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1.
Nucleic Acids Res ; 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38869059

ABSTRACT

Stress induces global stabilization of the mRNA poly(A) tail (PAT) and the assembly of untranslated poly(A)-tailed mRNA into mRNPs that accumulate in stress granules (SGs). While the mechanism behind stress-induced global PAT stabilization has recently emerged, the biological significance of PAT stabilization under stress remains elusive. Here, we demonstrate that stress-induced PAT stabilization is a prerequisite for SG formation. Perturbations in PAT length impact SG formation; PAT shortening, achieved by overexpressing mRNA deadenylases, inhibits SG formation, whereas PAT lengthening, achieved by overexpressing their dominant negative mutants or downregulating deadenylases, promotes it. PABPC1, which specifically binds to the PAT, is crucial for SG formation. Complementation analyses reveal that the PABC/MLLE domain of PABPC1, responsible for binding PAM2 motif-containing proteins, plays a key role. Among them, ataxin-2 is a known SG component. A dominant-negative approach reveals that the PAM2 motif of ataxin-2 is essential for SG formation. Notably, ataxin-2 increases stress sensitivity, lowering the threshold for SG formation, probably by promoting the aggregation of PABPC1-bound mRNA. The C-terminal region is responsible for the self-aggregation of ataxin-2. These findings underscore the critical roles of mRNA PAT, PABPC1 and ataxin-2 in SG formation and provide mechanistic insights into this process.

2.
Biochem Biophys Res Commun ; 719: 150103, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-38761636

ABSTRACT

The RNA-binding protein PKR serves as a crucial antiviral innate immune factor that globally suppresses translation by sensing viral double-stranded RNA (dsRNA) and by phosphorylating the translation initiation factor eIF2α. Recent findings have unveiled that single-stranded RNAs (ssRNAs), including in vitro transcribed (IVT) mRNA, can also bind to and activate PKR. However, the precise mechanism underlying PKR activation by ssRNAs, remains incompletely understood. Here, we developed a NanoLuc Binary Technology (NanoBiT)-based in vitro PKR dimerization assay to assess the impact of ssRNAs on PKR dimerization. Our findings demonstrate that, akin to double-stranded polyinosinic:polycytidylic acid (polyIC), an encephalomyocarditis virus (EMCV) RNA, as well as NanoLuc luciferase (Nluc) mRNA, can induce PKR dimerization. Conversely, homopolymeric RNA lacking secondary structure fails to promote PKR dimerization, underscoring the significance of secondary structure in this process. Furthermore, adenovirus VA RNA 1, another ssRNA, impedes PKR dimerization by competing with Nluc mRNA. Additionally, we observed structured ssRNAs capable of forming G-quadruplexes induce PKR dimerization. Collectively, our results indicate that ssRNAs have the ability to either induce or inhibit PKR dimerization, thus representing potential targets for the development of antiviral and anti-inflammatory agents.


Subject(s)
Encephalomyocarditis virus , Protein Multimerization , RNA, Double-Stranded , RNA, Viral , eIF-2 Kinase , eIF-2 Kinase/metabolism , eIF-2 Kinase/chemistry , Humans , RNA, Viral/metabolism , RNA, Viral/genetics , RNA, Viral/chemistry , Encephalomyocarditis virus/genetics , RNA, Double-Stranded/metabolism , RNA, Double-Stranded/chemistry , Poly I-C/pharmacology , Nucleic Acid Conformation
3.
Cells ; 12(19)2023 10 06.
Article in English | MEDLINE | ID: mdl-37830624

