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1.
Nature ; 588(7836): 157-163, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33239784

RESUMO

Janus kinases (JAKs) mediate responses to cytokines, hormones and growth factors in haematopoietic cells1,2. The JAK gene JAK2 is frequently mutated in the ageing haematopoietic system3,4 and in haematopoietic cancers5. JAK2 mutations constitutively activate downstream signalling and are drivers of myeloproliferative neoplasm (MPN). In clinical use, JAK inhibitors have mixed effects on the overall disease burden of JAK2-mutated clones6,7, prompting us to investigate the mechanism underlying disease persistence. Here, by in-depth phosphoproteome profiling, we identify proteins involved in mRNA processing as targets of mutant JAK2. We found that inactivation of YBX1, a post-translationally modified target of JAK2, sensitizes cells that persist despite treatment with JAK inhibitors to apoptosis and results in RNA mis-splicing, enrichment for retained introns and disruption of the transcriptional control of extracellular signal-regulated kinase (ERK) signalling. In combination with pharmacological JAK inhibition, YBX1 inactivation induces apoptosis in JAK2-dependent mouse and primary human cells, causing regression of the malignant clones in vivo, and inducing molecular remission. This identifies and validates a cell-intrinsic mechanism whereby differential protein phosphorylation causes splicing-dependent alterations of JAK2-ERK signalling and the maintenance of JAK2V617F malignant clones. Therapeutic targeting of YBX1-dependent ERK signalling in combination with JAK2 inhibition could thus eradicate cells harbouring mutations in JAK2.


Assuntos
Janus Quinase 2/genética , Janus Quinase 2/metabolismo , Neoplasias/genética , Neoplasias/patologia , Proteína 1 de Ligação a Y-Box/metabolismo , Animais , Apoptose/efeitos dos fármacos , Linhagem Celular , Células Cultivadas , Células Clonais/metabolismo , Células Clonais/patologia , Feminino , Xenoenxertos , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Íntrons/genética , Janus Quinase 2/antagonistas & inibidores , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Masculino , Camundongos , Mutação , Transplante de Neoplasias , Neoplasias/tratamento farmacológico , Fosfoproteínas/análise , Fosforilação , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Proteoma/análise , Proteômica , Splicing de RNA/genética , Indução de Remissão , Proteína 1 de Ligação a Y-Box/antagonistas & inibidores , Proteína 1 de Ligação a Y-Box/química
2.
Nucleic Acids Res ; 47(6): 3127-3141, 2019 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-30605522

RESUMO

The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity. The structure of the nucleoprotein filament indicates that the CSD of YB-1 preserved its chaperone activity also in eukaryotes and shows that mRNA is channeled between consecutive CSDs. The energy benefit needed for the formation of stable nucleoprotein filament relies on an electrostatic zipper mediated by positively charged amino acid residues in the YB-1 C-terminus. Thus, YB-1 displays a structural plasticity to unfold structured mRNAs into extended linear filaments. We anticipate that our findings will shed the light on the scanning of mRNAs by ribosomes during the initiation and elongation steps of mRNA translation.


Assuntos
Nucleoproteínas/química , Proteínas de Ligação a RNA/ultraestrutura , Proteína 1 de Ligação a Y-Box/ultraestrutura , Sequência de Aminoácidos/genética , Citoesqueleto/genética , Citoesqueleto/ultraestrutura , Escherichia coli/genética , Humanos , Nucleoproteínas/genética , Nucleoproteínas/ultraestrutura , Ligação Proteica/genética , Biossíntese de Proteínas/genética , Dobramento de Proteína , RNA Mensageiro/química , RNA Mensageiro/genética , Proteínas de Ligação a RNA/genética , Ribossomos/química , Ribossomos/genética , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/genética
3.
Int J Mol Sci ; 23(1)2021 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-35008856

RESUMO

YB-1 is a multifunctional DNA- and RNA-binding protein involved in cell proliferation, differentiation, and migration. YB-1 is a predominantly cytoplasmic protein that is transported to the nucleus in certain conditions, including DNA-damaging stress, transcription inhibition, and viral infection. In tumors, YB-1 nuclear localization correlates with high aggressiveness, multidrug resistance, and a poor prognosis. It is known that posttranslational modifications can regulate the nuclear translocation of YB-1. In particular, well-studied phosphorylation at serine 102 (S102) activates YB-1 nuclear import. Here, we report that Akt kinase phosphorylates YB-1 in vitro at serine 209 (S209), which is located in the vicinity of the YB-1 nuclear localization signal. Using phosphomimetic substitutions, we showed that S209 phosphorylation inhibits YB-1 nuclear translocation and prevents p-S102-mediated YB-1 nuclear import.


