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1.
Mol Cell ; 83(24): 4494-4508.e6, 2023 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-38016476

RESUMO

In the cytoplasm, mRNAs are dynamically partitioned into translating and non-translating pools, but the mechanism for this regulation has largely remained elusive. Here, we report that m6A regulates mRNA partitioning between polysome and P-body where a pool of non-translating mRNAs resides. By quantifying the m6A level of polysomal and cytoplasmic mRNAs with m6A-LAIC-seq and m6A-LC-MS/MS in HeLa cells, we observed that polysome-associated mRNAs are hypo-m6A-methylated, whereas those enriched in P-body are hyper-m6A-methylated. Downregulation of the m6A writer METTL14 enhances translation by switching originally hyper-m6A-modified mRNAs from P-body to polysome. Conversely, by proteomic analysis, we identify a specific m6A reader IGF2BP3 enriched in P-body, and via knockdown and molecular tethering assays, we demonstrate that IGF2BP3 is both necessary and sufficient to switch target mRNAs from polysome to P-body. These findings suggest a model for the dynamic regulation of mRNA partitioning between the translating and non-translating pools in an m6A-dependent manner.


Assuntos
Adenina , Corpos de Processamento , Biossíntese de Proteínas , Proteínas de Ligação a RNA , Humanos , Cromatografia Líquida , Células HeLa , Polirribossomos/genética , Proteômica , RNA Mensageiro/genética , Espectrometria de Massas em Tandem , Adenina/análogos & derivados , Adenina/metabolismo , Proteínas de Ligação a RNA/metabolismo
2.
Semin Cell Dev Biol ; 157: 24-32, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37407370

RESUMO

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.


Assuntos
Corpos de Processamento , Proteínas de Ligação a RNA , Animais , Proteínas de Ligação a RNA/genética , Células Germinativas/metabolismo , RNA Mensageiro/genética , Regulação da Expressão Gênica , Mamíferos/genética
3.
Proc Natl Acad Sci U S A ; 120(6): e2114747120, 2023 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-36716374

RESUMO

Biomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs) are a type of biomolecular condensate necessary for local protein synthesis and are involved in synaptic plasticity and long-term memory. Most of the proteins in RNPs possess low-complexity motifs (LCM), allowing for increased promiscuity of protein-protein interactions. Here, we describe the importance of protein-protein interactions mediated by the LCM of RNA-binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3). CPEB3 is necessary for long-term synaptic plasticity and memory persistence, but the mechanisms involved are still not completely elucidated. We now present key mechanisms involved in its regulation of synaptic plasticity. We find that CPEB3-LCM plays a role in appropriate local protein synthesis of messenger ribonucleic acid (mRNA) targets, through crucial protein-protein interactions that drive localization to neuronal Decapping protein 1 (DCP1)-bodies. Translation-promoting CPEB3 and translation-inhibiting CPEB1 are packaged into neuronal RNP granules immediately after chemical long-term potentiation is induced, but only translation-promoting CPEB3 is repackaged to these organelles at later time points. This localization to neuronal RNP granules is critical for functional influence on translation as well as overall local protein synthesis (measured as α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) insertion into the membrane and localization to the synapse). We therefore conclude that protein-protein interaction between the LCM of CPEB3 plays a critical role in local protein synthesis by utilizing neuronal RNP granules.


Assuntos
Memória de Longo Prazo , Neurônios , Neurônios/metabolismo , RNA Mensageiro/metabolismo , Plasticidade Neuronal/fisiologia , Proteínas de Ligação a RNA/metabolismo , Grânulos Citoplasmáticos/metabolismo
4.
Trends Biochem Sci ; 45(9): 764-778, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32475683

RESUMO

Ribonucleoprotein (RNP) granules are RNA-protein assemblies that are involved in multiple aspects of RNA metabolism and are linked to memory, development, and disease. Some RNP granules form, in part, through the formation of intermolecular RNA-RNA interactions. In vitro, such trans RNA condensation occurs readily, suggesting that cells require mechanisms to modulate RNA-based condensation. We assess the mechanisms of RNA condensation and how cells modulate this phenomenon. We propose that cells control RNA condensation through ATP-dependent processes, static RNA buffering, and dynamic post-translational mechanisms. Moreover, perturbations in these mechanisms can be involved in disease. This reveals multiple cellular mechanisms of kinetic and thermodynamic control that maintain the proper distribution of RNA molecules between dispersed and condensed forms.