ABSTRACT

During early embryonic development, the RNA-binding protein CPEB mediates cytoplasmic polyadenylation and translational activation through a combinatorial code defined by the cy-toplasmic polyadenylation element (CPE) present in maternal mRNAs. However, in non-neuronal somatic cells, CPEB accelerates deadenylation to repress translation of the target, including c-myc mRNA, through an ill-defined cis-regulatory mechanism. Using RNA mutagenesis and electrophoretic mobility shift assays, we demonstrated that a combination of tandemly arranged consensus (cCPE) and non-consensus (ncCPE) cytoplasmic polyadenylation elements (CPEs) constituted a combinatorial code for CPEB-mediated c-myc mRNA decay. CPEB binds to cCPEs with high affinity (Kd = ~250 nM), whereas it binds to ncCPEs with low affinity (Kd > ~900 nM). CPEB binding to a cCPE enhances CPEB binding to the proximal ncCPE. In contrast, while a cCPE did not activate mRNA degradation, an ncCPE was essential for the induction of degradation, and a combination of a cCPE and ncCPEs further promoted degradation. Based on these findings, we propose a model in which the high-affinity binding of CPEB to the cCPE accelerates the binding of the second CPEB to the ncCPEs, resulting in the recruitment of deadenylases, acceleration of deadenylation, and repression of c-myc mRNAs.


Subject(s)
Oocytes , mRNA Cleavage and Polyadenylation Factors , mRNA Cleavage and Polyadenylation Factors/metabolism , Oocytes/metabolism , RNA/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/metabolism , Transcription Factors/metabolism , Humans
4.
STAR Protoc ; 4(2): 102340, 2023 May 26.
Article in English | MEDLINE | ID: mdl-37243600

ABSTRACT

Poly(A) tail metabolism contributes to post-transcriptional regulation of gene expression. Here, we present a protocol for analyzing intact mRNA poly(A) tail length using nanopore direct RNA sequencing, which excludes truncated RNAs from the measurement. We describe steps for preparing recombinant eIF4E mutant protein, purifying m7G- capped RNAs, library preparation, and sequencing. Resulting data can be used not only for expression profiling and poly(A) tail length estimation but also for detecting alternative splicing and polyadenylation events and RNA base modification. For complete details on the use and execution of this protocol, please refer to Ogami et al. (2022).1.

5.
Cell Rep ; 41(4): 111548, 2022 10 25.
Article in English | MEDLINE | ID: mdl-36288708

ABSTRACT

Translation of 5' terminal oligopyrimidine (TOP) mRNAs encoding the protein synthesis machinery is strictly regulated by an amino-acid-sensing mTOR pathway. However, its regulatory mechanism remains elusive. Here, we demonstrate that TOP mRNA translation positively correlates with its poly(A) tail length under mTOR active/amino-acid-rich conditions, suggesting that TOP mRNAs are post-transcriptionally controlled by poly(A) tail-length regulation. Consistent with this, the tail length of TOP mRNAs dynamically fluctuates in response to amino acid availability. The poly(A) tail shortens under mTOR active/amino-acid-rich conditions, whereas the long-tailed TOP mRNAs accumulate under mTOR inactive/amino-acid-starved (AAS) conditions. An RNA-binding protein, LARP1, is indispensable for the process. LARP1 interacts with non-canonical poly(A) polymerases and induces post-transcriptional polyadenylation of the target. Our findings illustrate that LARP1 contributes to the selective accumulation of TOP mRNAs with long poly(A) tails under AAS, resulting in accelerated ribosomal loading onto TOP mRNAs for the resumption of translation after AAS.


Subject(s)
Autoantigens , Ribonucleoproteins , RNA, Messenger/metabolism , Ribonucleoproteins/metabolism , Autoantigens/metabolism , TOR Serine-Threonine Kinases/metabolism , Ribosomes/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Polynucleotide Adenylyltransferase/genetics , Amino Acids/metabolism , Protein Biosynthesis
6.
J Biol Chem ; 298(5): 101844, 2022 05.
Article in English | MEDLINE | ID: mdl-35307347

