited from prokaryotic times. While P-bodies and SGs are crucial to the HCV cycle, in the interferon-free era we still lack detailed knowledge of the mechanisms involved, processes that may underlie the long-term complications of HCV infection.
Topics: Cell Line; Cytoplasmic Granules; Gene Expression; Hepacivirus; Humans; Microscopy, Fluorescence; RNA, Messenger; RNA, Viral; Virus Replication
PubMed: 28782251
DOI: 10.1111/liv.13541 -
Proceedings of the National Academy of... Mar 2019Germinated plant seeds buried in soil undergo skotomorphogenic development before emergence to reach the light environment. Young seedlings transitioning from dark to...
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 in young 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 an mutant defective in p-body formation (Decapping 5; ) showed reduced fitness under both dark and light conditions. Comparative transcriptome and translatome analyses of wild-type and seedlings 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.
Topics: Arabidopsis; Arabidopsis Proteins; Co-Repressor Proteins; Darkness; Endoribonucleases; Gene Expression Regulation, Plant; Indoleacetic Acids; Light; Morphogenesis; Protochlorophyllide; RNA, Messenger; Seedlings; Transcriptome
PubMed: 30850529
DOI: 10.1073/pnas.1900084116 -
Cell Death & Disease Mar 2021The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically...
The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.
Topics: Adipogenesis; Animals; DEAD-box RNA Helicases; Humans; Mice; Proto-Oncogene Proteins; RNA Stability; Transfection
PubMed: 33731683
DOI: 10.1038/s41419-021-03537-7 -
Biochemical Society Transactions Feb 2010P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and... (Review)
Review
P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and trypanosomes. At the molecular level, P-bodies are dynamic aggregates of specific mRNAs and proteins that serve a dual function: first, they harbour mRNAs that are translationally silenced, and such mRNA can exit again from P-bodies to re-engage in translation. Secondly, P-bodies recruit mRNAs that are targeted for deadenylation and degradation by the decapping/Xrn1 pathway. Whereas certain proteins are core constituents of P-bodies, others involved in recognizing short-lived mRNAs can only be trapped in P-bodies when mRNA decay is attenuated. This reflects the very transient interactions by which many proteins associate with P-bodies. In the present review, we summarize recent findings on the function, assembly and motility of P-bodies. An updated list of proteins and RNAs that localize to P-bodies will help in keeping track of this fast-growing field.
Topics: Animals; Gene Silencing; Inclusion Bodies; MicroRNAs; Microtubules; RNA Caps; RNA Stability; RNA, Messenger; RNA-Binding Proteins
PubMed: 20074068
DOI: 10.1042/BST0380242 -
Science (New York, N.Y.) Jan 2020Tethered interactions between the endoplasmic reticulum (ER) and other membrane-bound organelles allow for efficient transfer of ions and/or macromolecules and provide a...
Tethered interactions between the endoplasmic reticulum (ER) and other membrane-bound organelles allow for efficient transfer of ions and/or macromolecules and provide a platform for organelle fission. Here, we describe an unconventional interface between membraneless ribonucleoprotein granules, such as processing bodies (P-bodies, or PBs) and stress granules, and the ER membrane. We found that PBs are tethered at molecular distances to the ER in human cells in a tunable fashion. ER-PB contact and PB biogenesis were modulated by altering PB composition, ER shape, or ER translational capacity. Furthermore, ER contact sites defined the position where PB and stress granule fission occurs. We thus suggest that the ER plays a fundamental role in regulating the assembly and disassembly of membraneless organelles.
Topics: Cell Line; Cytoplasmic Granules; Endoplasmic Reticulum; Humans; Intracellular Membranes; Organelles; Oxidative Stress; Protein Biosynthesis; Protein Unfolding; RNA, Messenger; Ribonucleoproteins
PubMed: 32001628
DOI: 10.1126/science.aay7108 -
Biochemical Society Transactions Oct 2016Intracellular compartments are necessary for the regulation of many biochemical processes that ensure cell survival, growth and proliferation. Compartmentalisation is... (Review)
Review
Intracellular compartments are necessary for the regulation of many biochemical processes that ensure cell survival, growth and proliferation. Compartmentalisation is commonly achieved in organelles with defined lipid membranes, such as mitochondria, endoplasmic reticulum or the Golgi apparatus. While these organelles are responsible for many localised biochemical processes, recent evidence points to another class of compartments that lack membrane boundaries. The structure and content of these bodies depend on their function and subcellular localisation, but they mainly incorporate proteins and RNA. Examples of these ribonucleoprotein bodies (RNPBs) include eukaryotic mRNA processing bodies (P-bodies) and stress granules (SGs). While most of these structures have been widely studied for their capacity to bind, store and process mRNAs under different conditions, their biological functions and physical properties are poorly understood. Recent intriguing data suggest that liquid-liquid phase separation (LLPS) represents an important mechanism seeding the formation and defining the function of RNPBs. In this review, we discuss how LLPS is transforming our ideas about the biological functions of SGs and P-bodies and their link to diseases.
Topics: Animals; Cytoplasmic Granules; Cytoskeleton; Humans; Models, Biological; Protein Stability; RNA Stability; RNA, Messenger; RNA-Binding Proteins; Ribonucleoproteins
PubMed: 27911723
DOI: 10.1042/BST20160117 -
Methods in Enzymology 2007The packaging of cytoplasmic mRNA into discrete RNA granules regulates gene expression by delaying the translation of specific transcripts. Specialized RNA granules... (Review)
Review
The packaging of cytoplasmic mRNA into discrete RNA granules regulates gene expression by delaying the translation of specific transcripts. Specialized RNA granules found in germ cells direct the timing of maternal mRNA translation to promote germ cell development in the early embryo and establish the germ line for the next generation. Similarly, select neuronal mRNA transcripts are packaged into translationally inert RNA granules, transported to sites where their protein products are required, and only then activated and translated. Following translation, however, newly inactivated mRNAs released from polysomes can also be packaged into dynamic, transient structures known as stress granules (SGs) and processing bodies (PBs). Stress granules are composed largely of stalled preinitiation complexes, and contain mRNA, small ribosomal subunits, eIF3, eIF4E, eIF4G, and PABP, as their core components. PBs are associated with mRNA decay and contain the decapping enzymes DCP1/2, the 5' to 3' exonuclease Xrn1, the Lsm proteins (1-7), and the scaffolding proteins hedls/GE-1 and GW182. Both SGs and PBs contain mRNA, eIF4E, microRNAs and argonaute proteins, and various regulators of mRNA stability and translation (TTP, RCK/p54, and CPEB). Thus, SGs and PBs share some protein and mRNA components, but also contain a number of unique markers specific to each structure. We describe markers and staining procedures used to identify these distinct types of RNA granules, describe conditions that promote their assembly and disassembly, and establish YB-1 as a useful marker of SGs and PBs.
Topics: Animals; Cytoplasmic Granules; Humans; Immunohistochemistry; Inclusion Bodies; Mammals; RNA; RNA Processing, Post-Transcriptional; RNA-Binding Proteins; Transfection
PubMed: 17923231
DOI: 10.1016/S0076-6879(07)31005-7 -
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