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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.
ACS Omega ; 9(6): 6873-6879, 2024 Feb 13.
Article in English | MEDLINE | ID: mdl-38371756

ABSTRACT

In this study, we devised a novel method to create heterologous producers of lethal antibiotics against host bacteria. Heterologous producers cannot be created when antibiotics are toxic to host bacteria. To overcome this challenge, we developed a novel method involving construction of a combinatorial library with various promoters and screening based on the production. To realize this, we utilized Combi-OGAB (Combinatorial Ordered Gene Assembly in Bacillus subtilis), which technology can effectively construct diverse combinatorial library and accelerate screening procedures. B. subtilis and Gramicidin S were selected as the host bacterium and the targeted antibiotic, respectively. The screened producer from Combi-OGAB screening cycles achieved >30-fold productivity over the lethal level. These results suggest that our strategy has the potential to maximize the phenotypic resistance of host bacteria to create heterologous lethal antibiotic producers.

3.
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
4.
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
5.
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
6.
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
7.
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
8.
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
9.
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
10.
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
11.
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.

12.
Sci Rep ; 8(1): 1455, 2018 01 23.
Article in English | MEDLINE | ID: mdl-29362417

ABSTRACT

Eukaryotic mature mRNAs possess a poly adenylate tail (poly(A)), to which multiple molecules of poly(A)-binding protein C1 (PABPC1) bind. PABPC1 regulates translation and mRNA metabolism by binding to regulatory proteins. To understand functional mechanism of the regulatory proteins, it is necessary to reveal how multiple molecules of PABPC1 exist on poly(A). Here, we characterize the structure of the multiple molecules of PABPC1 on poly(A), by using transmission electron microscopy (TEM), chemical cross-linking, and NMR spectroscopy. The TEM images and chemical cross-linking results indicate that multiple PABPC1 molecules form a wormlike structure in the PABPC1-poly(A) complex, in which the PABPC1 molecules are linearly arrayed. NMR and cross-linking analyses indicate that PABPC1 forms a multimer by binding to the neighbouring PABPC1 molecules via interactions between the RNA recognition motif (RRM) 2 in one molecule and the middle portion of the linker region of another molecule. A PABPC1 mutant lacking the interaction site in the linker, which possesses an impaired ability to form the multimer, reduced the in vitro translation activity, suggesting the importance of PABPC1 multimer formation in the translation process. We therefore propose a model of the PABPC1 multimer that provides clues to comprehensively understand the regulation mechanism of mRNA translation.


Subject(s)
Poly A/metabolism , Poly(A)-Binding Protein I/chemistry , Poly(A)-Binding Protein I/metabolism , Binding Sites , Humans , Magnetic Resonance Spectroscopy , Microscopy, Electron, Transmission , Mutation , Poly(A)-Binding Protein I/genetics , Protein Binding , Protein Multimerization , RNA, Messenger/chemistry , RNA, Messenger/metabolism
13.
J Biol Chem ; 292(49): 20113-20124, 2017 12 08.
Article in English | MEDLINE | ID: mdl-29038292

ABSTRACT

Prions are infectious proteins that cause fatal neurodegenerative disorders including Creutzfeldt-Jakob and bovine spongiform encephalopathy (mad cow) diseases. The yeast [PSI+] prion is formed by the translation-termination factor Sup35, is the best-studied prion, and provides a useful model system for studying such diseases. However, despite recent progress in the understanding of prion diseases, the cellular defense mechanism against prions has not been elucidated. Here, we report that proteolytic cleavage of Sup35 suppresses spontaneous de novo generation of the [PSI+] prion. We found that during yeast growth in glucose media, a maximum of 40% of Sup35 is cleaved at its N-terminal prion domain. This cleavage requires the vacuolar proteases PrA-PrB. Cleavage occurs in a manner dependent on translation but independently of autophagy between the glutamine/asparagine-rich (Q/N-rich) stretch critical for prion formation and the oligopeptide-repeat region required for prion maintenance, resulting in the removal of the Q/N-rich stretch from the Sup35 N terminus. The complete inhibition of Sup35 cleavage, by knocking out either PrA (pep4Δ) or PrB (prb1Δ), increased the rate of de novo formation of [PSI+] prion up to ∼5-fold, whereas the activation of Sup35 cleavage, by overproducing PrB, inhibited [PSI+] formation. On the other hand, activation of the PrB pathway neither cleaved the amyloid conformers of Sup35 in [PSI+] strains nor eliminated preexisting [PSI+]. These findings point to a mechanism antagonizing prion generation in yeast. Our results underscore the usefulness of the yeast [PSI+] prion as a model system to investigate defense mechanisms against prion diseases and other amyloidoses.