Assuntos
Núcleo Celular/metabolismo , Fosfosserina/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , Sequência de Aminoácidos , Animais , Células HeLa , Humanos , Camundongos , Células NIH 3T3 , Fosforilação , Ligação Proteica , Transporte Proteico , Proteínas Proto-Oncogênicas c-akt/metabolismo , RNA/metabolismo , Soro , Proteína 1 de Ligação a Y-Box/química
4.
RNA ; 24(12): 1706-1720, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30139801

RESUMO

Cytoplasmic localization, stability, and translation of mRNAs are controlled by their dynamic association of numerous mRNA-binding (mRNP) proteins, including cold shock domain (CSD)-containing proteins, heterogeneous nuclear ribonucleoproteins (hnRNPs), and serine/arginine-rich (SR) proteins. Here, we demonstrate that the most abundant human mRNP protein, the CSD-containing Y-box-binding protein 1 (YBX1), the closely related YBX3 protein, and other mRNP proteins, such as SRSF1, SRSF2, SRSF3, hnRNP A1, and H, specifically and efficiently interact with overlapping sets of mitochondrial tRNAs (mt tRNAs). In vitro reconstitution and in vivo binding experiments show that YBX1 recognizes the D- and/or T-stem-loop regions of mt tRNAs through relying on the RNA-binding capacity of its CSD. Cell fractionation and in vivo RNA-protein cross-linking experiments demonstrate that YBX1 and YBX3 interact with mt tRNAs in the cytosol outside of mitochondria. Cell fractionation and fluorescence in situ hybridization experiments provide evidence that mitochondrial autophagy promotes the release of mt tRNAs from the mitochondria into the cytoplasm. Association of mRNP proteins with mt tRNAs is highly dynamic; it is rapidly increased upon transcription inhibition and decreased during apoptosis. Although the cytoplasmic function of mt tRNAs remains elusive, their dynamic interactions with key mRNA-binding proteins may influence cytoplasmic mRNA stability and/or translation.


Assuntos
Citosol/química , Mitocôndrias/química , RNA de Transferência/química , Ribonucleoproteínas/química , Autofagia/genética , Ribonucleoproteína Nuclear Heterogênea A1/química , Ribonucleoproteína Nuclear Heterogênea A1/genética , Humanos , Hibridização in Situ Fluorescente , Mitocôndrias/genética , RNA Mensageiro/química , RNA Mensageiro/genética , RNA de Transferência/genética , Ribonucleoproteínas/genética , Fatores de Processamento de Serina-Arginina/química , Fatores de Processamento de Serina-Arginina/genética , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/genética
5.
Biochemistry (Mosc) ; 85(Suppl 1): S1-S19, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32087051

RESUMO

This review summarizes the features of cold shock domain (CSD) proteins in the context of their interactions with nucleic acids and describes similarities and differences in the structure of cold shock proteins of prokaryotes and CSD proteins of eukaryotes with special emphasis on the functions related to the RNA/DNA-binding ability of these proteins. The mechanisms and specificity of their interaction with nucleic acids in relation to the growing complexity of protein domain structure are described, as well as various complexes of the mammalian Y-box binding protein 1 (YB-1) with nucleic acids (filaments, globules, toroids). The role of particular amino acid residues in the binding of nitrogenous bases and the sugar-phosphate backbone of nucleic acids is emphasized. The data on the nucleic acid sequences recognized by the Y-box binding proteins are systematized. Post-translational modifications of YB-1, especially its phosphorylation, affect the recognition of specific sequences in the promoter regions of various groups of genes by YB-1 protein. The data on the interaction of Lin28 protein with let-7 miRNAs are summarized. The features of the domain structure of plant CSD proteins and their effect on the interaction with nucleic acids are discussed.


