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Svitkin YV, Yanagiya A, Karetnikov AE, Alain T, Fabian MR, Khoutorsky A, Perreault S, Topisirovic I, Sonenberg N. Control of translation and miRNA-dependent repression by a novel poly(A) binding protein, hnRNP-Q. PLoS Biol 2013; 11:e1001564. [PMID: 23700384 PMCID: PMC3660254 DOI: 10.1371/journal.pbio.1001564] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/10/2013] [Indexed: 02/05/2023] Open
Abstract
The heterogeneous nuclear ribonucleoprotein Q2 competitively binds mRNA poly(A) tails to regulate translational and miRNA-related functions of PABP. Translation control often operates via remodeling of messenger ribonucleoprotein particles. The poly(A) binding protein (PABP) simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation. PABP also promotes miRNA-dependent deadenylation and translational repression of target mRNAs. We demonstrate that isoform 2 of the mouse heterogeneous nuclear protein Q (hnRNP-Q2/SYNCRIP) binds poly(A) by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to poly(A) in vitro. Depleting hnRNP-Q2 from translation extracts stimulates cap-dependent and IRES-mediated translation that is dependent on the PABP/poly(A) complex. Adding recombinant hnRNP-Q2 to the extracts inhibited translation in a poly(A) tail-dependent manner. The displacement of PABP from the poly(A) tail by hnRNP-Q2 impaired the association of eIF4E with the 5′ m7G cap structure of mRNA, resulting in the inhibition of 48S and 80S ribosome initiation complex formation. In mouse fibroblasts, silencing of hnRNP-Q2 stimulated translation. In addition, hnRNP-Q2 impeded let-7a miRNA-mediated deadenylation and repression of target mRNAs, which require PABP. Thus, by competing with PABP, hnRNP-Q2 plays important roles in the regulation of global translation and miRNA-mediated repression of specific mRNAs. The regulation of mRNA translation and stability is of paramount importance for almost every cellular function. In eukaryotes, the poly(A) binding protein (PABP) is a central regulator of both global and mRNA-specific translation. PABP simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G). These interactions circularize the mRNA and stimulate translation. PABP also regulates specific mRNAs by promoting miRNA-dependent deadenylation and translational repression. A key step in understanding PABP's functions is to identify factors that affect its association with the poly(A) tail. Here we show that the cytoplasmic isoform of the mouse heterogeneous nuclear ribonucleoprotein Q (hnRNP-Q2/SYNCRIP), which exhibits binding preference to poly(A), interacts with the poly(A) tail by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to the poly(A) tail. Depleting hnRNP-Q2 stimulates translation in cell-free extracts and in cultured cells, in agreement with its function as translational repressor. In addition, hnRNP-Q2 impeded miRNA-mediated deadenylation and repression of target mRNAs, which requires PABP. Thus, competition from hnRNP-Q2 provides a novel mechanism by which multiple functions of PABP are regulated. This regulation could play important roles in various biological processes, such as development, viral infection, and human disease.
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Affiliation(s)
- Yuri V. Svitkin
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Akiko Yanagiya
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Alexey E. Karetnikov
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Tommy Alain
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Marc R. Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Arkady Khoutorsky
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Sandra Perreault
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Sasaki K, Kim MH, Imai R. Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 is a negative regulator of cold acclimation. THE NEW PHYTOLOGIST 2013; 198:95-102. [PMID: 23323758 DOI: 10.1111/nph.12118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/27/2012] [Indexed: 06/01/2023]
Abstract
Bacterial cold shock proteins (CSPs) act as RNA chaperones that destabilize mRNA secondary structures at low temperatures. Bacterial CSPs are composed solely of a nucleic acid-binding domain termed the cold shock domain (CSD). Plant CSD proteins contain an auxiliary domain in addition to the CSD but also show RNA chaperone activity. However, their biological functions are poorly understood. We examined Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 (AtCSP2) using overexpressing and mutant lines. A double mutant, with reduced AtCSP2 and no AtCSP4, showed higher freezing tolerance than the wild-type when cold-acclimated. The increase in freezing tolerance was associated with up-regulation of CBF transcription factors and their downstream genes. By contrast, overexpression of AtCSP2 resulted in decreased freezing tolerance when cold-acclimated. In addition, late flowering and shorter siliques were observed in the overexpressing lines. AtCSP2 negatively regulates freezing tolerance and is partially redundant with its closest paralog, AtCSP4.