Assuntos
Grânulos Citoplasmáticos , RNA , Grânulos Citoplasmáticos/metabolismo , Organelas/metabolismo , Processamento de Proteína Pós-Traducional , RNA/metabolismo , Ribonucleoproteínas/genética
5.
Development ; 148(22)2021 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-35020877

RESUMO

Numerous motors of the Kinesin family contribute to plus-end-directed microtubule transport. However, almost all transport towards the minus-end of microtubules involves Dynein. Understanding the mechanism by which Dynein transports this vast diversity of cargo is the focus of intense research. In selected cases, adaptors that link a particular cargo with Dynein have been identified. However, the sheer diversity of cargo suggests that additional adaptors must exist. We used the Drosophila egg chamber as a model to address this issue. Within egg chambers, Egalitarian is required for linking mRNA with Dynein. However, in the absence of Egalitarian, Dynein transport into the oocyte is severely compromised. This suggests that additional cargoes might be linked to Dynein in an Egalitarian-dependent manner. We therefore used proximity biotin ligation to define the interactome of Egalitarian. This approach yielded several novel interacting partners, including P body components and proteins that associate with Dynein in mammalian cells. We also devised and validated a nanobody-based proximity biotinylation strategy that can be used to define the interactome of any GFP-tagged protein.


Assuntos
Proteínas de Drosophila/genética , Dineínas/genética , Cinesinas/genética , Oócitos/crescimento & desenvolvimento , Animais , Biotina/química , Polaridade Celular/genética , Drosophila melanogaster/genética , Dineínas/química , Regulação da Expressão Gênica/genética , Cinesinas/química , Microtúbulos/genética , Oócitos/metabolismo , Corpos de Processamento/genética , Mapas de Interação de Proteínas/genética , Transporte Proteico , RNA Mensageiro/genética
6.
Mol Cell ; 62(6): 943-957, 2016 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-27315556

RESUMO

Signals and posttranslational modifications regulating the decapping step in mRNA degradation pathways are poorly defined. In this study we reveal the importance of K63-linked ubiquitylation for the assembly of decapping factors, P-body formation, and constitutive decay of instable mRNAs encoding mediators of inflammation by various experimental approaches. K63-branched ubiquitin chains also regulate IL-1-inducible phosphorylation of the P-body component DCP1a. The E3 ligase TRAF6 binds to DCP1a and indirectly regulates DCP1a phosphorylation, expression of decapping factors, and gene-specific mRNA decay. Mutation of six C-terminal lysines of DCP1a suppresses decapping activity and impairs the interaction with the mRNA decay factors DCP2, EDC4, and XRN1, but not EDC3, thus remodeling P-body architecture. The usage of ubiquitin chains for the proper assembly and function of the decay-competent mammalian decapping complex suggests an additional layer of control to allow a coordinated function of decapping activities and mRNA metabolism in higher eukaryotes.


Assuntos
Endorribonucleases/metabolismo , Lisina/metabolismo , Capuzes de RNA/metabolismo , Estabilidade de RNA , RNA Mensageiro/metabolismo , Fator 6 Associado a Receptor de TNF/metabolismo , Transativadores/metabolismo , Ubiquitinação , Animais , Linhagem Celular Tumoral , Endorribonucleases/genética , Exorribonucleases/metabolismo , Células HEK293 , Humanos , Interleucina-1alfa/farmacologia , Peptídeos e Proteínas de Sinalização Intracelular , Camundongos , Proteínas Associadas aos Microtúbulos/metabolismo , Mutação , Fosforilação , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas/metabolismo , Capuzes de RNA/genética , Estabilidade de RNA/efeitos dos fármacos , RNA Mensageiro/genética , Receptores de Interleucina-1/agonistas , Receptores de Interleucina-1/genética , Receptores de Interleucina-1/metabolismo , Fator 6 Associado a Receptor de TNF/genética , Fatores de Tempo , Transativadores/genética , Transfecção , Ubiquitinação/efeitos dos fármacos
7.
Cell Mol Life Sci ; 80(9): 247, 2023 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-37578641

