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1.
J Phys Chem B ; 128(27): 6449-6462, 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38941243

ABSTRACT

Microscopic understanding of protein-RNA interactions is important for different biological activities, such as RNA transport, translation, splicing, silencing, etc. Polyadenine (Poly(A)) binding proteins (PABPs) make up a class of regulatory proteins that play critical roles in protecting the poly(A) tails of cellular mRNAs from nuclease degradation. In this work, we performed molecular dynamics simulations to investigate the conformational modifications of human PABP protein and poly(A) RNA that occur during complexation. It is demonstrated that the intermediate linker domain of the protein transforms from a disordered coil-like structure to a helical form during the recognition process, leading to the formation of the complex. On the other hand, disordered collapsed coil-like RNA on complexation has been found to transform into a rigid extended conformation. Importantly, the binding free energy calculation showed that the thermodynamic stability of the complex is primarily guided by favorable hydrophobic interactions between the protein and the RNA.


Subject(s)
Molecular Dynamics Simulation , Poly A , Poly(A)-Binding Proteins , Thermodynamics , Humans , Poly A/chemistry , Poly A/metabolism , Poly(A)-Binding Proteins/chemistry , Poly(A)-Binding Proteins/metabolism , Protein Conformation , Protein Binding , Hydrophobic and Hydrophilic Interactions , RNA/chemistry , RNA/metabolism
2.
Mol Cell ; 84(11): 2119-2134.e5, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38848691

ABSTRACT

Protein synthesis is metabolically costly and must be tightly coordinated with changing cellular needs and nutrient availability. The cap-binding protein eIF4E makes the earliest contact between mRNAs and the translation machinery, offering a key regulatory nexus. We acutely depleted this essential protein and found surprisingly modest effects on cell growth and recovery of protein synthesis. Paradoxically, impaired protein biosynthesis upregulated genes involved in the catabolism of aromatic amino acids simultaneously with the induction of the amino acid biosynthetic regulon driven by the integrated stress response factor GCN4. We further identified the translational control of Pho85 cyclin 5 (PCL5), a negative regulator of Gcn4, that provides a consistent protein-to-mRNA ratio under varied translation environments. This regulation depended in part on a uniquely long poly(A) tract in the PCL5 5' UTR and poly(A) binding protein. Collectively, these results highlight how eIF4E connects protein synthesis to metabolic gene regulation, uncovering mechanisms controlling translation during environmental challenges.


Subject(s)
Amino Acids , Eukaryotic Initiation Factor-4E , Gene Expression Regulation, Fungal , Protein Biosynthesis , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Eukaryotic Initiation Factor-4E/metabolism , Eukaryotic Initiation Factor-4E/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Amino Acids/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , RNA, Messenger/metabolism , RNA, Messenger/genetics , 5' Untranslated Regions , Basic-Leucine Zipper Transcription Factors/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , Cyclins/genetics , Cyclins/metabolism , Poly(A)-Binding Proteins/metabolism , Poly(A)-Binding Proteins/genetics
3.
Reproduction ; 168(2)2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38819377

ABSTRACT

In brief: Ovarian aging results in reactive oxygen species accumulation and mitochondrial deterioration. During the aging process, GRSF1 deficiency attenuates mitochondrial function in aging granulosa cells. Abstract: Ovarian aging critically influences reproductive potential, with a marked decrease in oocyte quality and quantity and an increase in oxidative stress and mitochondrial dysfunction. This study elucidates the role of guanine-rich RNA sequence binding factor 1 (GRSF1) in the aging of ovarian granulosa cells (GCs). We observed a significant reduction in GRSF1 within GCs correlating with patient age, utilizing clinical samples from IVF patients. Using an siRNA-mediated knockdown technique, we established that diminished GRSF1 expression exacerbates mitochondrial dysfunction, elevates reactive oxygen species, and impairs ATP production. Furthermore, RNA immunoprecipitation revealed GRSF1's interaction with superoxide dismutase 2 (SOD2) mRNA, a key antioxidant enzyme, suggesting a mechanism whereby GRSF1 modulates oxidative stress. Downregulation of SOD2 reversed the protective effects of GRSF1 overexpression on mitochondrial function. These insights into the role of GRSF1 in ovarian aging may guide the development of interventions to improve fertility outcomes in advanced age.