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Affiliation(s)
- Kentaro Sasaki
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Myung-Hee Kim
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
| | - Ryozo Imai
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
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Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 synthesis is regulated by mTOR signaling pathway. PLoS One 2012; 7:e52527. [PMID: 23285076 PMCID: PMC3527543 DOI: 10.1371/journal.pone.0052527] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/16/2012] [Indexed: 02/07/2023] Open
Abstract
YB-1 is a eukaryotic protein with numerous intra- and extracellular functions based on its ability to interact with RNA, DNA, and many proteins. In spite of achievements in studying its functions, regulation of YB-1 synthesis in the cell remains poorly understood. In the current study Western and Northern blotting were used to determine the amounts of YB-1 and YB-1 mRNA in rabbit organs and several cell lines. As found, in the majority of studied eukaryotic cells a considerable proportion of YB-1 mRNA was stored in free mRNPs, i.e., was poorly translated. Also, we demonstrated that YB-1 synthesis depended on conditions that determined the rate of cell division. Specific suppression of YB-1 synthesis resulted from inhibition of the mTOR signaling pathway with inhibitor PP242, but not rapamycin. Experiments on reporter constructs showed that dependence of YB-1 mRNA translation on activity of the mTOR signaling pathway was dictated by 5′ untranslated regions of this mRNA, irrelatively of the TOP-like sequences at the beginning of 5′ UTR.
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Affiliation(s)
- Dmitry N. Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Irina A. Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Lev P. Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
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54
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Li W, Wang X, Gao G. Expression of YB-1 enhances production of murine leukemia virus vectors by stabilizing genomic viral RNA. Protein Cell 2012; 3:943-9. [PMID: 23225179 DOI: 10.1007/s13238-012-2090-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 09/04/2012] [Indexed: 12/25/2022] Open
Abstract
Murine leukemia virus (MLV)-based retroviral vectors is widely used for gene transfer and basic research, and production of high-titer retroviral vectors is very important. Here we report that expression of the Y-box binding protein 1 (YB-1) enhanced the production of infectious MLV vectors. YB-1 specifically increased the stability of viral genomic RNA in virus-producing cells, and thus increasing viral RNA levels in both producer cells and virion particles. The viral element responsive to YB-1 was mapped to the repeat sequence (R region) in MLV genomic RNA. These results identified YB-1 as a MLV mRNA stabilizer, which can be used for improving production of MLV vectors.
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Affiliation(s)
- Wei Li
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Somasekharan SP, Stoynov N, Rotblat B, Leprivier G, Galpin JD, Ahern CA, Foster LJ, Sorensen PHB. Identification and quantification of newly synthesized proteins translationally regulated by YB-1 using a novel Click-SILAC approach. J Proteomics 2012; 77:e1-10. [PMID: 22967496 DOI: 10.1016/j.jprot.2012.08.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/03/2012] [Accepted: 08/27/2012] [Indexed: 01/03/2023]
Abstract
Messenger RNA-binding translational regulatory proteins determine in large part the spectrum of transcripts that are translated under specific cellular contexts. Y-box binding protein-1 (YB-1) is a conserved eukaryotic translational regulator that is implicated in cancer progression. To identify specific proteins that are translationally regulated by YB-1, we established a pulse-labelling approach combining Click chemistry and stable isotope labelling by amino acids in cell culture (SILAC). The proteome of TC32 human Ewing sarcoma cells, which robustly express YB-1, was compared with or without YB-1 siRNA knockdown. Cells labelled with light or heavy isotopologs of Arg and Lys were then cotranslationally pulsed with the methionine derivative, azidohomoalanine (AHA). Cells were lysed and newly synthesized proteins were selectively derivatized via a Click (3+2 cycloaddition) reaction to add an alkyne biotin tag. They were then affinity purified and subjected to liquid chromatography-tandem mass spectrometry. This combined Click-SILAC approach enabled us to catalog and quantify newly synthesized proteins regulated by YB-1 after only 45 min of labelling. Bioinformatic analysis revealed that YB-1 regulated proteins are involved in diverse biological pathways. We anticipate that this Click-SILAC strategy will be useful for studying short-term protein synthesis in different cell culture systems and under diverse biological contexts.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada BC V6T 1Z4
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Y-box binding protein 1 and RNase UK114 mediate monocyte chemoattractant protein 1 mRNA stability in vascular smooth muscle cells. Mol Cell Biol 2012; 32:3768-75. [PMID: 22801372 DOI: 10.1128/mcb.00846-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Monocyte chemoattractant protein 1 (MCP-1) plays a pivotal role in many inflammatory processes, including the progression of atherosclerosis and the response of the arterial wall to injury. We previously demonstrated that dexamethasone (Dex) inhibits MCP-1 mRNA accumulation in smooth muscle cells by decreasing its half-life. The effect of Dex was dependent upon the glucocorticoid receptor (GR) and independent of new transcription. Using RNA affinity and column chromatography, we have identified two proteins involved in regulating MCP-1 mRNA stability: Y-box binding protein 1 (YB-1), a multifunctional DNA/RNA-binding protein, and endoribonuclease UK114 (UK). By immunoprecipitation, YB and GR formed a complex present in equal amounts in extracts from untreated and Dex-treated cells. YB-1, UK, and GR small interfering RNA (siRNA) substantially inhibited the effect of Dex on MCP-1 mRNA accumulation. In addition, YB-1 antibody blocked the degradation of MCP-1 mRNA by cytoplasmic extracts from the Dex-treated cells. The degradative activity of extracts immunoprecipitated with antibodies to either YB-1 or GR was blocked with UK antibody. UK did not degrade MCP-1 mRNA; however, upon addition to nondegrading control extracts, it rapidly degraded MCP-1 mRNA. These studies define new roles for GR, YB-1, and UK in the formation of a molecular complex that degrades MCP-1 mRNA.