RESUMO

Controlled mRNA storage and stability is essential for oocyte meiosis and early embryonic development. However, how to regulate mRNA storage and stability in mammalian oogenesis remains elusive. Here we showed that LSM14B, a component of membraneless compartments including P-body-like granules and mitochondria-associated ribonucleoprotein domain (MARDO) in germ cell, is indispensable for female fertility. To reveal loss of LSM14B disrupted primordial follicle assembly and caused mRNA reduction in non-growing oocytes, which was concomitant with the impaired assembly of P-body-like granules. 10× Genomics single-cell RNA-sequencing and immunostaining were performed. Meanwhile, we conducted RNA-seq analysis of GV-stage oocytes and found that Lsm14b deficiency not only impaired the maternal mRNA accumulation but also disrupted the translation in fully grown oocytes, which was closely associated with dissolution of MARDO components. Moreover, Lsm14b-deficient oocytes reassembled a pronucleus containing decondensed chromatin after extrusion of the first polar body, through compromising the activation of maturation promoting factor, while the defects were restored via WEE1/2 inhibitor. Together, our findings reveal that Lsm14b plays a pivotal role in mammalian oogenesis by specifically controlling of oocyte mRNA storage and stability.


Assuntos
Oócitos , Oogênese , Animais , Feminino , RNA Mensageiro/genética , Oogênese/genética , Folículo Ovariano , Meiose/genética , Fertilidade/genética , Mamíferos
8.
Biol Reprod ; 109(1): 73-82, 2023 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-37067907

RESUMO

Oocyte maturation and subsequent ovulation during the reproductive lifespan ensure long-term reproduction in mammalian females. This is achieved by tight regulation for the maintenance and growth of primordial follicles. However, the underlying mechanisms remain unsolved. We herein report that posttranscriptional gene regulation mediated by an RNA helicase, DEAD-box helicase 6 (DDX6), and phosphoinositide-3-kinase (PI3K)-AKT signaling exhibits an antagonistic interaction in mouse primordial follicles. DDX6 forms P-body-like cytoplasmic foci in oocytes, which colocalize to a P-body component, DCP1A. Interestingly, the P-body-like granules predominantly assemble in primordial follicles, but disperse once follicle growth is initiated, suggesting that they play a role in the maintenance of primordial follicles. Oocyte-specific knockout of Ddx6 using Gdf9-iCre revealed that Ddx6-deficient oocytes are defective in foci assembly and are abnormally enlarged, resulting in premature depletion of primordial follicles. These results indicate that DDX6 is required to maintain primordial follicles. The abnormal oocyte enlargement is because of enhanced PI3K-AKT signaling, a pivotal signaling pathway in the growth of primordial follicles. Conversely, the forced activation of PI3K-AKT signaling by knocking out Pten disassembles P-body-like granules in primordial follicles. These data suggest that DDX6 and PI3K-AKT signaling mutually antagonize the assembly of P-body-like granules and the growth of primordial follicles. We propose this mutual antagonism as an oocyte-intrinsic mechanism controlling the maintenance and growth of primordial follicles, ensuring the longevity of female reproduction.


Assuntos
Fosfatidilinositol 3-Quinases , Proteínas Proto-Oncogênicas c-akt , Feminino , Camundongos , Animais , Proteínas Proto-Oncogênicas c-akt/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Fosfatidilinositol 3-Quinase/metabolismo , Oócitos/metabolismo , Transdução de Sinais/fisiologia , RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , Mamíferos/metabolismo , Proteínas Proto-Oncogênicas/metabolismo
9.
RNA ; 2021 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-33931500

RESUMO

Severe environmental stress can trigger a plethora of physiological changes and, in the process, significant cytoplasmic reorganization. Stress-activated RNA-protein granules have been implicated in this cellular overhaul by sequestering pre-existing mRNAs and influencing their fates during and after stress acclimation. While the composition and dynamics of stress-activated granule formation has been well studied, their function and impact on RNA-cargo has remained murky. Several recent studies challenge the view that these granules degrade and silence mRNAs present at the onset of stress and instead suggest new roles for these structures in mRNA storage, transit, and inheritance. Here we discuss recent evidence for revised models of stress-activated granule functions and the role of these granules in stress survival and recovery.