Assuntos
Proteínas e Peptídeos de Choque Frio/química , Proteínas e Peptídeos de Choque Frio/metabolismo , Ácidos Nucleicos/metabolismo , Domínios Proteicos , Processamento de Proteína Pós-Traducional , Proteína 1 de Ligação a Y-Box/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas e Peptídeos de Choque Frio/genética , Temperatura Baixa , Regulação da Expressão Gênica , Humanos , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Proteína 1 de Ligação a Y-Box/química
6.
Fish Shellfish Immunol ; 93: 406-415, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31369857

RESUMO

Mandarin fish (Siniperca chuatsi) is a universally farmed fish species in China and has a large farming scale and economic value. With the high-density cultural mode in mandarin fish, viral diseases, such as infectious spleen and kidney necrosis virus (ISKNV) and Siniperca chuatsi rhabdovirus (SCRV), have increased loss, which has seriously restricted the development of aquaculture. Y-Box binding protein 1 (YB-1) is a member of cold shock protein family that regulates multiple cellular processes. The roles of mammalian YB-1 protein in environmental stress and innate immunity have been studied well, but its roles in teleost fishes remain unknown. In the present study, the characteristic of S. chuatsi YB-1 (scYB-1) and its roles in cold stress and virus infection were investigated. The scYB-1 obtained an 1541 bp cDNA that contains a 903 bp open reading frame encoding a protein of 300 amino acids. Tissue distribution results showed that the scYB-1 is a ubiquitously expressed gene found among tissues from mandarin fish. Overexpression of scYB-1 can increase the expression levels of cold shock-responsive genes, such as scHsc70a, scHsc70b, and scp53. Furthermore, the role of scYB-1 in innate immunity was also investigated in mandarin fish fry (MFF-1) cells. The expression level of scYB-1 was significant change in response to poly (I:C), poly (dG:dC), PMA, ISKNV, or SCRV stimulation. The overexpression of scYB-1 can significantly increase the expression levels of NF-κB-responsive genes, including scIL-8, scTNF-α, and scIFN-h. The NF-κB-luciferase report assay results showed that the relative expression of luciferin was significantly increased in the cells overexpressed with scYB-1 compared with those in cells overexpressed with control plasmid. These results indicate that scYB-1 can induce the NF-κB signaling pathway in MFF-1 cells. Overexpressed scYB-1 can downregulate the expression of ISKNV viral major capsid protein (mcp) gene but upregulates the expression of SCRV mcp gene. Moreover, knockdown of scYB-1 using siRNA can upregulate the expression of ISKNV mcp gene but downregulates the expression of SCRV mcp gene. These results indicate that scYB-1 suppresses ISKNV infection while enhancing SCRV infection. The above observations suggest that scYB-1 is involved in cold stress and virus infection. Our study will provide an insight into the roles of teleost fish YB-1 protein in stress response and innate immunity.


Assuntos
Doenças dos Peixes/imunologia , Peixes/genética , Peixes/imunologia , Regulação da Expressão Gênica/imunologia , Imunidade Inata/genética , Proteína 1 de Ligação a Y-Box/genética , Proteína 1 de Ligação a Y-Box/imunologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Infecções por Vírus de DNA/imunologia , Infecções por Vírus de DNA/veterinária , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/imunologia , Perfilação da Expressão Gênica/veterinária , Iridoviridae/fisiologia , Filogenia , Poli I-C/farmacologia , Polidesoxirribonucleotídeos/farmacologia , Rhabdoviridae/fisiologia , Infecções por Rhabdoviridae/imunologia , Infecções por Rhabdoviridae/veterinária , Alinhamento de Sequência/veterinária , Acetato de Tetradecanoilforbol/farmacologia , Proteína 1 de Ligação a Y-Box/química
7.
J Biol Chem ; 292(2): 539-550, 2017 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-27856639

RESUMO

Human YVH1 (hYVH1), also known as dual specificity phosphatase 12 (DUSP12), is a poorly characterized atypical dual specificity phosphatase widely conserved throughout evolution. Recent findings have demonstrated that hYVH1 expression affects cellular DNA content and is a novel cell survival phosphatase preventing both thermal and oxidative stress-induced cell death, whereas studies in yeast have established YVH1 as a novel 60S ribosome biogenesis factor. In this study, we have isolated novel hYVH1-associating proteins from human U2OS osteosarcoma cells using affinity chromatography coupled to mass spectrometry employing ion mobility separation. Numerous ribosomal proteins were identified, confirming the work done in yeast. Furthermore, proteins known to be present on additional RNP particles were identified, including Y box-binding protein 1 (YB-1) and fragile X mental retardation protein, proteins that function in translational repression and stress granule regulation. Follow-up studies demonstrated that hYVH1 co-localizes with YB-1 and fragile X mental retardation protein on stress granules in response to arsenic treatment. Interestingly, hYVH1-positive stress granules were significantly smaller, whereas knocking down hYVH1 expression attenuated stress granule breakdown during recovery from arsenite stress, indicating a possible role for hYVH1 in stress granule disassembly. These results propagate a role for dual specificity phosphatases at RNP particles and suggest that hYVH1 may affect a variety of fundamental cellular processes by regulating messenger ribonucleoprotein (mRNP) dynamics.