Subject(s)
Fungal Proteins/metabolism , Peptide Termination Factors/metabolism , Prion Proteins/metabolism , Prions/antagonists & inhibitors , Proteolysis , Saccharomyces cerevisiae Proteins/metabolism , Peptide Hydrolases/metabolism , Prions/metabolism , Vacuoles/enzymology , Yeasts/metabolism
14.
Polymers (Basel) ; 8(3)2016 Feb 29.
Article in English | MEDLINE | ID: mdl-30979161

ABSTRACT

This study deals with the fabrication of biodegradable porous materials from bacterial polyester, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P3HB3HHx), via thermally induced phase separation. P3HB3HHx monoliths with topological porous structure were prepared by dissolution of P3HB3HHx in dimethyl sulfoxide (DMSO) at 85 °C and subsequent quenching. The microstructure of the resulting P3HB3HHx monoliths was changed by the P3HB3HHx concentration of the polymer solution. Differential scanning calorimetry and polarized optical microscope analysis revealed that the P3HB3HHx monoliths crystallized during phase separation and the subsequent aging. The mechanical properties, such as compression modulus and stress, of the monoliths depended on the 3-hydroxyhexanoate content of P3HB3HHx. Furthermore, the P3HB3HHx monolith absorbed linseed oil in preference to water in a plant oil⁻water mixture. In combination with the biodegradable character of P3HB3HHx, the present study is expected to contribute to the development of bio-based materials.

15.
Biochem Biophys Res Commun ; 455(3-4): 323-31, 2014 Dec 12.
Article in English | MEDLINE | ID: mdl-25446091

ABSTRACT

The poly(A) tail of mRNAs plays pivotal roles in the posttranscriptional control of gene expression at both translation and mRNA stability. Recent findings demonstrate that the poly(A) tail is globally stabilized by some stresses. However, the mechanism underlying this phenomenon has not been elucidated. Here, we show that arsenite-induced oxidative stress inhibits deadenylation of mRNA primarily through downregulation of Tob and Pan3, both of which mediate the recruitment of deadenylases to mRNA. Arsenite selectively induces the proteolytic degradation of Tob and Pan3, and siRNA-mediated knockdown of Tob and Pan3 recapitulates stabilization of the mRNA poly(A) tail observed during arsenite stress. Although arsenite also inhibits translation by activating the eIF2α kinase HRI, arsenite-induced mRNA stabilization can be observed under HRI-depleted conditions. These results highlight the essential role of Tob and Pan3 in the stress-induced global stabilization of mRNA.


Subject(s)
Arsenites/chemistry , Carrier Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Proteasome Endopeptidase Complex/metabolism , RNA, Messenger/metabolism , Tumor Suppressor Proteins/metabolism , Amino Acid Motifs , Down-Regulation , HeLa Cells , Humans , Oxidative Stress , Poly A/chemistry , Protein Binding , Proteolysis , RNA Stability , RNA, Small Interfering/metabolism
16.
Biochem Biophys Res Commun ; 445(3): 639-44, 2014 Mar 14.
Article in English | MEDLINE | ID: mdl-24569073

ABSTRACT

The eukaryotic releasing factor eRF3 is a multifunctional protein that plays pivotal roles in translation termination as well as the initiation of mRNA decay. eRF3 also functions in the regulation of apoptosis; eRF3 is cleaved at Ala73 by an as yet unidentified protease into processed isoform of eRF3 (p-eRF3), which interacts with the inhibitors of apoptosis proteins (IAPs). The binding of p-eRF3 with IAPs leads to the release of active caspases from IAPs, which promotes apoptosis. Although full-length eRF3 is localized exclusively in the cytoplasm, p-eRF3 localizes in the nucleus as well as the cytoplasm. We here focused on the role of p-eRF3 in the nucleus. We identified leptomycin-sensitive nuclear export signal (NES) at amino acid residues 61-71 immediately upstream of the cleavage site Ala73. Thus, the proteolytic cleavage of eRF3 into p-eRF3 leads to release an amino-terminal fragment containing NES to allow the relocalization of eRF3 into the nucleus. Consistent with this, p-eRF3 more strongly interacted with the nuclear ARF tumor suppressor than full-length eRF3. These results suggest that while p-eRF3 interacts with IAPs to promote apoptosis in the cytoplasm, p-eRF3 also has some roles in regulating cell death in the nucleus.