10.
J Virol ; 96(6): e0000222, 2022 03 23.
Artigo em Inglês | MEDLINE | ID: mdl-35107372

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has the largest RNA genome, approximately 30 kb, among RNA viruses. The DDX DEAD box RNA helicase is a multifunctional protein involved in all aspects of RNA metabolism. Therefore, host RNA helicases may regulate and maintain such a large viral RNA genome. In this study, I investigated the potential role of several host cellular RNA helicases in SARS-CoV-2 infection. Notably, DDX21 knockdown markedly accumulated intracellular viral RNA and viral production, as well as viral infectivity of SARS-CoV-2, indicating that DDX21 strongly restricts the SARS-CoV-2 infection. In addition, MOV10 RNA helicase also suppressed the SARS-CoV-2 infection. In contrast, DDX1, DDX5, and DDX6 RNA helicases were required for SARS-CoV-2 replication. Indeed, SARS-CoV-2 infection dispersed the P-body formation of DDX6 and MOV10 RNA helicases as well as XRN1 exonuclease, while the viral infection did not induce stress granule formation. Accordingly, the SARS-CoV-2 nucleocapsid (N) protein interacted with DDX1, DDX3, DDX5, DDX6, DDX21, and MOV10 and disrupted the P-body formation, suggesting that SARS-CoV-2 N hijacks DDX6 to carry out viral replication. Conversely, DDX21 and MOV10 restricted SARS-CoV-2 infection through an interaction of SARS-CoV-2 N with host cellular RNA helicases. Altogether, host cellular RNA helicases seem to regulate the SARS-CoV-2 infection. IMPORTANCE SARS-CoV-2 has a large RNA genome, of approximately 30 kb. To regulate and maintain such a large viral RNA genome, host RNA helicases may be involved in SARS-CoV-2 replication. In this study, I have demonstrated that DDX21 and MOV10 RNA helicases limit viral infection and replication. In contrast, DDX1, DDX5, and DDX6 are required for SARS-CoV-2 infection. Interestingly, SARS-CoV-2 infection disrupted P-body formation and attenuated or suppressed stress granule formation. Thus, SARS-CoV-2 seems to hijack host cellular RNA helicases to play a proviral role by facilitating viral infection and replication and by suppressing the host innate immune system.


Assuntos
COVID-19 , Interações entre Hospedeiro e Microrganismos , RNA Helicases , RNA Viral , COVID-19/enzimologia , Interações entre Hospedeiro e Microrganismos/fisiologia , Humanos , RNA Helicases/genética , RNA Helicases/metabolismo , RNA Viral/metabolismo , SARS-CoV-2 , Replicação Viral/fisiologia
11.
EMBO Rep ; 22(7): e51342, 2021 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-33973704

RESUMO

PIWI-interacting RNAs (piRNAs) guide PIWI proteins to silence transposable elements and safeguard fertility in germ cells. Many protein factors required for piRNA biogenesis localize to perinuclear ribonucleoprotein (RNP) condensates named nuage, where target silencing and piRNA amplification are thought to occur. In mice, some of the piRNA factors are found in discrete cytoplasmic foci called processing bodies (P-bodies). However, the dynamics and biological significance of such compartmentalization of the piRNA pathway remain unclear. Here, by analyzing the subcellular localization of functional mutants of piRNA factors, we show that piRNA factors are actively compartmentalized into nuage and P-bodies in silkworm cells. Proper demixing of nuage and P-bodies requires target cleavage by the PIWI protein Siwi and ATP hydrolysis by the DEAD-box helicase BmVasa, disruption of which leads to promiscuous overproduction of piRNAs deriving from non-transposable elements. Our study highlights a role of dynamic subcellular compartmentalization in ensuring the fidelity of piRNA biogenesis.


Assuntos
Bombyx , Proteínas de Drosophila , Animais , Proteínas Argonautas/genética , Bombyx/genética , Bombyx/metabolismo , Elementos de DNA Transponíveis , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Células Germinativas/metabolismo , Camundongos , RNA Interferente Pequeno/genética , Ribonucleoproteínas
12.
RNA Biol ; 20(1): 573-587, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-37553798

RESUMO

Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte's posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of oskar mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup's recruitment to oskar mRNA and indispensable for oskar's translational repression. We now report that this Bruno1-Cup interaction leads to precise oskar mRNA regulation during early oogenesis and, importantly, the two proteins mutually influence each other's mRNA expression and protein distribution in the egg chamber. We show that these factors stably associate with oskar mRNA in vivo. Cup associates with oskar mRNA without Bruno1, while surprisingly Bruno1's stable association with oskar mRNA depends on Cup. We demonstrate that the essential factor for oskar mRNA repression in early oogenesis is Cup, not Bruno1. Furthermore, we find that Cup is a key P-body component that maintains functional P-body morphology during oogenesis and is necessary for oskar mRNA's association with P-bodies. Therefore, Cup drives the translational repression and stability of oskar mRNA. These experimental results point to a regulatory feedback loop between Bruno 1 and Cup in early oogenesis that appears crucial for oskar mRNA to reach the posterior pole and its expression in the egg chamber for accurate embryo development.