Assuntos
Grânulos Citoplasmáticos/metabolismo , Fosfatase 1 de Especificidade Dupla/metabolismo , Ribonucleoproteínas/metabolismo , Arsenitos/farmacologia , Linhagem Celular Tumoral , Grânulos Citoplasmáticos/química , Fosfatase 1 de Especificidade Dupla/química , Fosfatase 1 de Especificidade Dupla/isolamento & purificação , Humanos , Ribonucleoproteínas/química , Ribonucleoproteínas/isolamento & purificação , Proteínas Ribossômicas/química , Proteínas Ribossômicas/isolamento & purificação , Proteínas Ribossômicas/metabolismo , Estresse Fisiológico/efeitos dos fármacos , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/isolamento & purificação , Proteína 1 de Ligação a Y-Box/metabolismo
8.
Arch Biochem Biophys ; 660: 129-136, 2018 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-30321499

RESUMO

The transduction of signal by the Notch receptors to the intracellular domain is highly regulated and relies on binding of the ligands to the Epidermal growth factor Like Repeats (ELRs) of receptor's extracellular domain. Both canonical and non-canonical ligands are known to interact with different ELRs and activate Notch receptors. The aim of this study was to investigate the interaction of a soluble non-canonical ligand, Y box-1 (Yb-1) with Notch3 receptor ELRs. Polyclonal antibodies were employed as novel tools to identify the binding site of this ligand. Using various ligand binding and signaling assays, soluble Yb-1 was found to interact specifically with the Notch3 receptor, but not with Notch1. The ELRs 17-24 of Notch3 were identified as the binding site for Yb-1. Further, Yb-1 and Notch3 ELRs 17-24 structures were modelled and the Yb-1-Notch3 interaction interface was predicted to be Notch3 ELRs 20-23. Binding of the Yb-1 with Notch3 ELRs different from those reported for canonical DSL ligands also transduced the signal to the intracellular domain through the negative regulatory region. In conclusion, study highlights the importance of molecular modifications in different Notch3 ELRs for the transduction of signal to the negative regulatory region.


Assuntos
Fator de Crescimento Epidérmico/química , Receptor Notch3/metabolismo , Sequências Repetitivas de Aminoácidos , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/metabolismo , Animais , Células CHO , Cricetulus , Proteína Jagged-1/metabolismo , Ligantes , Ligação Proteica , Domínios Proteicos , Transdução de Sinais , Solubilidade
9.
RNA Biol ; 15(3): 359-368, 2018 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-29028411

RESUMO

PAR-CLIP (photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation) facilitates the identification and mapping of protein/RNA interactions. So far, it has been limited to select cell-lines as it requires efficient 4SU uptake. To increase transcriptome complexity and thus identify additional RNA-protein interaction sites we fused HEK 293 T-Rex cells (HEK293-Y) that express the RNA binding protein YBX1 with PC12 cells expressing eGFP (PC12-eGFP). The resulting hybrids enable PAR-CLIP on a neuronally expanded transcriptome (Fusion-CLIP) and serve as a proof of principle. The fusion cells express both parental marker genes YBX1 and eGFP and the expanded transcriptome contains human and rat transcripts. PAR-CLIP of fused cells versus the parental HEK293-Y identified 768 novel RNA targets of YBX1. We were able to trace the origin of the majority of the short PAR-CLIP reads as they differentially mapped to the human and rat genome. Furthermore, Fusion-CLIP expanded the CAUC RNA binding motif of YBX1 to UCUUUNNCAUC. The fusion of HEK293-Y and PC12-eGFP cells resulted in cells with a diverse genome expressing human and rat transcripts that enabled the identification of novel YBX1 substrates. The technique allows the expansion of the HEK 293 transcriptome and makes PAR-CLIP available to fusion cells of diverse origin.