ABSTRACT

Eukaryotic mRNAs possess a poly(A) tail at their 3'-end, to which poly(A)-binding protein C1 (PABPC1) binds and recruits other proteins that regulate translation. Enhanced poly(A)-dependent translation, which is also PABPC1 dependent, promotes cellular and viral proliferation. PABP-interacting protein 2A (Paip2A) effectively represses poly(A)-dependent translation by causing the dissociation of PABPC1 from the poly(A) tail; however, the underlying mechanism remains unknown. This study was conducted to investigate the functional mechanisms of Paip2A action by characterizing the PABPC1-poly(A) and PABPC1-Paip2A interactions. Isothermal titration calorimetry and NMR analyses indicated that both interactions predominantly occurred at the RNA recognition motif (RRM)2-RRM3 regions of PABPC1, which have comparable affinities for poly(A) and Paip2A (dissociation constant, Kd = 1 nM). However, the Kd values of isolated RRM2 were 200 and 4 µM in their interactions with poly(A) and Paip2A, respectively; Kd values of 5 and 1 µM were observed for the interactions of isolated RRM3 with poly(A) and Paip2A, respectively. NMR analyses also revealed that Paip2A can bind to the poly(A)-binding interfaces of the RRM2 and RRM3 regions of PABPC1. Based on these results, we propose the following functional mechanism for Paip2A: Paip2A initially binds to the RRM2 region of poly(A)-bound PABPC1, and RRM2-anchored Paip2A effectively displaces the RRM3 region from poly(A), resulting in dissociation of the whole PABPC1 molecule. Together, our findings provide insight into the translation repression effect of Paip2A and may aid in the development of novel anticancer and/or antiviral drugs.


Subject(s)
Poly A , Poly(A)-Binding Proteins , Protein Biosynthesis , RNA Recognition Motif , Poly A/metabolism , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , Protein Binding , RNA, Messenger/genetics , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism
7.
Biochem Biophys Res Commun ; 553: 9-16, 2021 05 14.
Article in English | MEDLINE | ID: mdl-33756349

ABSTRACT

The RNA-binding protein Ataxin-2 regulates translation and mRNA stability through cytoplasmic polyadenylation of the targets. Here we newly identified DDX6 as a positive regulator of the cytoplasmic polyadenylation. Analysis of Ataxin-2 interactome using LC-MS/MS revealed prominent interaction with the DEAD-box RNA helicase DDX6. DDX6 interacted with components of the Ataxin-2 polyadenylation machinery; Ataxin-2, PABPC1 and PAPD4. As in the case for Ataxin-2 downregulation, DDX6 downregulation led to an increase in Ataxin-2 target mRNAs with short poly(A) tails as well as a reduction in their protein expression. In contrast, Ataxin-2 target mRNAs with short poly(A) tails were decreased by the overexpression of Ataxin-2, which was compromised by the DDX6 downregulation. However, polyadenylation induced by Ataxin-2 tethering was not affected by the DDX6 downregulation. Taken together, these results suggest that DDX6 positively regulates Ataxin-2-induced cytoplasmic polyadenylation to maintain poly(A) tail length of the Ataxin-2 targets provably through accelerating binding of Ataxin-2 to the target mRNAs.


Subject(s)
Ataxin-2/metabolism , Cytoplasm/metabolism , DEAD-box RNA Helicases/metabolism , Polyadenylation , Polynucleotide Adenylyltransferase/metabolism , Proto-Oncogene Proteins/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Chromatography, Liquid , HEK293 Cells , Humans , Poly A/genetics , Poly A/metabolism , Protein Binding , Protein Interaction Maps , RNA Stability , RNA, Messenger/genetics , RNA, Messenger/metabolism , Tandem Mass Spectrometry
8.
J Biol Chem ; 295(47): 15810-15825, 2020 11 20.
Article in English | MEDLINE | ID: mdl-32989052

ABSTRACT

The RNA-binding protein Ataxin-2 binds to and stabilizes a number of mRNA sequences, including that of the transactive response DNA-binding protein of 43 kDa (TDP-43). Ataxin-2 is additionally involved in several processes requiring translation, such as germline formation, long-term habituation, and circadian rhythm formation. However, it has yet to be unambiguously demonstrated that Ataxin-2 is actually involved in activating the translation of its target mRNAs. Here we provide direct evidence from a polysome profile analysis showing that Ataxin-2 enhances translation of target mRNAs. Our recently established method for transcriptional pulse-chase analysis under conditions of suppressing deadenylation revealed that Ataxin-2 promotes post-transcriptional polyadenylation of the target mRNAs. Furthermore, Ataxin-2 binds to a poly(A)-binding protein PABPC1 and a noncanonical poly(A) polymerase PAPD4 via its intrinsically disordered region (amino acids 906-1095) to recruit PAPD4 to the targets. Post-transcriptional polyadenylation by Ataxin-2 explains not only how it activates translation but also how it stabilizes target mRNAs, including TDP-43 mRNA. Ataxin-2 is known to be a potent modifier of TDP-43 proteinopathies and to play a causative role in the neurodegenerative disease spinocerebellar ataxia type 2, so these findings suggest that Ataxin-2-induced cytoplasmic polyadenylation and activation of translation might impact neurodegeneration (i.e. TDP-43 proteinopathies), and this process could be a therapeutic target for Ataxin-2-related neurodegenerative disorders.