Assuntos
Proteínas de Drosophila , Drosophila melanogaster , Oogênese , Animais , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Oócitos , Oogênese/genética , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
13.
J Am Soc Nephrol ; 33(11): 2040-2058, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35918145

RESUMO

BACKGROUND: Ureteral obstruction is marked by disappearance of the vasopressin-dependent water channel aquaporin-2 (AQP2) in the renal collecting duct and polyuria upon reversal. Most studies of unilateral ureteral obstruction (UUO) models have examined late time points, obscuring the early signals that trigger loss of AQP2. METHODS: We performed RNA-Seq on microdissected rat cortical collecting ducts (CCDs) to identify early signaling pathways after establishment of UUO. RESULTS: Vasopressin V2 receptor (AVPR2) mRNA was decreased 3 hours after UUO, identifying one cause of AQP2 loss. Collecting duct principal cell differentiation markers were lost, including many not regulated by vasopressin. Immediate early genes in CCDs were widely induced 3 hours after UUO, including Myc, Atf3, and Fos (confirmed at the protein level). Simultaneously, expression of NF-κB signaling response genes known to repress Aqp2 increased. RNA-Seq for CCDs at an even earlier time point (30 minutes) showed widespread mRNA loss, indicating a "stunned" profile. Immunocytochemical labeling of markers of mRNA-degrading P-bodies DDX6 and 4E-T indicated an increase in P-body formation within 30 minutes. CONCLUSIONS: Immediately after establishment of UUO, collecting ducts manifest a stunned state with broad disappearance of mRNAs. Within 3 hours, there is upregulation of immediate early and inflammatory genes and disappearance of the V2 vasopressin receptor, resulting in loss of AQP2 (confirmed by lipopolysaccharide administration). The inflammatory response seen rapidly after UUO establishment may be relevant to both UUO-induced polyuria and long-term development of fibrosis in UUO kidneys.


Assuntos
Túbulos Renais Coletores , Obstrução Ureteral , Ratos , Animais , Aquaporina 2/genética , Aquaporina 2/metabolismo , Obstrução Ureteral/complicações , Obstrução Ureteral/metabolismo , Poliúria/metabolismo , Rim/metabolismo , Vasopressinas , RNA Mensageiro/metabolismo , Túbulos Renais Coletores/metabolismo
14.
J Cell Sci ; 133(24)2020 12 29.
Artigo em Inglês | MEDLINE | ID: mdl-33262313

RESUMO

Defective intracellular trafficking and export of microRNAs (miRNAs) have been observed in growth-retarded mammalian cells having impaired mitochondrial potential and dynamics. Here, we found that uncoupling protein 2 (Ucp2)-mediated depolarization of mitochondrial membrane also results in progressive sequestration of miRNAs within polysomes and lowers their release via extracellular vesicles. Interestingly, the impaired miRNA-trafficking process in growth-retarded human cells could be reversed in the presence of Genipin, an inhibitor of Ucp2. Mitochondrial detethering of endoplasmic reticulum (ER), observed in cells with depolarized mitochondria, was found to be responsible for defective compartmentalization of translation initiation factor eIF4E to polysomes attached to ER. This caused a retarded translation process accompanied by enhanced retention of miRNAs and target mRNAs within ER-attached polysomes to restrict extracellular export of miRNAs. Reduced compartment-specific activity of the mammalian target of rapamycin complex 1 (mTORC1), the master regulator of protein synthesis, in cells with defective mitochondria or detethered ER, caused reduced phosphorylation of eIF4E-BP1 and prevented eIF4E targeting to ER-attached polysomes and miRNA export. These data suggest how mitochondrial membrane potential and dynamics, by affecting mTORC1 activity and compartmentalization, determine the subcellular localization and export of miRNAs.