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Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. Y-box-binding protein 1 (YB-1) and its functions. BIOCHEMISTRY (MOSCOW) 2012; 76:1402-33. [PMID: 22339596 DOI: 10.1134/s0006297911130049] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the structure and functions of Y-box binding protein 1 (YB-1) and its homologs. Interactions of YB-1 with DNA, mRNAs, and proteins are considered. Data on the participation of YB-1 in DNA reparation and transcription, mRNA splicing and translation are systematized. Results on interactions of YB-1 with cytoskeleton components and its possible role in mRNA localization are discussed. Data on intracellular distribution of YB-1, its redistribution between the nucleus and the cytoplasm, and its secretion and extracellular functions are summarized. The effect of YB-1 on cell differentiation, its involvement in extra- and intracellular signaling pathways, and its role in early embryogenesis are described. The mechanisms of regulation of YB-1 expression in the cell are presented. Special attention is paid to the involvement of YB-1 in oncogenic cell transformation, multiple drug resistance, and dissemination of tumors. Both the oncogenic and antioncogenic activities of YB-1 are reviewed. The potential use of YB-1 in diagnostics and therapy as an early cancer marker and a molecular target is discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Ribonucleoprotein Y-box-binding protein-1 regulates mitochondrial oxidative phosphorylation (OXPHOS) protein expression after serum stimulation through binding to OXPHOS mRNA. Biochem J 2012; 443:573-84. [PMID: 22280412 DOI: 10.1042/bj20111728] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play key roles in essential cellular functions, such as energy production, metabolic pathways and aging. Growth factor-mediated expression of the mitochondrial OXPHOS (oxidative phosphorylation) complex proteins has been proposed to play a fundamental role in metabolic homoeostasis. Although protein translation is affected by general RNA-binding proteins, very little is known about the mechanism involved in mitochondrial OXPHOS protein translation. In the present study, serum stimulation induced nuclear-encoded OXPHOS protein expression, such as NDUFA9 [NADH dehydrogenase (ubiquinone) 1α subcomplex, 9, 39 kDa], NDUFB8 [NADH dehydrogenase (ubiquinone) 1β subcomplex, 8, 19 kDa], SDHB [succinate dehydrogenase complex, subunit B, iron sulfur (Ip)] and UQCRFS1 (ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1), and mitochondrial ATP production, in a translation-dependent manner. We also observed that the major ribonucleoprotein YB-1 (Y-box-binding protein-1) preferentially bound to these OXPHOS mRNAs and regulated the recruitment of mRNAs from inactive mRNPs (messenger ribonucleoprotein particles) to active polysomes. YB-1 depletion led to up-regulation of mitochondrial function through induction of OXPHOS protein translation from inactive mRNP release. In contrast, YB-1 overexpression suppressed the translation of these OXPHOS mRNAs through reduced polysome formation, suggesting that YB-1 regulated the translation of mitochondrial OXPHOS mRNAs through mRNA binding. Taken together, our findings suggest that YB-1 is a critical factor for translation that may control OXPHOS activity.