Subject(s)
Ataxin-2/metabolism , Cytoplasm/metabolism , Polyadenylation , Protein Biosynthesis , RNA Stability , RNA, Messenger/metabolism , Ataxin-2/genetics , Cytoplasm/genetics , HEK293 Cells , HeLa Cells , Humans , Poly(A)-Binding Protein I/genetics , Poly(A)-Binding Protein I/metabolism , Polynucleotide Adenylyltransferase/genetics , Polynucleotide Adenylyltransferase/metabolism , Protein Binding , RNA, Messenger/genetics , mRNA Cleavage and Polyadenylation Factors/genetics , mRNA Cleavage and Polyadenylation Factors/metabolism
9.
Viruses ; 12(2)2020 02 04.
Article in English | MEDLINE | ID: mdl-32033097

ABSTRACT

The 2'-5'-oligoadenylate synthetase (OAS)/RNase L system protects hosts against pathogenic viruses through cleavage of the exogenous single-stranded RNA. In this system, an evolutionally conserved RNA quality control factor Dom34 (known as Pelota (Pelo) in higher eukaryotes) forms a surveillance complex with RNase L to recognize and eliminate the exogenous RNA in a manner dependent on translation. Here, we newly identified that ATP-binding cassette sub-family E member 1 (ABCE1), which is also known as RNase L inhibitor (RLI), is involved in the regulation of exogenous RNA decay. ABCE1 directly binds to form a complex with RNase L and accelerates RNase L dimer formation in the absence of 2'-5' oligoadenylates (2-5A). Depletion of ABCE1 represses 2-5A-induced RNase L activation and stabilizes exogenous RNA to a level comparable to that seen in RNase L depletion. The increased half-life of the RNA by the single depletion of either protein is not significantly affected by the double depletion of both proteins, suggesting that RNase L and ABCE1 act together to eliminate exogenous RNA. Our results indicate that ABCE1 functions as a positive regulator of exogenous RNA decay rather than an inhibitor of RNase L.


Subject(s)
ATP-Binding Cassette Transporters/genetics , ATP-Binding Cassette Transporters/metabolism , Gene Expression Regulation , RNA Stability , Endoribonucleases/metabolism , HeLa Cells , Humans , Protein Binding
10.
J Biol Chem ; 295(2): 390-402, 2020 01 10.
Article in English | MEDLINE | ID: mdl-31792053

ABSTRACT

MicroRNA-122 (miR-122) is highly expressed in hepatocytes, where it plays an important role in regulating cholesterol and fatty acid metabolism, and it is also a host factor required for hepatitis C virus replication. miR-122 is selectively stabilized by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2 (also known as PAPD4 or TENT2). However, it is unclear how GLD-2 specifically stabilizes miR-122. Here, we show that QKI7 KH domain-containing RNA binding (QKI-7), one of three isoforms of the QKI proteins, which are members of the signal transduction and activation of RNA (STAR) family of RNA-binding proteins, is involved in miR-122 stabilization. QKI down-regulation specifically decreased the steady-state level of mature miR-122, but did not affect the pre-miR-122 level. We also found that QKI-7 uses its C-terminal region to interact with GLD-2 and its QUA2 domain to associate with the RNA-induced silencing complex protein Argonaute 2 (Ago2), indicating that the GLD-2-QKI-7 interaction recruits GLD-2 to Ago2. QKI-7 exhibited specific affinity to miR-122 and significantly promoted GLD-2-mediated 3' adenylation of miR-122 in vitro Taken together, our findings indicate that miR-122 binds Ago2-interacting QKI-7, which recruits GLD-2 for 3' adenylation and stabilization of miR-122.