Subject(s)
Aging , Cellular Senescence , Granulosa Cells , Mitochondria , Oxidative Stress , Reactive Oxygen Species , Female , Granulosa Cells/metabolism , Humans , Mitochondria/metabolism , Reactive Oxygen Species/metabolism , Aging/metabolism , Adult , Superoxide Dismutase/metabolism , Superoxide Dismutase/genetics , Cells, Cultured , Poly(A)-Binding Proteins
4.
PLoS Genet ; 20(5): e1011251, 2024 May.
Article in English | MEDLINE | ID: mdl-38768217

ABSTRACT

Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Experiments with transgenic Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.


Subject(s)
Ataxin-2 , Drosophila Proteins , Drosophila melanogaster , RNA, Messenger , Ribonucleoproteins , Ataxin-2/genetics , Ataxin-2/metabolism , Animals , Humans , Ribonucleoproteins/genetics , Ribonucleoproteins/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Poly(A)-Binding Proteins/metabolism , Poly(A)-Binding Proteins/genetics , Animals, Genetically Modified , Cytoplasmic Granules/metabolism , Cytoplasmic Granules/genetics , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/metabolism , Protein Biosynthesis , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Intrinsically Disordered Proteins/genetics , Intrinsically Disordered Proteins/metabolism , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , DNA-Binding Proteins
5.
PLoS One ; 19(5): e0300287, 2024.
Article in English | MEDLINE | ID: mdl-38696388

ABSTRACT

The phosphorylation of eukaryotic translational initiation factors has been shown to play a significant role in controlling the synthesis of protein. Viral infection, environmental stress, and growth circumstances cause phosphorylation or dephosphorylation of plant initiation factors. Our findings indicate that casein kinase 2 can phosphorylate recombinant wheat eIFiso4E and eIFiso4G generated from E. coli in vitro. For wheat eIFiso4E, Ser-207 was found to be the in vitro phosphorylation site. eIFiso4E lacks an amino acid that can be phosphorylated at the position corresponding to Ser-209, the phosphorylation site in mammalian eIF4E, yet phosphorylation of eIFiso4E has effects on VPg binding affinity that are similar to those of phosphorylation of mammalian eIF4E. The addition of VPg and phosphorylated eIFiso4F to depleted wheat germ extract (WGE) leads to enhancement of translation of both uncapped and capped viral mRNA. The addition of PABP together with eIFiso4Fp and eIF4B to depleted WGE increases both uncapped and capped mRNA translation. However, it exhibits a translational advantage specifically for uncapped mRNA, implying that the phosphorylation of eIFiso4F hinders cap binding while promoting VPg binding, thereby facilitating uncapped translation. These findings indicate TEV virus mediates VPg-dependent translation by engaging a mechanism entailing phosphorylated eIFiso4Fp and PABP. To elucidate the molecular mechanisms underlying these observed effects, we studied the impact of PABP and/or eIF4B on the binding of VPg with eIFiso4Fp. The inclusion of PABP and eIF4B with eIFiso4Fp resulted in about 2-fold increase in affinity for VPg (Kd = 24 ± 1.7 nM), as compared to the affinity of eIFiso4Fp alone (Kd = 41.0 ± 3.1 nM). The interactions between VPg and eIFiso4Fp were determined to be both enthalpically and entropically favorable, with the enthalpic contribution accounting for 76-97% of the ΔG at 25°C, indicating a substantial role of hydrogen bonding in enhancing the stability of the complex. The binding of PABP to eIFiso4Fp·4B resulted in a conformational alteration, leading to a significant enhancement in the binding affinity to VPg. These observations suggest PABP enhances the affinity between eIFiso4Fp and VPg, leading to an overall conformational change that provides a stable platform for efficient viral translation.


Subject(s)
Eukaryotic Initiation Factors , Poly(A)-Binding Proteins , Potyvirus , Protein Binding , Protein Biosynthesis , Triticum , Phosphorylation , Potyvirus/metabolism , Potyvirus/genetics , Triticum/virology , Triticum/metabolism , Triticum/genetics , Eukaryotic Initiation Factors/metabolism , Eukaryotic Initiation Factors/genetics , Poly(A)-Binding Proteins/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/genetics , Casein Kinase II/metabolism , Casein Kinase II/genetics
6.
Nat Commun ; 15(1): 3127, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38605014

ABSTRACT

Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.


Subject(s)
Heat-Shock Response , Stress, Physiological , Heat-Shock Response/genetics , Stress, Physiological/genetics , Biological Evolution , Poly(A)-Binding Proteins/genetics
7.
Proc Natl Acad Sci U S A ; 121(13): e2321606121, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38513106

ABSTRACT

Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen, Nat. Rev. Mol. Cell Biol. 18, 285-298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond, J. Biol. Chem. 294, 7151-7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Riback et al., Cell 168, 1028-1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen-deuterium exchange/mass spectrometry to investigate the mechanism of Pab1's condensation. Pab1's four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate's interaction network. Our data yield a picture of Pab1's stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.