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Evdokimova V, Tognon CE, Sorensen PHB. On translational regulation and EMT. Semin Cancer Biol 2012; 22:437-45. [PMID: 22554796 DOI: 10.1016/j.semcancer.2012.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/16/2012] [Indexed: 12/28/2022]
Abstract
Translational regulation is increasingly recognized as a critical mediator of gene expression. It endows cells with the ability to decide when a particular protein is expressed, thereby ensuring proper and prompt cellular responses to environmental cues. This ability to reprogram protein synthesis and to permit the translation of the respective regulatory messages is particularly important in complex changing environments, including embryonic development, wound healing and environmental stress. Not surprisingly, mistakes in this process can lead to cancer. This review will focus on the mechanisms of translational control operating in normal and cancer cells. We discuss the possibility that progression of primary epithelial tumors into a motile mesenchymal-like phenotype during the invasive phase of metastasis is driven, in part, by a switch from cap-dependent to cap-independent translation.
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Affiliation(s)
- Valentina Evdokimova
- Institute of Protein Research, Pushchino, Moscow Region 142290, Russian Federation
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60
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Yang C, Wang L, Siva VS, Shi X, Jiang Q, Wang J, Zhang H, Song L. A novel cold-regulated cold shock domain containing protein from scallop Chlamys farreri with nucleic acid-binding activity. PLoS One 2012; 7:e32012. [PMID: 22359656 PMCID: PMC3281114 DOI: 10.1371/journal.pone.0032012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/20/2012] [Indexed: 11/26/2022] Open
Abstract
Background The cold shock domain (CSD) containing proteins (CSDPs) are one group of the evolutionarily conserved nucleic acid-binding proteins widely distributed in bacteria, plants, animals, and involved in various cellular processes, including adaptation to low temperature, cellular growth, nutrient stress and stationary phase. Methodology The cDNA of a novel CSDP was cloned from Zhikong scallop Chlamys farreri (designated as CfCSP) by expressed sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The full length cDNA of CfCSP was of 1735 bp containing a 927 bp open reading frame which encoded an N-terminal CSD with conserved nucleic acids binding motif and a C-terminal domain with four Arg-Gly-Gly (RGG) repeats. The CSD of CfCSP shared high homology with the CSDs from other CSDPs in vertebrate, invertebrate and bacteria. The mRNA transcripts of CfCSP were mainly detected in the tissue of adductor and also marginally detectable in gill, hepatopancreas, hemocytes, kidney, mantle and gonad of healthy scallop. The relative expression level of CfCSP was up-regulated significantly in adductor and hemocytes at 1 h and 24 h respectively after low temperature treatment (P<0.05). The recombinant CfCSP protein (rCfCSP) could bind ssDNA and in vitro transcribed mRNA, but it could not bind dsDNA. BX04, a cold sensitive Escherichia coli CSP quadruple-deletion mutant, was used to examine the cold adaptation ability of CfCSP. After incubation at 17°C for 120 h, the strain of BX04 containing the vector pINIII showed growth defect and failed to form colonies, while strain containing pINIII-CSPA or pINIII-CfCSP grew vigorously, indicating that CfCSP shared a similar function with E. coli CSPs for the cold adaptation. Conclusions These results suggest that CfCSP is a novel eukaryotic cold-regulated nucleic acid-binding protein and may function as an RNA chaperone in vivo during the cold adaptation process.
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Affiliation(s)
- Chuanyan Yang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Lingling Wang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- * E-mail: (LW); (LS)
| | - Vinu S. Siva
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Shi
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Qiufen Jiang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Jingjing Wang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Huan Zhang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
| | - Linsheng Song
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- * E-mail: (LW); (LS)
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Inoue I, Matsumoto K, Yu Y, Bay BH. Surmounting Chemoresistance by Targeting the Y-Box Binding Protein-1. Anat Rec (Hoboken) 2011; 295:215-22. [DOI: 10.1002/ar.22401] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/30/2011] [Indexed: 12/23/2022]
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Miki T, Kamikawa Y, Kurono S, Kaneko Y, Katahira J, Yoneda Y. Cell type-dependent gene regulation by Staufen2 in conjunction with Upf1. BMC Mol Biol 2011; 12:48. [PMID: 22087843 PMCID: PMC3226675 DOI: 10.1186/1471-2199-12-48] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 11/16/2011] [Indexed: 12/01/2022] Open
Abstract
Background Staufen2 (Stau2), a double-stranded RNA-binding protein, is a component of neuronal RNA granules, which are dendritic mRNA transport machines. Although Stau2 is thought to be involved in the dendritic targeting of several mRNAs in neurons, the mechanism whereby Stau2 regulates these mRNAs is unknown. To elucidate the functions of Stau2, we screened for novel binding partners by affinity purification of GST-tagged Stau2 from 293F cells. Results Three RNA helicases, RNA helicase A, Upf1 and Mov10, were identified in Stau2-containing complexes. We focused our studies on Upf1, a key player in nonsense-mediated mRNA decay. Stau2 was found to bind directly to Upf1 in an RNA-independent manner in vitro. Tethering Stau2 to the 3'-untranslated region (UTR) of a reporter gene had little effect on its expression in HeLa cells. In contrast, when the same tethering assay was performed in 293F cells, we observed an increase in reporter protein levels. This upregulation of protein expression by Stau2 turned out to be dependent on Upf1. Moreover, we found that in 293F cells, Stau2 upregulates the reporter mRNA level in an Upf1-independent manner. Conclusions These results indicate that the recruitment of Stau2 alone or in combination with Upf1 differentially affects the fate of mRNAs. Moreover, the results suggest that Stau2-mediated fate determination could be executed in a cell type-specific manner.