Subject(s)
MicroRNAs/metabolism , Polynucleotide Adenylyltransferase/metabolism , RNA-Binding Proteins/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Argonaute Proteins/metabolism , Cell Line, Tumor , Humans , Polyadenylation , Protein Interaction Maps , RNA Stability
11.
Nagoya J Med Sci ; 81(2): 227-232, 2019 May.
Article in English | MEDLINE | ID: mdl-31239591

ABSTRACT

Neonates who swallow a considerable amount of maternal blood may exhibit vomiting and suckling disorder during the first few days of the postnatal period. Some clinicians treat these neonates with gastric lavage (GL) to prevent vomiting and the establishment of enteral feeding empirically, but there was no study assessing the effect of GL for neonates with coffee-ground emesis. We designed a multicenter randomized controlled trial to evaluate the efficacy and safety of GL in neonates with coffee-ground emesis. Vigorous neonates with birth weight ranging from 2500 g to 3999 g and gestational age between 37w0d and 41w6d who presented with coffee-ground emesis on more than twice and diagnosed as false melena, were divided into two groups using computerized randomization. We defined feeding intolerance (FI) as (1) ≥2 vomiting episodes in 4h or ≥3 episodes in 24h and/or (2) feeding failure on at least two occasions because of retching or poor sucking. Primary outcome is percentage of infants who present FI within 24 hours from admission. We also assessed the residual volumes, number of vomiting episodes, percentage of weight reduction at postnatal day 4, rates of body weight gain at 1 month of age, and peak serum total bilirubin value before discharge. To our knowledge, this is the first study to evaluate the safety and efficacy of GL for neonates with coffee-ground emesis. This trial is registered at UMIN Clinical Trials Registry as UMIN000026483.


Subject(s)
Gastric Lavage/methods , Vomiting/therapy , Birth Weight/physiology , Female , Humans , Infant, Newborn , Male , Meconium/chemistry , Prospective Studies , Software
13.
Jpn J Infect Dis ; 72(4): 237-242, 2019 Jul 24.
Article in English | MEDLINE | ID: mdl-30814460

ABSTRACT

Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are the leading causes of acute respiratory tract infection in children, and clinical manifestations of these virus infections are considered similar. To investigate the differences in clinical characteristics between HMPV and RSV infections in young children, we prospectively enrolled children < 3 years old who required hospitalization with acute respiratory tract infection due to HMPV or RSV at 10 hospitals in Japan. We enrolled 48 children with HMPV infection and 141 with RSV infection. Patients with HMPV infection were older than those with RSV infection. High-grade fever was more frequently observed in patients with HMPV infection, whereas no significant differences in respiratory symptoms were apparent. Abnormal serum lactate dehydrogenase values and consolidation shadows on chest X-ray were more frequently observed in patients with HMPV infection. During hospitalization, nasal mucus suction was more frequently required in patients with RSV infection. On the other hand, ß2-adrenergic agonists, corticosteroids, and leukotriene receptor antagonists were more frequently used in patients with HMPV infection. These findings suggest that HMPV and RSV infections show similar respiratory symptoms, but HMPV infection is more likely to lead to the development of pneumonia, at least among hospitalized young children.


Subject(s)
Metapneumovirus , Paramyxoviridae Infections/pathology , Respiratory Syncytial Virus Infections/pathology , Respiratory Syncytial Virus, Human , Respiratory Tract Infections/pathology , Respiratory Tract Infections/virology , Acute Disease , Child, Preschool , Female , Hospitalization , Humans , Infant , Japan , Male , Nasopharynx/virology , Paramyxoviridae Infections/therapy , Pneumonia, Viral/pathology , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , Respiratory Syncytial Virus Infections/therapy , Respiratory Tract Infections/therapy
14.
J Infect Chemother ; 25(5): 346-350, 2019 May.
Article in English | MEDLINE | ID: mdl-30718192