Subject(s)
Cell Nucleus/metabolism , Peptide Termination Factors/analysis , Peptide Termination Factors/metabolism , Tumor Suppressor Protein p14ARF/metabolism , Active Transport, Cell Nucleus , Amino Acid Sequence , Apoptosis , Cell Nucleus/ultrastructure , HeLa Cells , Humans , Karyopherins/metabolism , Molecular Sequence Data , Nuclear Export Signals , Open Reading Frames , Peptide Chain Termination, Translational , Protein Interaction Maps , Protein Isoforms/analysis , Protein Isoforms/metabolism , Receptors, Cytoplasmic and Nuclear/metabolism , Tumor Suppressor Protein p14ARF/analysis , Exportin 1 Protein
17.
J Biol Chem ; 288(24): 17832-43, 2013 Jun 14.
Article in English | MEDLINE | ID: mdl-23667253

ABSTRACT

In yeast, aberrant mRNAs lacking in-frame termination codons are recognized and degraded by the non-stop decay (NSD) pathway. The recognition of non-stop mRNAs involves a member of the eRF3 family of GTP-binding proteins, Ski7. Ski7 is thought to bind the ribosome stalled at the 3'-end of the mRNA poly(A) tail and recruit the exosome to degrade the aberrant message. However, Ski7 is not found in mammalian cells, and even the presence of the NSD mechanism itself has remained enigmatic. Here, we show that unstable non-stop mRNA is degraded in a translation-dependent manner in mammalian cells. The decay requires another eRF3 family member (Hbs1), its binding partner Dom34, and components of the exosome-Ski complex (Ski2/Mtr4 and Dis3). Hbs1-Dom34 binds to form a complex with the exosome-Ski complex. Also, the elimination of aberrant proteins produced from non-stop transcripts requires the RING finger protein listerin. These findings demonstrate that the NSD mechanism exists in mammalian cells and involves Hbs1, Dom34, and the exosome-Ski complex.


Subject(s)
GTP-Binding Proteins/physiology , HSP70 Heat-Shock Proteins/physiology , Microfilament Proteins/metabolism , Peptide Elongation Factors/physiology , RNA Stability , RNA, Messenger/metabolism , Endonucleases , Exosome Multienzyme Ribonuclease Complex/genetics , Exosome Multienzyme Ribonuclease Complex/metabolism , Gene Expression , Gene Knockdown Techniques , Half-Life , HeLa Cells , Humans , Nuclear Proteins , Protein Binding , Protein Biosynthesis , RNA, Messenger/genetics , RNA, Small Interfering/genetics , RNA-Binding Proteins/metabolism
18.
Apoptosis ; 17(12): 1287-99, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23054082

ABSTRACT

Polypeptide chain release factor eRF3 plays pivotal roles in translation termination and post-termination events including ribosome recycling and mRNA decay. It is not clear, however, if eRF3 is targeted for the regulation of gene expression. Here we show that DNA-damaging agents (UV and etoposide) induce the immediate cleavage and degradation of eRF3 in a caspase-dependent manner. The effect is selective since the binding partners of eRF3, eRF1 and PABP, and an unrelated control, GAPDH, were not affected. Point mutations of aspartate residues within overlapping DXXD motifs near the amino terminus of eRF3 prevented the appearance of the UV-induced cleavage product, identifying D32 as the major cleavage site. The cleavage and degradation occurred in a similar time-dependent manner to those of eIF4G, a previously established caspase-3 target involved in the inhibition of translation during apoptosis. siRNA-mediated knockdown of eRF3 led to inhibition of cellular protein synthesis, supporting the idea that the decrease in the amount of eRF3 caused by the caspase-mediated degradation contributes to the inhibition of translation during apoptosis. This is the first report showing that eRF3 could serve as a target in the regulation of gene expression.