Assuntos
Fusão Celular/métodos , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/metabolismo , RNA Mensageiro/metabolismo , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/metabolismo , Motivos de Aminoácidos , Animais , Sítios de Ligação , Reagentes de Ligações Cruzadas , Perfilação da Expressão Gênica/métodos , Células HEK293 , Humanos , Imunoprecipitação , Células PC12 , Ligação Proteica , Ratos
10.
Nucleic Acids Res ; 44(14): 6949-60, 2016 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-27174937

RESUMO

Stress-induced angiogenin (ANG)-mediated tRNA cleavage promotes a cascade of cellular events that starts with production of tRNA-derived stress-induced RNAs (tiRNAs) and culminates with enhanced cell survival. This stress response program relies on a subset tiRNAs that inhibit translation initiation and induce the assembly of stress granules (SGs), cytoplasmic ribonucleoprotein complexes with cytoprotective and pro-survival properties. SG-promoting tiRNAs bear oligoguanine motifs at their 5'-ends, assemble G-quadruplex-like structures and interact with the translational silencer YB-1. We used CRISPR/Cas9-based genetic manipulations and biochemical approaches to examine the role of YB-1 in tiRNA-mediated translational repression and SG assembly. We found that YB-1 directly binds to tiRNAs via its cold shock domain. This interaction is required for packaging of tiRNA-repressed mRNAs into SGs but is dispensable for tiRNA-mediated translational repression. Our studies reveal the functional role of YB-1 in the ANG-mediated stress response program.


Assuntos
Grânulos Citoplasmáticos/metabolismo , Biossíntese de Proteínas , RNA de Transferência/metabolismo , Estresse Fisiológico , Proteína 1 de Ligação a Y-Box/metabolismo , Sequência de Aminoácidos , Arsenitos/farmacologia , Sequência de Bases , Sistemas CRISPR-Cas/genética , Proliferação de Células , Sobrevivência Celular , Grânulos Citoplasmáticos/efeitos dos fármacos , Fator de Iniciação 4F em Eucariotos/metabolismo , Deleção de Genes , Técnicas de Inativação de Genes , Heterogeneidade Genética , Humanos , Células MCF-7 , Modelos Moleculares , Biossíntese de Proteínas/efeitos dos fármacos , RNA Guia de Cinetoplastídeos/metabolismo , RNA de Transferência/genética , Compostos de Sódio/farmacologia , Estresse Fisiológico/efeitos dos fármacos , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/genética
11.
Biochim Biophys Acta ; 1864(12): 1631-1640, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27544639

RESUMO

Base excision repair (BER) is a flagship DNA repair system responsible for maintaining genome integrity. Apart from basal enzymes, this system involves several accessory factors essential for coordination and regulation of DNA processing during substrate channeling. Y-box-binding protein 1 (YB-1), a multifunctional factor that can interact with DNA, RNA, poly(ADP-ribose) and plenty of proteins including DNA repair enzymes, is increasingly considered as a non-canonical protein of BER. Here we provide quantitative characterization of YB-1 physical interactions with key BER factors such as PARP1, PARP2, APE1, NEIL1 and pol ß and comparison of the full-length YB-1 and its C-terminally truncated nuclear form in regard to their binding affinities for BER proteins. Data on functional interactions reveal strong stimulation of PARP1 autopoly(ADP-ribosyl)ation and inhibition of poly(ADP-ribose) degradation by PARG in the presence of YB-1. Moreover, YB-1 is shown to stimulate AP lyase activity of NEIL1 and to inhibit dRP lyase activity of pol ß on model DNA duplex structure. We also demonstrate for the first time YB-1 poly(ADP-ribosyl)ation in the presence of RNA.


Assuntos
Reparo do DNA/fisiologia , Proteína 1 de Ligação a Y-Box/metabolismo , Animais , Dano ao DNA , DNA Glicosilases/metabolismo , DNA Polimerase beta/metabolismo , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/química , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/genética , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/metabolismo , Humanos , Camundongos , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Poli(ADP-Ribose) Polimerase-1/genética , Poli(ADP-Ribose) Polimerase-1/metabolismo , Poli(ADP-Ribose) Polimerases/genética , Poli(ADP-Ribose) Polimerases/metabolismo , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Espectrometria de Fluorescência , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/genética
12.
Genes Cells ; 21(6): 648-60, 2016 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-27168020