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Affiliation(s)
- Takashi Miki
- Department of Frontier Bioscience, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
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Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 2011; 43:613-23. [PMID: 21855800 DOI: 10.1016/j.molcel.2011.06.022] [Citation(s) in RCA: 704] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 04/05/2011] [Accepted: 06/04/2011] [Indexed: 11/16/2022]
Abstract
Angiogenin is a stress-activated ribonuclease that cleaves tRNA within anticodon loops to produce tRNA-derived stress-induced fragments (tiRNAs). Transfection of natural or synthetic tiRNAs inhibits protein synthesis and triggers the phospho-eIF2α-independent assembly of stress granules (SGs), essential components of the stress response program. We show that selected tiRNAs inhibit protein synthesis by displacing eIF4G/eIF4A from uncapped > capped RNAs. tiRNAs also displace eIF4F, but not eIF4E:4EBP1, from isolated m(7)G cap. We identify a terminal oligoguanine motif that is required to displace the eIF4F complex, inhibit translation, and induce SG assembly. We show that the tiRNA-associated translational silencer YB-1 contributes to angiogenin-, tiRNA-, and oxidative stress-induced translational repression. Our data reveal some of the mechanisms by which stress-induced tRNA cleavage inhibits protein synthesis and activates a cytoprotective stress response program.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA.
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Lyabin DN, Eliseeva IA, Skabkina OV, Ovchinnikov LP. Interplay between Y-box-binding protein 1 (YB-1) and poly(A) binding protein (PABP) in specific regulation of YB-1 mRNA translation. RNA Biol 2011; 8:883-92. [PMID: 21788731 DOI: 10.4161/rna.8.5.16022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
YB-1 is a DNA- and RNA-binding protein that regulates expression of many important genes. Its deficiency or excess may pose threats, including malignant cellular transformation and metastasis, which explains the necessity of strict control over its amount at every level. As we showed previously, the 3' untranslated region (UTR) of YB-1 mRNA contains a regulatory element specifically binding to YB-1 and PABP (PABPC1). Also, we showed that YB-1 selectively inhibits YB-1 mRNA translation, while PABP stimulates it in a poly(A) tail-independent manner. It was suggested that regulation of YB-1 mRNA translation involves competition between PABP and YB-1 for binding to the regulatory element. Here we offer cogent evidence for this model and add novel details to the mechanism of regulation of YB-1 synthesis. In experiments on regulatory element deletion we showed that it is this element that is responsible for a specific effect of YB-1 and PABP on YB-1 mRNA translation. Mutations eliminating only specific YB-1 affinity for this element suppressed the inhibitory effect of YB-1 and concurrently dramatically decreased the PABP stimulating effect. Mutations reducing only specific PABP affinity for this element, as well as spatial separation of the YB-1- and PABP binding sites, did not affect the YB-1 inhibitory action but completely abolished the positive PABP effect. Together, these results unambiguously prove direct inhibitory action of YB-1 on its mRNA translation, while the positive effect of PABP is realized through displacing YB-1 from the regulatory element.
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Affiliation(s)
- Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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Abstract
The regulation of translation has emerged as a major determinant of gene expression and is critical for both normal cellular function and the development of disease. Numerous studies have highlighted the diverse, and sometimes related, mechanisms which underlie the regulation of global translation rates and the translational control of specific mRNAs. In the present paper, we discuss the emerging roles of the basal translation factor PABP [poly(A)-binding protein] in mRNA-specific translational control in metazoa which suggest that PABP function is more complex than first recognized.