Subject(s)
Apoptosis , Caspase 3/metabolism , DNA Damage/radiation effects , Peptide Termination Factors/metabolism , Apoptosis/radiation effects , Caspase 3/genetics , Cell Line , Gene Expression Regulation , Humans , Peptide Chain Termination, Translational , Peptide Termination Factors/genetics , Proteolysis/radiation effects , Ultraviolet Rays
19.
RNA ; 18(11): 1957-67, 2012 Nov.
Article in English | MEDLINE | ID: mdl-23019593

ABSTRACT

Eukaryotic releasing factor GSPT/eRF3 mediates translation termination-coupled mRNA decay via interaction with a cytosolic poly(A)-binding protein (PABPC1). A region of eRF3 containing two overlapping PAM2 (PABPC1-interacting motif 2) motifs is assumed to bind to the PABC domain of PABPC1, on the poly(A) tail of mRNA. PAM2 motifs are also found in the major deadenylases Caf1-Ccr4 and Pan2-Pan3, whose activities are enhanced upon PABPC1 binding to these motifs. Their deadenylase activities are regulated by eRF3, in which two overlapping PAM2 motifs competitively prevent interaction with PABPC1. However, it is unclear how these overlapping motifs recognize PABC and regulate deadenylase activity in a translation termination-coupled manner. We used a dominant-negative approach to demonstrate that the N-terminal PAM2 motif is critical for eRF3 binding to PABPC1 and that both motifs are required for function. Isothermal titration calorimetry (ITC) and NMR analyses revealed that the interaction is in equilibrium between the two PAM2-PABC complexes, where only one of the two overlapping PAM2 motifs is PABC-bound and the other is PABC-unbound and partially accessible to the other PABC. Based on these results, we proposed a biological role for the overlapping PAM2 motifs in the regulation of deadenylase accessibility to PABPC1 at the 3' end of poly(A).


Subject(s)
Peptide Termination Factors/physiology , RNA Processing, Post-Transcriptional , RNA Stability , RNA, Messenger/metabolism , Amino Acid Sequence , Binding Sites , Calorimetry , Gene Expression Regulation , Green Fluorescent Proteins/genetics , Half-Life , HeLa Cells , Humans , Models, Molecular , Molecular Sequence Data , Peptide Termination Factors/chemistry , Peptide Termination Factors/genetics , Poly A/metabolism , Poly(A)-Binding Protein I/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Quaternary , RNA, Messenger/genetics , Thermodynamics , Titrimetry , beta-Globins/genetics
20.
EMBO J ; 30(7): 1311-23, 2011 Apr 06.
Article in English | MEDLINE | ID: mdl-21336257

ABSTRACT

Tob is a member of the anti-proliferative protein family, which functions in transcription and mRNA decay. We have previously demonstrated that Tob is involved in the general mechanism of mRNA decay by mediating mRNA deadenylation through interaction with Caf1 and a general RNA-binding protein, PABPC1. Here, we focus on the role of Tob in the regulation of specific mRNA. We show that Tob binds directly to a sequence-specific RNA-binding protein, cytoplasmic polyadenylation element-binding protein 3 (CPEB3). CPEB3 negatively regulates the expression of a target by accelerating deadenylation and decay of its mRNA, which it achieves by tethering to the mRNA. The carboxyl-terminal RNA-binding domain of CPEB3 binds to the carboxyl-terminal unstructured region of Tob. Tob then binds Caf1 deadenylase and recruits it to CPEB3 to form a ternary complex. The CPEB3-accelerated deadenylation was abrogated by a dominant-negative mutant of either Caf1 or Tob. Together, these results indicate that Tob mediates the recruitment of Caf1 to the target of CPEB3 and elicits deadenylation and decay of the mRNA. Our results provide an explanation of how Tob regulates specific biological processes.


Subject(s)
Gene Expression Regulation , Intracellular Signaling Peptides and Proteins/metabolism , RNA-Binding Proteins/antagonists & inhibitors , Transcription Factors/antagonists & inhibitors , Tumor Suppressor Proteins/metabolism , Animals , COS Cells , Chlorocebus aethiops , HeLa Cells , Humans , Protein Binding , Protein Interaction Domains and Motifs , Protein Interaction Mapping , RNA Stability , RNA, Messenger/metabolism
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