ABSTRACT

BACKGROUND: Mycoplasma pneumoniae pneumonia (MPP) is generally a self-limiting disease, but it may become refractory. It is thought that refractory MPP is linked to the excessive immunologic responses of the host. Consequently, the use of adjunctive systemic corticosteroids may have beneficial effects. In this study, we compared the effects of high- and low-dose corticosteroid therapy in a pediatric population with refractory MPP. METHODS: We retrospectively collected data from 91 pediatric MPP patients treated with adjunctive systemic corticosteroids between April 2014 and October 2016. The patients were divided into the following two groups: high-dose corticosteroid group (2 mg/kg/day or more of prednisolone equivalents; n = 38) and low-dose corticosteroid group (<2 mg/kg/day; n = 53). Additionally, we compared the number of febrile days post-corticosteroid administration. We used 25 paired patients in a propensity score matching analysis to correct for confounding factors both by age and by days (from onset till corticosteroid therapy initiation). RESULTS: We observed that in the high-dose corticosteroid group defervescence following corticosteroid therapy initiation was achieved significantly earlier and length of hospitalization was significantly shorter (0.8 ± 1.0 vs. 1.5 ± 1.4 days and 8.2 ± 2.4 vs. 10.7 ± 2.7 days, respectively). In the propensity score matching, we observed that significant differences in the length of fever following corticosteroid therapy initiation and hospitalization were still present. Further, neither of the groups developed corticosteroid-related adverse events. CONCLUSION: Our results suggest that patients with refractory MPP treated with high-dose corticosteroid could achieve defervescence earlier and have a shorter hospitalization.


Subject(s)
Fever/drug therapy , Glucocorticoids/administration & dosage , Mycoplasma pneumoniae/drug effects , Pneumonia, Mycoplasma/drug therapy , Child , Child, Preschool , Dose-Response Relationship, Drug , Drug Resistance, Bacterial , Female , Fever/microbiology , Glucocorticoids/adverse effects , Humans , Length of Stay/statistics & numerical data , Male , Mycoplasma pneumoniae/isolation & purification , Mycoplasma pneumoniae/physiology , Pneumonia, Mycoplasma/microbiology , Retrospective Studies , Time Factors , Treatment Outcome
15.
Biochem Biophys Res Commun ; 511(2): 422-426, 2019 04 02.
Article in English | MEDLINE | ID: mdl-30799083

ABSTRACT

MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate gene expression at post-transcriptional level via translational repression and/or mRNA degradation. miRNAs are associated with many cellular processes, and down-regulation of miRNAs causes numerous diseases including cancer, neurological disorders, inflammation, and cardiovascular diseases, for which miRNA replacement therapy has emerged as a promising approach. This approach aims to restore down-regulated miRNAs using synthetic miRNA mimics. However, it remains a critical issue that miRNA mimics are unstable and transient in cells. Here, we first show that miRNA mimics are rapidly degraded by a mechanism different from Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay, which degrades endogenous miRNAs, and newly identified 2'-5'-oligoadenylate synthetase (OAS)/RNase L as key factors responsible for the degradation of miRNA mimics in human cells. Our results suggest that the OAS1 recognizes miRNA mimics and produces 2'-5'-oligoadenylates (2-5A), which leads to the activation of latent endoribonuclease RNase L to degrade miRNA mimics. A small-molecule inhibitor that blocks RNase L can stabilize miRNA mimics. These findings provide a promising method for the stabilization of miRNA mimics, as well as for the efficient miRNA replacement therapy.


Subject(s)
2',5'-Oligoadenylate Synthetase/metabolism , Endoribonucleases/metabolism , MicroRNAs/metabolism , RNA Stability , HeLa Cells , Humans , MicroRNAs/chemistry
16.
Nucleic Acids Res ; 47(1): 432-449, 2019 01 10.
Article in English | MEDLINE | ID: mdl-30395302

ABSTRACT

The 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway is an innate immune system that protects hosts against pathogenic viruses and bacteria through cleavage of exogenous single-stranded RNA; however, this system's selective targeting mechanism remains unclear. Here, we identified an mRNA quality control factor Dom34 as a novel restriction factor for a positive-sense single-stranded RNA virus. Downregulation of Dom34 and RNase L increases viral replication, as well as half-life of the viral RNA. Dom34 directly binds RNase L to form a surveillance complex to recognize and eliminate the exogenous RNA in a manner dependent on translation. Interestingly, the feature detected by the surveillance complex is not the specific sequence of the viral RNA but the 'exogenous nature' of the RNA. We propose the following model for the selective targeting of exogenous RNA; OAS3 activated by the exogenous RNA releases 2'-5'-oligoadenylates (2-5A), which in turn converts latent RNase L to an active dimer. This accelerates formation of the Dom34-RNase L surveillance complex, and its selective localization to the ribosome on the exogenous RNA, thereby promoting degradation of the RNA. Our findings reveal that the selective targeting of exogenous RNA in antiviral defense occurs via a mechanism similar to that in the degradation of aberrant transcripts in RNA quality control.