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Blifernez O, Wobbe L, Niehaus K, Kruse O. Protein arginine methylation modulates light-harvesting antenna translation in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:119-130. [PMID: 21175895 DOI: 10.1111/j.1365-313x.2010.04406.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylation of protein arginines represents an important post-translational modification mechanism, which has so far primarily been characterized in mammalian cells. In this work, we successfully identified and characterized arginine methylation as a crucial type of post-translational modification in the activity regulation of the cytosolic translation repressor protein NAB1 in the plant model organism Chlamydomonas reinhardtii. NAB1 represses the cytosolic translation of light-harvesting protein encoding mRNAs by sequestration into translationally silent messenger ribonucleoprotein complexes (mRNPs). Protein arginine methylation of NAB1 could be demonstrated by PRMT1 catalyzed methylation of recombinant NAB1 in vitro, and by immunodetection of methylated NAB1 arginines in vivo. Mass spectrometric analyses of NAB1 purified from C. reinhardtii revealed the asymmetric dimethylation of Arg90 and Arg92 within GAR motif I. Inhibition of arginine methylation by either adenosine-2'-3'-dialdehyde (AdOx) or 7,7'-carbonylbis(azanediyl)bis(4-hydroxynaphthalene-2-sulfonic acid) sodium salt hydrate (AMI-1) caused a dark-green phenotype characterized by the increased accumulation of light-harvesting complex proteins, and indicating a reduced translation repressor activity of NAB1. The extent of NAB1 arginine methylation depends on the growth conditions, with phototrophic growth causing a high methylation state and heterotrophic growth resulting in lowered methylation of the protein. In addition, we could show that NAB1 activity regulation by arginine methylation operates independently from cysteine-based redox control, which has previously been shown to control the activity of NAB1.
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Affiliation(s)
- Olga Blifernez
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Lutz Wobbe
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Olaf Kruse
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Hou H, Wang F, Zhang W, Wang D, Li X, Bartlam M, Yao X, Rao Z. Structure-functional analyses of CRHSP-24 plasticity and dynamics in oxidative stress response. J Biol Chem 2010; 286:9623-35. [PMID: 21177848 DOI: 10.1074/jbc.m110.177436] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cold shock domain (CSD) is an evolutionarily conserved nucleic acid binding domain that exhibits binding activity to RNA, ssDNA, and dsDNA. Mammalian CRHSP-24 contains CSD, but its structure-functional relationship has remained elusive. Here we report the crystal structure of human CRHSP-24 and characterization of the molecular trafficking of CRHSP-24 between stress granules and processing bodies in response to oxidative stress. The structure of CRHSP-24 determined by single-wavelength anomalous dispersion exhibits an α-helix and a compact β-barrel formed by five curved anti-parallel β strands. Ligand binding activity of the CSD is orchestrated by residues Ser(41) to Leu(43). Interestingly, a phosphomimetic S41D mutant abolishes the ssDNA binding in vitro and causes CRHSP-24 liberated from stress granules in vivo without apparent alternation of its localization to the processing bodies. This new class of phosphorylation-regulated interaction between the CSD and nucleic acids is unique in stress granule plasticity. Importantly, the association of CRHSP-24 with stress granules is blocked by PP4/PP2A inhibitor calyculin A as PP2A catalyzes the dephosphorylation of Ser(41) of CRHSP-24. Therefore, we speculate that CRHSP-24 participates in oxidative stress response via a dynamic and temporal association between stress granules and processing bodies.
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Affiliation(s)
- Hai Hou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Jenkins RH, Bennagi R, Martin J, Phillips AO, Redman JE, Fraser DJ. A conserved stem loop motif in the 5'untranslated region regulates transforming growth factor-β(1) translation. PLoS One 2010; 5:e12283. [PMID: 20865036 PMCID: PMC2928724 DOI: 10.1371/journal.pone.0012283] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/16/2010] [Indexed: 01/10/2023] Open
Abstract
Transforming growth factor-β1 (TGF-β1) regulates cellular proliferation, differentiation, migration, and survival. The human TGF-β1 transcript is inherently poorly translated, and translational activation has been documented in relation to several stimuli. In this paper, we have sought to identify in cis regulatory elements within the TGF-β1 5′Untranslated Region (5′UTR). In silico analysis predicted formation of stable secondary structure in a G/C-rich element between nucleotides +77 to +106, and demonstrated that this element is highly conserved across species. Circular dichroism spectroscopy confirmed the presence of secondary structure in this region. The proximal 5′UTR was inhibitory to translation in reporter gene experiments, and mutation of the secondary structure motif increased translational efficiency. Translational regulation of TGF-β1 mRNA is linked to altered binding of YB-1 protein to its 5′UTR. Immunoprecipitation-RT-qPCR demonstrated a high basal association of YB-1 with TGF-β1 mRNA. However, mutation of the secondary structure motif did not prevent interaction of YB-1 with the 5′UTR, suggesting that YB-1 binds to this region due to its G/C-rich composition, rather than a specific, sequence-dependent, binding site. These data identify a highly conserved element within the TGF-β1 5′UTR that forms stable secondary structure, and is responsible for the inherent low translation efficiency of this cytokine.