Subject(s)
Heat-Shock Proteins , Poly(A)-Binding Proteins , Poly(A)-Binding Proteins/genetics , Temperature , Heat-Shock Proteins/metabolism , Thermodynamics , Heat-Shock Response , Deuterium Exchange Measurement/methods
8.
Mol Cell ; 84(9): 1727-1741.e12, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38547866

ABSTRACT

Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying mechanism is unclear. We report that HS in budding yeast induces the disassembly of the eIF4F complex, where eIF4G and eIF4E assemble into translationally arrested mRNA ribonucleoprotein particles (mRNPs) and HS granules (HSGs), whereas eIF4A promotes HS translation. Using in vitro reconstitution biochemistry, we show that a conformational rearrangement of the thermo-sensing eIF4A-binding domain of eIF4G dissociates eIF4A and promotes the assembly with mRNA into HS-mRNPs, which recruit additional translation factors, including Pab1p and eIF4E, to form multi-component condensates. Using extracts and cellular experiments, we demonstrate that HS-mRNPs and condensates repress the translation of associated mRNA and deplete translation factors that are required for housekeeping translation, whereas HS mRNAs can be efficiently translated by eIF4A. We conclude that the eIF4F complex is a thermo-sensing node that regulates translation during HS.


Subject(s)
Eukaryotic Initiation Factor-4F , Eukaryotic Initiation Factor-4G , Heat-Shock Response , Poly(A)-Binding Proteins , Protein Biosynthesis , RNA, Messenger , Ribonucleoproteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Heat-Shock Response/genetics , Eukaryotic Initiation Factor-4F/metabolism , Eukaryotic Initiation Factor-4F/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Eukaryotic Initiation Factor-4G/metabolism , Eukaryotic Initiation Factor-4G/genetics , Ribonucleoproteins/metabolism , Ribonucleoproteins/genetics , Eukaryotic Initiation Factor-4E/metabolism , Eukaryotic Initiation Factor-4E/genetics , Eukaryotic Initiation Factor-4A/metabolism , Eukaryotic Initiation Factor-4A/genetics , Gene Expression Regulation, Fungal , Protein Binding , RNA, Fungal/metabolism , RNA, Fungal/genetics
9.
Adv Sci (Weinh) ; 11(14): e2308496, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38308190

ABSTRACT

During maternal-to-zygotic transition (MZT) in the embryo, mRNA undergoes complex post-transcriptional regulatory processes. However, it is unclear whether and how alternative splicing plays a functional role in MZT. By analyzing transcriptome changes in mouse and human early embryos, dynamic changes in alternative splicing during MZT are observed and a previously unnoticed process of zygotic splicing activation (ZSA) following embryonic transcriptional activation is described. As the underlying mechanism of RNA splicing, splicing factors undergo dramatic maternal-to-zygotic conversion. This conversion relies on the key maternal factors BTG4 and PABPN1L and is zygotic-transcription-dependent. CDK11-dependent phosphorylation of the key splicing factor, SF3B1, and its aggregation with SRSF2 in the subnuclear domains of 2-cell embryos are prerequisites for ZSA. Isoforms generated by erroneous splicing, such as full-length Dppa4, hinder normal embryonic development. Moreover, alternative splicing regulates the conversion of early embryonic blastomeres from totipotency to pluripotency, thereby affecting embryonic lineage differentiation. ZSA is an essential post-transcriptional process of MZT and has physiological significance in generating new life. In addition to transcriptional activation, appropriate expression of transcript isoforms is also necessary for preimplantation embryonic development.