Assuntos
Fator de Iniciação 4E em Eucariotos , MicroRNAs , Fator de Iniciação 4E em Eucariotos/metabolismo , Humanos , Alvo Mecanístico do Complexo 1 de Rapamicina/genética , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Mitocôndrias/genética , Mitocôndrias/metabolismo , Fosforilação , Polirribossomos/metabolismo
15.
Dev Growth Differ ; 64(9): 537-547, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36353942

RESUMO

The transcriptome dynamically changes via several transcriptional and post-transcriptional mechanisms. RNA-binding proteins contribute to such mechanisms to regulate the cellular status. DDX6 is one such protein and a core component of processing bodies (P-bodies), membrane-less cytosolic substructures where RNA and proteins localize and are functionally regulated. Despite the importance of DDX6, owing to the lack of tightly controlled methods for protein knockdown, it was difficult to assess in high time resolution how its depletion exactly affects the P-body assembly structure. Therefore, we adopted an advanced protein degradation method, the auxin-induced degron (AID) system, to degrade DDX6 acutely in ES cells. By introducing AID-tagged DDX6 and the E3 ligase subunit of OsTIR1 into ES cells, we successfully degraded DDX6 following auxin analog (indole-3-acetic acid, IAA) treatment. The degradation rate of DDX6 was slower than that of the cytosolic reporter protein EGFP but was enhanced by increasing the OsTIR1 dosage. Lastly, we confirmed that a substantial portion of P-bodies disappears around the time of 1 hr after IAA addition consistent with DDX6 depletion detected by western blot. In accordance with this, we detected transcriptome changes by 6 hr after IAA treatment. Therefore, we demonstrated the applicability of the AID method to gain insight into the function of P-bodies and their protein components.


Assuntos
Corpos de Processamento , RNA , Proteólise , Proteínas de Ligação a RNA , Ácidos Indolacéticos/farmacologia
16.
Int J Mol Sci ; 23(13)2022 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-35806385

RESUMO

The condensation of nuclear promyelocytic leukemia bodies, cytoplasmic P-granules, P-bodies (PBs), and stress granules is reversible and dynamic via liquid-liquid phase separation. Although each condensate comprises hundreds of proteins with promiscuous interactions, a few key scaffold proteins are required. Essential scaffold domain sequence elements, such as poly-Q, low-complexity regions, oligomerizing domains, and RNA-binding domains, have been evaluated to understand their roles in biomolecular condensation processes. However, the underlying mechanisms remain unclear. We analyzed Nst1, a PB-associated protein that can intrinsically induce PB component condensations when overexpressed. Various Nst1 domain deletion mutants with unique sequence distributions, including intrinsically disordered regions (IDRs) and aggregation-prone regions, were constructed based on structural predictions. The overexpression of Nst1 deletion mutants lacking the aggregation-prone domain (APD) significantly inhibited self-condensation, implicating APD as an oligomerizing domain promoting self-condensation. Remarkably, cells overexpressing the Nst1 deletion mutant of the polyampholyte domain (PD) in the IDR region (Nst1∆PD) rarely accumulate endogenous enhanced green fluorescent protein (EGFP)-tagged Dcp2. However, Nst1∆PD formed self-condensates, suggesting that Nst1 requires PD to interact with Dcp2, regardless of its self-condensation. In Nst1∆PD-overexpressing cells treated with cycloheximide (CHX), Dcp2, Xrn1, Dhh1, and Edc3 had significantly diminished condensation compared to those in CHX-treated Nst1-overexpressing cells. These observations suggest that the PD of the IDR in Nst1 functions as a hub domain interacting with other PB components.


Assuntos
Corpos de Processamento , Proteínas de Saccharomyces cerevisiae , Cicloeximida/farmacologia , Grânulos Citoplasmáticos/metabolismo , Domínios Proteicos , Proteínas de Saccharomyces cerevisiae/metabolismo
17.
Int J Mol Sci ; 23(5)2022 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-35269643

RESUMO

Membrane-less biomolecular compartmentalization is a core phenomenon involved in many physiological activities that occur ubiquitously in cells. Condensates, such as promyelocytic leukemia (PML) bodies, stress granules, and P-bodies (PBs), have been investigated to understand the process of membrane-less cellular compartmentalization. In budding yeast, PBs dispersed in the cytoplasm of exponentially growing cells rapidly accumulate in response to various stresses such as osmotic stress, glucose deficiency, and heat stress. In addition, cells start to accumulate PBs chronically in post-exponential phases. Specific protein-protein interactions are involved in accelerating PB accumulation in each circumstance, and discovering the regulatory mechanism for each is the key to understanding cellular condensation. Here, we demonstrate that Nst1 of budding yeast Saccharomyces cerevisiae is far more densely associated with PBs in post-exponentially growing phases from the diauxic shift to the stationary phase than during glucose deprivation of exponentially growing cells, while the PB marker Dcp2 exhibits a similar degree of condensation under these conditions. Similar to Edc3, ectopic Nst1 overexpression induces self-condensation and the condensation of other PB components, such as Dcp2 and Dhh1, which exhibit liquid-like properties. Altogether, these results suggest that Nst1 has the intrinsic potential for self-condensation and the condensation of other PB components, specifically in post-exponential phases.