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Affiliation(s)
- Robert H. Jenkins
- Institute of Nephrology, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - Rasha Bennagi
- Institute of Nephrology, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - John Martin
- Institute of Nephrology, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - Aled O. Phillips
- Institute of Nephrology, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - James E. Redman
- School of Chemistry, Cardiff University, Park Place, Cardiff, Wales, United Kingdom
| | - Donald J. Fraser
- Institute of Nephrology, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
- * E-mail:
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Maher-Laporte M, Berthiaume F, Moreau M, Julien LA, Lapointe G, Mourez M, DesGroseillers L. Molecular composition of staufen2-containing ribonucleoproteins in embryonic rat brain. PLoS One 2010; 5:e11350. [PMID: 20596529 PMCID: PMC2893162 DOI: 10.1371/journal.pone.0011350] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 06/08/2010] [Indexed: 01/21/2023] Open
Abstract
Messenger ribonucleoprotein particles (mRNPs) are used to transport mRNAs along neuronal dendrites to their site of translation. Numerous mRNA-binding and regulatory proteins within mRNPs finely regulate the fate of bound-mRNAs. Their specific combination defines different types of mRNPs that in turn are related to specific synaptic functions. One of these mRNA-binding proteins, Staufen2 (Stau2), was shown to transport dendritic mRNAs along microtubules. Its knockdown expression in neurons was shown to change spine morphology and synaptic functions. To further understand the molecular mechanisms by which Stau2 modulates synaptic function in neurons, it is important to identify and characterize protein co-factors that regulate the fate of Stau2-containing mRNPs. To this end, a proteomic approach was used to identify co-immunoprecipitated proteins in Staufen2-containing mRNPs isolated from embryonic rat brains. The proteomic approach identified mRNA-binding proteins (PABPC1, hnRNP H1, YB1 and hsc70), proteins of the cytoskeleton (α- and β-tubulin) and RUFY3 a poorly characterized protein. While PABPC1 and YB1 associate with Stau2-containing mRNPs through RNAs, hsc70 is directly bound to Stau2 and this interaction is regulated by ATP. PABPC1 and YB1 proteins formed puncta in dendrites of embryonic rat hippocampal neurons. However, they poorly co-localized with Stau2 in the large dendritic complexes suggesting that they are rather components of Stau2-containing mRNA particles. All together, these results represent a further step in the characterization of Stau2-containing mRNPs in neurons and provide new tools to study and understand how Stau2-containing mRNPs are transported, translationally silenced during transport and/or locally expressed according to cell needs.
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Affiliation(s)
| | - Frédéric Berthiaume
- Pathologie et Microbiologie, Université de Montréal, Montréal, Québec, Canada
| | - Mireille Moreau
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Louis-André Julien
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Gabriel Lapointe
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Michael Mourez
- Pathologie et Microbiologie, Université de Montréal, Montréal, Québec, Canada
| | - Luc DesGroseillers
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Mihailovich M, Militti C, Gabaldón T, Gebauer F. Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays 2010; 32:109-18. [PMID: 20091748 DOI: 10.1002/bies.200900122] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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.