Subject(s)
Transcriptome , Zygote , Humans , Animals , Mice , Transcriptome/genetics , Zygote/metabolism , Embryonic Development/genetics , RNA Splicing , Protein Isoforms/genetics , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , Nuclear Proteins/genetics
11.
Biol Reprod ; 110(4): 834-847, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38281153

ABSTRACT

Besides ubiquitous poly(A)-binding protein, cytoplasmic 1 (PABPC1), testis-specific PABPC2/PABPt (in humans, referred to as PABPC3), and female and male germline-specific PABPC1L/ePAB, have been reported in the mouse testis. Recent in silico analysis additionally identified testis-specific Pabpc6 in the mouse. In this study, we characterized PABPC6 and its mutant mice. PABPC6 was initially detectable in the cytoplasm of pachytene spermatocytes, increased in abundance in round spermatids, and decreased in elongating spermatids. PABPC6 was capable of binding to poly(A) tails of various mRNAs and interacting with translation-associated factors, including EIF4G, PAIP1, and PAIP2. Noteworthy was that PABPC6, unlike PABPC1, was barely associated with translationally active polysomes and enriched in chromatoid bodies of round spermatids. Despite these unique characteristics, neither synthesis of testicular proteins nor spermatogenesis was affected in the mutant mice lacking PABPC6, suggesting that PABPC6 is functionally redundant with other co-existing PABPC proteins during spermatogenesis.


Subject(s)
Spermatogenesis , Testis , Humans , Male , Mice , Female , Animals , Testis/metabolism , Spermatogenesis/genetics , Spermatids/metabolism , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , Cytoplasm/metabolism , RNA, Messenger/metabolism , Peptide Initiation Factors/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism
12.
Cell Death Dis ; 14(11): 717, 2023 11 03.
Article in English | MEDLINE | ID: mdl-37923734

ABSTRACT

Age-associated hypercoagulability is accompanied by the increase of plasma levels of some coagulation factors including fibrinogen which may contribute to the increased risk of cardiovascular, cerebrovascular, and thrombotic diseases in elderly people. However, the underlying mechanism of increased plasma fibrinogen concentration during aging is still elusive. GRSF1 belongs to the heterogeneous nuclear ribonucleoproteins F/H (hnRNP F/H) subfamily. Here, we report that GRSF1 attenuates hypercoagulability via negative modulation of fibrinogen expression. We demonstrated that GRSF1 negatively regulated fibrinogen expression at both mRNA and protein levels. GRSF1 directly interacted with the coding region (CDS) of FGA, FGB, and FGG mRNAs, and decreased their stability thus mitigating fibrinogen expression. We further identified that only a few G-tracts within the Fib C domain of FGA, FGB, and FGG CDS and the qRRM2 domain of GRSF1 were required for their interaction. Moreover, we confirmed hypercoagulability and the decrease of GRSF1 expression level during mice aging. Functionally, GRSF1 overexpression in old mice liver decreased fibrinogen plasma level, reduced hypercoagulability, and mitigated blood coagulation activity, whereas GRSF1 knockdown in young mice liver increased fibrinogen plasma level and promoted blood coagulation activity. Collectively, our findings unveil a novel posttranscriptional regulation of fibrinogen by GRSF1 and uncover a critical role of GRSF1 in regulating blood coagulation activity.


Subject(s)
Fibrinogen , Thrombophilia , Aged , Animals , Humans , Mice , Fibrinogen/genetics , Fibrinogen/metabolism , Gene Expression Regulation , Poly(A)-Binding Proteins/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism
13.
EMBO Rep ; 24(12): e57741, 2023 Dec 06.
Article in English | MEDLINE | ID: mdl-38009565

ABSTRACT

N6-methyladenosine (m6 A) in mRNA is key to eukaryotic gene regulation. Many m6 A functions involve RNA-binding proteins that recognize m6 A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Animals , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , RNA-Binding Proteins/metabolism , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , RNA, Messenger/genetics , Intracellular Signaling Peptides and Proteins/metabolism
14.
Genes Dev ; 37(15-16): 760-777, 2023 08 01.
Article in English | MEDLINE | ID: mdl-37704377

ABSTRACT

The mRNA 3' poly(A) tail plays a critical role in regulating both mRNA translation and turnover. It is bound by the cytoplasmic poly(A) binding protein (PABPC), an evolutionarily conserved protein that can interact with translation factors and mRNA decay machineries to regulate gene expression. Mammalian PABPC1, the prototypical PABPC, is expressed in most tissues and interacts with eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation in specific contexts. In this study, we uncovered a new mammalian PABPC, which we named neural PABP (neuPABP), as it is predominantly expressed in the brain. neuPABP maintains a unique architecture as compared with other PABPCs, containing only two RNA recognition motifs (RRMs) and maintaining a unique N-terminal domain of unknown function. neuPABP expression is activated in neurons as they mature during synaptogenesis, where neuPABP localizes to the soma and postsynaptic densities. neuPABP interacts with the noncoding RNA BC1, as well as mRNAs coding for ribosomal and mitochondrial proteins. However, in contrast to PABPC1, neuPABP does not associate with actively translating mRNAs in the brain. In keeping with this, we show that neuPABP has evolved such that it does not bind eIF4G and as a result fails to support protein synthesis in vitro. Taken together, these results indicate that mammals have expanded their PABPC repertoire in the brain and propose that neuPABP may support the translational repression of select mRNAs.