Assuntos
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Citoplasma , RNA Helicases DEAD-box , Glucose , Corpos de Processamento , Proteínas de Saccharomyces cerevisiae/genética
18.
J Biol Chem ; 295(6): 1426-1438, 2020 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-31896577

RESUMO

Stress granules (SGs) are ribonucleoprotein (RNP) assemblies that form in eukaryotic cells as a result of limited translation in response to stress. SGs form during viral infection and are thought to promote the antiviral response because many viruses encode inhibitors of SG assembly. However, the antiviral endoribonuclease RNase L also alters SG formation, whereby only small punctate SG-like bodies that we term RNase L-dependent bodies (RLBs) form during RNase L activation. How RLBs relate to SGs and their mode of biogenesis is unknown. Herein, using immunofluorescence, live-cell imaging, and MS-based analyses, we demonstrate that RLBs represent a unique RNP granule with a protein and RNA composition distinct from that of SGs in response to dsRNA lipofection in human cells. We found that RLBs are also generated independently of SGs and the canonical dsRNA-induced SG biogenesis pathway, because RLBs did not require protein kinase R, phosphorylation of eukaryotic translation initiation factor 2 subunit 1 (eIF2α), the SG assembly G3BP paralogs, or release of mRNAs from ribosomes via translation elongation. Unlike the transient interactions between SGs and P-bodies, RLBs and P-bodies extensively and stably interacted. However, despite both RLBs and P-bodies exhibiting liquid-like properties, they remained distinct condensates. Taken together, these observations reveal that RNase L promotes the formation of a unique RNP complex that may have roles during the RNase L-mediated antiviral response.


Assuntos
Grânulos Citoplasmáticos/metabolismo , Endorribonucleases/metabolismo , Ribonucleoproteínas/metabolismo , Células A549 , Linhagem Celular , Grânulos Citoplasmáticos/ultraestrutura , Células HEK293 , Humanos
19.
FASEB J ; 34(7): 9433-9449, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32496609

RESUMO

Mov10 is a processing body (P-body) protein and an interferon-stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P-body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P-bodies. However, in HCV-infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P-body localization, helicase, and ATP-binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR-Cas9-based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.


Assuntos
Hepacivirus/fisiologia , Hepatite C/prevenção & controle , Interações Hospedeiro-Patógeno , RNA Helicases/metabolismo , Replicação Viral , Hepacivirus/isolamento & purificação , Hepatite C/patologia , Hepatite C/virologia , Humanos , RNA Helicases/genética
20.
EMBO Rep ; 20(12): e48251, 2019 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-31657143

RESUMO

Formation of primordial follicles is a fundamental, early process in mammalian oogenesis. However, little is known about the underlying mechanisms. We herein report that the RNA-binding proteins ELAVL2 and DDX6 are indispensable for the formation of quiescent primordial follicles in mouse ovaries. We show that Elavl2 knockout females are infertile due to defective primordial follicle formation. ELAVL2 associates with mRNAs encoding components of P-bodies (cytoplasmic RNP granules involved in the decay and storage of RNA) and directs the assembly of P-body-like granules by promoting the translation of DDX6 in oocytes prior to the formation of primordial follicles. Deletion of Ddx6 disturbs the assembly of P-body-like granules and severely impairs the formation of primordial follicles, indicating the potential importance of P-body-like granules in the formation of primordial follicles. Furthermore, Ddx6-deficient oocytes are abnormally enlarged due to misregulated PI3K-AKT signaling. Our data reveal that an ELAVL2-directed post-transcriptional network is essential for the formation of quiescent primordial follicles.


Assuntos
Proteína Semelhante a ELAV 2/metabolismo , Redes Reguladoras de Genes , Infertilidade Feminina/genética , Folículo Ovariano/metabolismo , Animais , Células Cultivadas , RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , Proteína Semelhante a ELAV 2/genética , Feminino , Camundongos , Oogênese , Folículo Ovariano/citologia , Proteínas Proto-Oncogênicas/genética , Proteínas Proto-Oncogênicas/metabolismo
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