RESUMO

Y-box binding protein 1 (YBX-1 or YB-1) is an oncoprotein that promotes replicative immortality, tumor cell invasion and metastasis. The increase in the abundance of YB-1 in the cell or YB-1 translocation from the cytoplasm to the nucleus is characteristic of malignant cell growth. We have previously reported that ΔNp63α, a transcription factor that is known to play a pivotal role in keratinocyte proliferation and differentiation, promotes YB-1 nuclear accumulation. Here, we show that YB-1 is highly expressed in proliferating keratinocytes and is down-regulated during keratinocyte differentiation. ΔNp63α reduces YB-1 protein turnover and leads to accumulation of ubiquitin-conjugated YB-1 into the nucleus. Reduction of YB-1 protein level, following treatment with a DNA-damaging agent, is inhibited by ΔNp63α suggesting that YB-1 and ΔNp63α interplay can support keratinocyte proliferation and protect cells from apoptosis under genotoxic stress.


Assuntos
Queratinócitos/citologia , Fatores de Transcrição/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Proteína 1 de Ligação a Y-Box/química , Ciclo Celular , Diferenciação Celular , Linhagem Celular Tumoral , Regulação para Baixo , Humanos , Queratinócitos/metabolismo , Estabilidade Proteica , Proteína 1 de Ligação a Y-Box/metabolismo
13.
Biochim Biophys Acta Proteins Proteom ; 1865(6): 664-673, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28341602

RESUMO

Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC. RNA hairpins other than those mentioned above pull out neither YB-1 nor NSUN2. Both these proteins are found in exosomes secreted by HEK293 cells. YB-1 for all that is detected as a form having a slightly higher electrophoretic mobility than that of YB-1 associated with the above RNA hairpins, assuming changes in posttranslational modifications of the protein during its transfer from cytoplasm into exosomes. Next generation sequencing of total exosomal RNA (eRNA) reveals a large representative set of RNA species, including mRNAs containing the above-mentioned motifs. The degree of enrichment in exosomes with this kind of mRNAs strongly depends on the locations of eRNA-specific motifs within the mRNA sequences. Altogether, our findings point to YB-1 and NSUN2 as possible mediators of the process of transfer of specific mRNAs into exosomes, allowing us to speculate on an involvement of these proteins in the mRNA sorting via the recognition of the above motifs.


Assuntos
Citosol/metabolismo , Exossomos/metabolismo , Metiltransferases/metabolismo , RNA Mensageiro/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , Sequência de Aminoácidos , Citometria de Fluxo , Células HEK293 , Humanos , Metiltransferases/química , Microscopia Imunoeletrônica , RNA Mensageiro/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Proteína 1 de Ligação a Y-Box/química
14.
Nucleic Acids Res ; 43(19): 9457-73, 2015 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-26271991

RESUMO

Translation is tightly regulated in cells for keeping adequate protein levels, this task being notably accomplished by dedicated mRNA-binding proteins recognizing a specific set of mRNAs to repress or facilitate their translation. To select specific mRNAs, mRNA-binding proteins can strongly bind to specific mRNA sequences/structures. However, many mRNA-binding proteins rather display a weak specificity to short and redundant sequences. Here we examined an alternative mechanism by which mRNA-binding proteins could inhibit the translation of specific mRNAs, using YB-1, a major translation regulator, as a case study. Based on a cooperative binding, YB-1 forms stable homo-multimers on some mRNAs while avoiding other mRNAs. Via such inhomogeneous distribution, YB-1 can selectively inhibit translation of mRNAs on which it has formed stable multimers. This novel mechanistic view on mRNA selection may be shared by other proteins considering the elevated occurrence of multimerization among mRNA-binding proteins. Interestingly, we also demonstrate how, by using the same mechanism, YB-1 can form multimers on specific DNA structures, which could provide novel insights into YB-1 nuclear functions in DNA repair and multi-drug resistance.