Subject(s)
Eukaryotic Initiation Factor-4G , Poly(A)-Binding Proteins , Animals , Poly(A)-Binding Proteins/genetics , Neurons , Brain , Mammals
15.
RNA ; 29(12): 1870-1880, 2023 12.
Article in English | MEDLINE | ID: mdl-37699651

ABSTRACT

The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In Saccharomyces cerevisiae, TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here, we present the structural analysis of the endogenous TREX complex of S. cerevisiae purified from its native environment. To this end, we used cross-linking mass spectrometry to gain structural information on regions of the complex that are not accessible to classical structural biology techniques. We also used negative-stain electron microscopy to investigate the organization of the cross-linked complex used for XL-MS by comparing our endogenous TREX complex with recently published structural models of recombinant THO-Sub2 complexes. According to our analysis, the endogenous yeast TREX complex preferentially assembles into a dimer.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , RNA, Messenger/genetics , RNA Transport , Transcription, Genetic , Nucleocytoplasmic Transport Proteins/genetics , Poly(A)-Binding Proteins/genetics
16.
J Biol Chem ; 299(8): 104959, 2023 08.
Article in English | MEDLINE | ID: mdl-37356722

ABSTRACT

Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.


Subject(s)
Poly(A)-Binding Protein I , Polyadenylation , Animals , Humans , Mice , Poly(A)-Binding Protein I/genetics , Poly(A)-Binding Protein I/metabolism , Poly(A)-Binding Proteins/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism
17.
Eur J Cancer Prev ; 32(3): 229-237, 2023 05 01.
Article in English | MEDLINE | ID: mdl-37010104

ABSTRACT

OBJECTIVE: Esophageal squamous cell carcinoma (ESCC) has high mortality worldwide, but its early diagnosis and prognosis are very difficult. Cytoplasmic poly(A)-binding protein 1 (PABPC1) plays an important role in regulating most cellular processes, resulting in a close relationship to tumor genesis and malignant development. Therefore, this work aimed to evaluate the clinical value of PABPC1 as a biomarker for the early diagnosis and prognosis of ESCC in endoscopic patients. METHODS: A total of 185 patients with lesions found by endoscopy were involved in this study, including 116 finally diagnosed with ESCCs and 69 with nonmalignant lesions. Biopsy fragments and surgical specimens were collected to assess PABPC1 expression by immunohistochemistry, and the association between the expression and survival was analyzed and compared in both samples. RESULTS: The average ratio of positive tumor cells to total tumor cells in the biopsy fragments was lower than that in surgical specimens, leading to a cutoff value of only 10% for the former in ROC analysis (AOC = 0.808, P < 0.001). However, PABPC1 high expression (PABPC1-HE) in both biopsy fragments and surgical specimens was associated with poor survival. When PABPC1 expression was used as a biomarker to diagnose ESCC in biopsy fragments, sensitivity, specificity, positive predictive value, and negative predictive value reached 44.8, 100.0, 100.0, and 51.9%, respectively. Among the 116 ESCC patients, 32 received postoperative concurrent chemoradiotherapy. Postoperative treatment increased the overall survival (OS) but not disease-free survival in lymph node-positive patients (P = 0.007 and 0.957, respectively). Nevertheless, PABPC1-HE predicted shorter OS regardless of the postoperative treatment in both endoscopic biopsy samples and surgical specimens. CONCLUSION: PABPC1 expression can be used as a biomarker to detect ESCC from endoscopic lesions. At the same time, PABPC1-HE is a predictor of poor survival regardless of postoperative chemoradiotherapy in endoscopic biopsy samples of ESCC.