Subject(s)
2',5'-Oligoadenylate Synthetase/genetics , Endonucleases/metabolism , Nuclear Proteins/metabolism , Signal Transduction/genetics , Virus Diseases/genetics , Viruses/genetics , Adenine Nucleotides/genetics , Adenine Nucleotides/metabolism , Endonucleases/genetics , Endoribonucleases/genetics , Gene Expression Regulation, Viral , Humans , Nuclear Proteins/genetics , Oligoribonucleotides/genetics , Oligoribonucleotides/metabolism , RNA Stability/genetics , RNA, Double-Stranded/genetics , RNA, Viral/genetics , Ribosomes/genetics , Ribosomes/virology , Virus Diseases/virology , Virus Replication/genetics , Viruses/pathogenicity
17.
FEBS Lett ; 593(3): 277-287, 2019 02.
Article in English | MEDLINE | ID: mdl-30520513

ABSTRACT

TAR DNA-binding protein 43 (TDP-43) is an RNA-binding protein, whose loss-of-function mutation causes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. Recent studies demonstrated that TDP-43 binds to the 3' untranslated region (UTR) of target mRNAs to promote mRNA instability. Here, we show that TDP-43 recruits Caf1 deadenylase to mRNA targets and accelerates their deadenylation. Tethering TDP-43 to the mRNA 3'UTR recapitulates destabilization of the mRNA, and TDP-43 accelerates their deadenylation. This accelerated deadenylation is inhibited by a dominant negative mutant of Caf1. We find that TDP-43 physically interacts with Caf1. In addition, we provide evidence that TDP-43 regulates poly(A) tail length of endogenous Progranulin (GRN) mRNA. These results may shed light on the link between dysregulation of TDP-43-mediated mRNA deadenylation and pathogenesis of neurodegenerative diseases.


Subject(s)
3' Untranslated Regions , Amyotrophic Lateral Sclerosis/metabolism , DNA-Binding Proteins/metabolism , Exoribonucleases/metabolism , Progranulins/biosynthesis , RNA Stability , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/pathology , DNA-Binding Proteins/genetics , Exoribonucleases/genetics , HEK293 Cells , HeLa Cells , Humans , Progranulins/genetics
18.
PLoS One ; 13(12): e0209595, 2018.
Article in English | MEDLINE | ID: mdl-30576373

ABSTRACT

OBJECTIVE: Urinary tract infection (UTI), one of the most common bacterial infections occurring during infancy and early childhood, is frequently associated with vesicoureteral reflux (VUR). Although several guidelines recommend performing ultrasonography as a screening test, its utility is not adequate and appropriate screening tests are strongly desirable. In this study, we evaluate the use of magnetic resonance imaging (MRI) as a screening test for VUR in children with UTI. METHODS: We prospectively studied 108 patients with suspected UTI between April 2014 and March 2016. UTI was diagnosed on the basis of diffusion-weighted MRI (DW-MRI) and urine culture findings. We measured ureteral dilatation using MRI in 96 patients with UTI and assessed the relationship between ureteral dilatation in MRI and VUR in 46 patients who underwent voiding cystourethrography (VCUG). RESULTS: Among 108 patients, 88 and 8 were diagnosed with upper and lower UTI, respectively. Among 46 patients who underwent VCUG, 23 had VUR (14 low grade and 9 high grade). Patients with ureteral dilatation detected on MRI had VUR more frequently than those without ureteral dilatation (any grades VUR, 71% vs. 32%; P = 0.02; high-grade VUR, 38% vs. 2%, P = 0.007). Overall, ureteral dilatation findings on MRI achieved sensitivity 65.2% and specificity 73.9% as a screening test for VUR. In addition, DW-MRI achieved sensitivity 100% and specificity 81.8% in the diagnosis of upper UTI. CONCLUSION: These findings suggested that MRI is a valuable tool for screening of VUR as well as diagnosis of upper UTI.