Assuntos
DNA/metabolismo , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , Animais , Células Cultivadas , DNA/ultraestrutura , DNA Topoisomerases Tipo II/metabolismo , DNA Super-Helicoidal/metabolismo , Microscopia de Força Atômica , Ligação Proteica , Biossíntese de Proteínas , Multimerização Proteica , Estrutura Terciária de Proteína , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/ultraestrutura , Ratos , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/ultraestrutura
15.
Biochem Biophys Res Commun ; 480(4): 629-634, 2016 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-27794479

RESUMO

The DNA/RNA-binding protein YB-1 (Y-box binding protein 1) performs multiple functions both in the cytoplasm and the nucleus of the cell. Generally localized to the cytoplasm, under certain conditions YB-1 is translocated to the nucleus. Here we report for the first time a transport factor that mediates YB-1 nuclear import - transportin-1. The YB-1/transportin-1 complex can be isolated from HeLa cell extract. Nuclear import of YB-1 and its truncated form YB-1 (1-219) in in vitro transport assay was diminished in the presence of a competitor substrate and ceased in the presence of transportin-1 inhibitor M9M. Inhibitors of importin ß1 had no effect on YB-1 transport. Furthermore, transport of YB-1 (P201A/Y202A) and YB-1 (1-219) (P201A/Y202A) bearing inactivating mutations in the transportin-1-dependent nuclear localization signal was practically abolished. Together, these results indicate that transportin-1 mediates YB-1 nuclear translocation.


Assuntos
Núcleo Celular/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , beta Carioferinas/metabolismo , Transporte Ativo do Núcleo Celular/fisiologia , Sítios de Ligação , Células HeLa , Humanos , Ligação Proteica , Proteína 1 de Ligação a Y-Box/química , beta Carioferinas/química
16.
Biochim Biophys Acta ; 1834(2): 559-67, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23220387

RESUMO

YB-1 is a major mRNP protein participating in the regulation of transcription and translation of a wide range of eukaryotic genes in many organisms probably due to its influence on mRNA packing into mRNPs. While the functional properties of YB-1 are extensively studied, little is known about its structural properties. In the present work we focused on studying its secondary structure, rigidity of its tertiary structure, compactness, and oligomerization in vitro by using far UV-CD, DSC, one-dimensional (1)H NMR, SAXS, sedimentation and FPLC. It was shown that only the cold shock domain within the entire YB-1 chain has a well-packed tertiary structure undergoing cooperative heat and cold denaturation transitions. In contrast, the rest of the YB-1 molecule is not rigidly packed and consists of PP II-like helical secondary structure elements and coil-like regions. At the same time, the overall dimension of the protein molecule is unexpectedly small. The polypeptide chains of YB-1 have a high tendency to form oligomers at neutral pH, while the extent and structural organization of the oligomers depend on protein concentration and ionic strength varying from compact monomeric units up to high molecular weight oligomers. These oligomers in solution are unstable and dissociate upon protein concentration decrease.


Assuntos
Multimerização Proteica/fisiologia , Ribonucleoproteínas/química , Proteína 1 de Ligação a Y-Box/química , Animais , Concentração de Íons de Hidrogênio , Ressonância Magnética Nuclear Biomolecular , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Coelhos , Ribonucleoproteínas/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo
17.
Nucleic Acids Res ; 40(17): 8622-36, 2012 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-22730292

RESUMO

The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein-protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3' splice sites in mammalian cells.


Assuntos
Processamento Alternativo , Éxons , Íntrons , Proteínas Nucleares/metabolismo , Proteínas de Ligação a RNA/metabolismo , Ribonucleoproteínas/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , Sítios de Ligação , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Células HEK293 , Humanos , Receptores de Hialuronatos/genética , Receptores de Hialuronatos/metabolismo , Proteínas Nucleares/química , Motivos de Nucleotídeos , Domínios e Motivos de Interação entre Proteínas , RNA/química , RNA/metabolismo , Precursores de RNA/metabolismo , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/química , Ribonucleoproteínas/química , Técnica de Seleção de Aptâmeros , Fator de Processamento U2AF , Proteína 1 de Ligação a Y-Box/química
18.
BMC Mol Biol ; 14: 14, 2013 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-23822148

RESUMO

BACKGROUND: Tip110 plays important roles in tumor immunobiology, pre-mRNA splicing, expression regulation of viral and host genes, and possibly protein turnover. It is clear that our understanding of Tip110 biological function remains incomplete. RESULTS: Herein, we employed an immunoaffinity-based enrichment approach combined with protein mass spectrometry and attempted to identify Tip110-interacting cellular proteins. A total of 13 major proteins were identified to be complexed with Tip110. Among them was Y-box binding protein 1 (YB-1). The interaction of Tip110 with YB-1 was further dissected and confirmed to be specific and involve the N-terminal of both Tip110 and YB-1 proteins. A HIV-1 LTR promoter-driven reporter gene assay and a CD44 minigene in vivo splicing assay were chosen to evaluate the functional relevance of the Tip110/YB-1 interaction. We showed that YB-1 potentiates the Tip110/Tat-mediated transactivation of the HIV-1 LTR promoter while Tip110 promotes the inclusion of the exon 5 in CD44 minigene alternative splicing. CONCLUSIONS: Tip110 and YB-1 interact to form a complex and mutually regulate each other's biological functions.