Subject(s)
Carcinoma, Squamous Cell , Esophageal Neoplasms , Esophageal Squamous Cell Carcinoma , Humans , Esophageal Squamous Cell Carcinoma/diagnosis , Carcinoma, Squamous Cell/pathology , Prognosis , Biopsy , Biomarkers, Tumor/metabolism , Early Diagnosis , Poly(A)-Binding Proteins
18.
Genome Biol ; 24(1): 103, 2023 04 30.
Article in English | MEDLINE | ID: mdl-37122016

ABSTRACT

BACKGROUND: RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and ECT4 are m6A readers that are known to redundantly regulate trichome branching and leaf growth, but their molecular functions remain unclear. RESULTS: Here, we show that ECT2, ECT3, and ECT4 directly interact with each other in the cytoplasm and perform genetically redundant functions in abscisic acid (ABA) response regulation during seed germination and post-germination growth. We reveal that ECT2/ECT3/ECT4 promote the stabilization of their targeted m6A-modified mRNAs, but have no function in alternative polyadenylation and translation. We find that ECT2 directly interacts with the poly(A) binding proteins, PAB2 and PAB4, and maintains the stabilization of m6A-modified mRNAs. Disruption of ECT2/ECT3/ECT4 destabilizes mRNAs of ABA signaling-related genes, thereby promoting the accumulation of ABI5 and leading to ABA hypersensitivity. CONCLUSION: Our study reveals a unified functional model of m6A mediated by m6A readers in plants. In this model, ECT2/ECT3/ECT4 promote stabilization of their target mRNAs in the cytoplasm.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , Basic-Leucine Zipper Transcription Factors/metabolism , Abscisic Acid , Germination/genetics , RNA Stability , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism , Seeds/genetics , Gene Expression Regulation, Plant , Intracellular Signaling Peptides and Proteins/genetics
19.
Nat Struct Mol Biol ; 30(3): 330-338, 2023 03.
Article in English | MEDLINE | ID: mdl-36849640

ABSTRACT

Deadenylation generally constitutes the first and pivotal step in eukaryotic messenger RNA decay. Despite its importance in posttranscriptional regulations, the kinetics of deadenylation and its regulation remain largely unexplored. Here we identify La ribonucleoprotein 1, translational regulator (LARP1) as a general decelerator of deadenylation, which acts mainly in the 30-60-nucleotide (nt) poly(A) length window. We measured the steady-state and pulse-chased distribution of poly(A)-tail length, and found that deadenylation slows down in the 30-60-nt range. LARP1 associates preferentially with short tails and its depletion results in accelerated deadenylation specifically in the 30-60-nt range. Consistently, LARP1 knockdown leads to a global reduction of messenger RNA abundance. LARP1 interferes with the CCR4-NOT-mediated deadenylation in vitro by forming a ternary complex with poly(A)-binding protein (PABP) and poly(A). Together, our work reveals a dynamic nature of deadenylation kinetics and a role of LARP1 as a poly(A) length-specific barricade that creates a threshold for deadenylation.


Subject(s)
Exoribonucleases , RNA-Binding Proteins , Exoribonucleases/metabolism , RNA-Binding Proteins/metabolism , Poly(A)-Binding Proteins/genetics , Gene Expression Regulation , RNA, Messenger/genetics , RNA, Messenger/metabolism , Poly A/metabolism
20.
J Assist Reprod Genet ; 40(4): 929-941, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36823316

ABSTRACT

Expression of the embryonic poly(A)-binding protein (EPAB) in frog, mouse, and human oocytes and early-stage embryos is maintained at high levels until embryonic genome activation (EGA) after which a significant decrease occurs in EPAB levels. Studies on the vertebrate oocytes and early embryos revealed that EPAB plays key roles in the translational regulation, stabilization, and protection of maternal mRNAs during oocyte maturation and early embryogenesis. However, it remains elusive whether EPAB interacts with other cellular proteins and undergoes phosphorylation to perform these roles. For this purpose, we identified a group of Epab-interacting proteins and its phosphorylation status in mouse germinal vesicle (GV)- and metaphase II (MII)-stage oocytes, and in 1-cell, 2-cell, and 4-cell preimplantation embryos. In the oocytes and early preimplantation embryos, Epab-interacting proteins were found to play roles in the translation and transcription processes, intracellular signaling and transport, maintenance of structural integrity, metabolism, posttranslational modifications, and chromatin remodeling. Moreover, we discovered that Epab undergoes phosphorylation on the serine, threonine, and tyrosine residues, which are localized in the RNA recognition motifs 2, 3, and 4 or C-terminal. Conclusively, these findings suggest that Epab not only functions in the translational control of maternal mRNAs through binding to their poly(A) tails but also participates in various cellular events through interacting with certain group proteins. Most likely, Epab undergoes a dynamic phosphorylation during the oocyte maturation and the early embryo development to carry out these functions.


Subject(s)
Serine , Tyrosine , Humans , Animals , Mice , Phosphorylation , Tyrosine/metabolism , Serine/metabolism , Threonine/metabolism , Oocytes , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/metabolism
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