Subject(s)
Urethra/diagnostic imaging , Urinary Tract Infections/diagnostic imaging , Vesico-Ureteral Reflux/diagnosis , Child, Preschool , Diffusion Magnetic Resonance Imaging , Dilatation/methods , Female , Humans , Infant , Infant, Newborn , Magnetic Resonance Imaging , Male , Ultrasonography , Urethra/pathology , Urinalysis , Urinary Tract Infections/diagnosis , Urinary Tract Infections/urine , Urography/methods , Vesico-Ureteral Reflux/diagnostic imaging , Vesico-Ureteral Reflux/urine
19.
Prion ; : 1-7, 2018 Sep 09.
Article in English | MEDLINE | ID: mdl-30198379

ABSTRACT

The yeast Saccharomyces cerevisiae has proven to be a useful model system to investigate the mechanism of prion generation and inheritance, to which studies in Sup35 made a great contribution. Recent studies demonstrated that 'protein misfolding and aggregation' (i.e. amyloidogenesis) is a common principle underlying the pathogenesis of neurodegenerative diseases including prion, amyotrophic lateral sclerosis (ALS), Perkinson's (PD), Alzheimer's (AD) diseases and polyglutamine (polyQ) diseases such as spinocerebellar ataxia (SCA) and Hantington's disease (HD). By these findings, the yeast has again been drawing increased attention as a useful system for studying neurodegenerative proteinopathies. So far, it has been reported that proteolytic cleavage of causative amyloidogenic proteins might affect the pathogenesis of the respective neurodegenerative diseases. Although those reports provide a clear phenomenological description, in the majority of cases, it has remained elusive if proteolysis is directly involved in the pathogenesis of the diseases. Recently, we have demonstrated in yeast that proteolysis suppresses prion generation. The yeast-based strategy might make a breakthrough to the unsolved issues.

20.
Genes Cells ; 23(5): 332-344, 2018 May.
Article in English | MEDLINE | ID: mdl-29626383

ABSTRACT

MicroRNAs are small noncoding RNAs that regulate translation and mRNA stability by binding target mRNAs in complex with Argonaute (AGO) proteins. AGO interacts with a member of the TNRC6 family proteins to form a microRNP complex, which recruits the CCR4-NOT complex to accelerate deadenylation and inhibits translation. MicroRNAs primarily repress translation of target mRNAs but have been shown to enhance translation of a specific type of target reporter mRNAs in various experimental systems: G0 quiescent mammalian cells, Xenopus laevis oocytes, Drosophila embryo extracts, and HeLa cells. In all of the cases mentioned, a common feature of the activated target mRNAs is the lack of a poly(A) tail. Here, we show let-7-microRNP-mediated translational activation of nonadenylated target mRNAs in a mammalian cell-free system, which contains over-expressed AGO2, TNRC6B, and PAPD7 (TUTase5, TRF4-1). Importantly, translation of nonadenylated mRNAs was activated also by tethered TNRC6B silencing domain (SD), in the presence of PAPD7. Deletion of the poly(A)-binding protein (PABP) interacting motif (PAM2) from the TNRC6B-SD abolished the translational activation, suggesting the involvement of PABP in the process. Similar results were also obtained in cultured HEK293T cells. This work may provide novel insights into microRNP-mediated mRNA regulation.


Subject(s)
Cell-Free System , MicroRNAs/metabolism , Protein Biosynthesis , RNA, Messenger/metabolism , Argonaute Proteins/genetics , Argonaute Proteins/metabolism , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , DNA-Directed DNA Polymerase/genetics , DNA-Directed DNA Polymerase/metabolism , HEK293 Cells , Humans , MicroRNAs/genetics , Poly(A)-Binding Protein I/genetics , Poly(A)-Binding Protein I/metabolism , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , Polyadenylation , RNA, Messenger/genetics , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism
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