Assuntos
Antígenos de Neoplasias/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo , Motivos de Aminoácidos , Antígenos de Neoplasias/química , Antígenos de Neoplasias/genética , Linhagem Celular , Repetição Terminal Longa de HIV , Humanos , Ligação Proteica , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Ativação Transcricional , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/genética , Produtos do Gene tat do Vírus da Imunodeficiência Humana/genética , Produtos do Gene tat do Vírus da Imunodeficiência Humana/metabolismo
19.
Cell Commun Signal ; 11: 63, 2013 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-24103640

RESUMO

BACKGROUND: The Y-box protein-1 (YB-1) fulfills pleiotropic functions relating to gene transcription, mRNA processing, and translation. It remains elusive how YB-1 shuttling into the nuclear and cytoplasmic compartments is regulated and whether limited proteolysis by the 20S proteasome releases fragments with distinct function(s) and subcellular distribution(s). RESULTS: To address these questions, mapping of domains responsible for subcellular targeting was performed. Three nuclear localization signals (NLS) were identified. NLS-1 (aa 149-156) and NLS-2 (aa 185-194) correspond to residues with unknown function(s), whereas NLS-3 (aa 276-292) matches with a designated multimerization domain. Nuclear export signal(s) were not identified. Endoproteolytic processing by the 20S proteasome before glycine 220 releases a carboxy-terminal fragment (CTF), which localized to the nucleus, indicating that NLS-3 is operative. Genotoxic stress induced proteolytic cleavage and nuclear translocation of the CTF. Co-expression of the CTF and full-length YB-1 resulted in an abrogated transcriptional activation of the MMP-2 promoter, indicating an autoregulatory inhibitory loop, whereas it fulfilled similar trans-repressive effects on the collagen type I promoter. CONCLUSION: Compartmentalization of YB-1 protein derivatives is controlled by distinct NLS, one of which targets a proteolytic cleavage product to the nucleus. We propose a model for an autoregulatory negative feedback loop that halts unlimited transcriptional activation.


Assuntos
Proteína 1 de Ligação a Y-Box/metabolismo , Animais , Linhagem Celular , Linhagem Celular Tumoral , Células Cultivadas , Humanos , Células Mesangiais/metabolismo , Sinais de Exportação Nuclear , Sinais de Localização Nuclear/metabolismo , Estrutura Terciária de Proteína , Proteólise , Ratos , Transcrição Gênica , Proteína 1 de Ligação a Y-Box/química
20.
Bioessays ; 32(2): 109-18, 2010 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-20091748

RESUMO

Cold shock domain (CSD)-containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post-transcriptional gene regulation. The CSD is an ancient beta-barrel fold that serves to bind nucleic acids. The CSD is structurally and functionally similar to the S1 domain, a fold with otherwise unrelated primary sequence. The flexibility of the CSD/S1 domain for RNA recognition confers an enormous functional versatility to the proteins that contain them. This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD.


Assuntos
Células Eucarióticas/metabolismo , Fatores de Iniciação em Eucariotos/metabolismo , Proteínas de Choque Térmico/metabolismo , Animais , Proteínas de Caenorhabditis elegans/química , Proteínas de Caenorhabditis elegans/classificação , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Fatores de Iniciação em Eucariotos/química , Fatores de Iniciação em Eucariotos/classificação , Fatores de Iniciação em Eucariotos/genética , Exossomos/metabolismo , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica/fisiologia , Proteínas de Choque Térmico/química , Proteínas de Choque Térmico/classificação , Proteínas de Choque Térmico/genética , Humanos , Filogenia , Estrutura Secundária de Proteína , Proteínas Repressoras/química , Proteínas Repressoras/classificação , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Proteína 1 de Ligação a Y-Box/química , Proteína 1 de Ligação a Y-Box/classificação , Proteína 1 de Ligação a Y-Box/genética , Proteína 1 de Ligação a Y-Box/metabolismo
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