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Affiliation(s)
- Marija Mihailovich
- Gene Regulation Programme, Centre de Regulació Genòmica (CRG-UPF), Barcelona, Spain
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Chaikam V, Karlson DT. Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins. BMB Rep 2010; 43:1-8. [DOI: 10.5483/bmbrep.2010.43.1.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kim MH, Sasaki K, Imai R. Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana. J Biol Chem 2009; 284:23454-60. [PMID: 19556243 PMCID: PMC2749119 DOI: 10.1074/jbc.m109.025791] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 06/24/2009] [Indexed: 11/06/2022] Open
Abstract
In response to cold, Escherichia coli produces cold shock proteins (CSPs) that have essential roles in cold adaptation as RNA chaperones. Here, we demonstrate that Arabidopsis cold shock domain protein 3 (AtCSP3), which shares a cold shock domain with bacterial CSPs, is involved in the acquisition of freezing tolerance in plants. AtCSP3 complemented a cold-sensitive phenotype of the E. coli CSP quadruple mutant and displayed nucleic acid duplex melting activity, suggesting that AtCSP3 also functions as an RNA chaperone. Promoter-GUS transgenic plants revealed tissue-specific expression of AtCSP3 in shoot and root apical regions. When exposed to low temperature, GUS activity was extensively induced in a broader region of the roots. In transgenic plants expressing an AtCSP3-GFP fusion, GFP signals were detected in both the nucleus and cytoplasm. An AtCSP3 knock-out mutant (atcsp3-2) was sensitive to freezing compared with wild-type plants under non-acclimated and cold-acclimated conditions, whereas expression of C-repeat-binding factors and their downstream genes during cold acclimation was not altered in the atcsp3-2 mutant. Overexpression of AtCSP3 in transgenic plants conferred enhanced freezing tolerance over wild-type plants. Together, the data demonstrated an essential role of RNA chaperones for cold adaptation in higher plants.
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Affiliation(s)
- Myung-Hee Kim
- From the Crop Cold Tolerance Research Team, National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan
| | - Kentaro Sasaki
- From the Crop Cold Tolerance Research Team, National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan
| | - Ryozo Imai
- From the Crop Cold Tolerance Research Team, National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan
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73
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Nakaminami K, Hill K, Perry SE, Sentoku N, Long JA, Karlson DT. Arabidopsis cold shock domain proteins: relationships to floral and silique development. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1047-62. [PMID: 19269998 PMCID: PMC2652047 DOI: 10.1093/jxb/ern351] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 12/09/2008] [Accepted: 12/09/2008] [Indexed: 05/21/2023]
Abstract
Cold shock domain proteins (CSPs) are highly conserved from bacteria to higher plants and animals. Bacterial cold shock proteins function as RNA chaperones by destabilizing RNA secondary structures and promoting translation as an adaptative mechanism to low temperature stress. In animals, cold shock domain proteins exhibit broad functions related to growth and development. In order to understand better the function of CSPs in planta, detailed analyses were performed for Arabidopsis thaliana CSPs (AtCSPs) on the transcript and protein levels using an extensive series of tissue harvested throughout developmental stages within the entire life cycle of Arabidopsis. On both the transcript and protein levels, AtCSPs were enriched in shoot apical meristems and siliques. Although all AtCSPs exhibited similar expression patterns, AtCSP2 was the most abundantly expressed gene. In situ hybridization analyses were also used to confirm that AtCSP2 and AtCSP4 transcripts accumulate in developing embryos and shoot apices. AtCSPs transcripts were also induced during a controlled floral induction study. In vivo ChIP analysis confirmed that an embryo expressed MADS box transcription factor, AGL15, interacts within two AtCSP promoter regions and alters the respective patterns of AtCSP transcription. Comparative analysis of AtCSP gene expression between Landsberg and Columbia ecotypes confirmed a 1000-fold reduction of AtCSP4 gene expression in the Landsberg background. Analysis of the AtCSP4 genomic locus identified multiple polymorphisms in putative regulatory cis-elements between the two ecotypes. Collectively, these data support the hypothesis that AtCSPs are involved in the transition to flowering and silique development in Arabidopsis.
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Affiliation(s)
- Kentaro Nakaminami
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506-6108, USA
- Present address and to whom correspondence should be sent: Monsanto Company, 110 TW Alexander Drive, RTP, NC 27709, USA. E-mail:
| | - Kristine Hill
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Naoki Sentoku
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Jeffrey A. Long
- Plant Biology Laboratory, Salk Institute for Biological Sciences, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dale T. Karlson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506-6108, USA
- Present address and to whom correspondence should be sent: Monsanto Company, 110 TW Alexander Drive, RTP, NC 27709, USA. E-mail:
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General RNA-binding proteins have a function in poly(A)-binding protein-dependent translation. EMBO J 2008; 28:58-68. [PMID: 19078965 DOI: 10.1038/emboj.2008.259] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 11/12/2008] [Indexed: 12/29/2022] Open
Abstract
The interaction between the poly(A)-binding protein (PABP) and eukaryotic translational initiation factor 4G (eIF4G), which brings about circularization of the mRNA, stimulates translation. General RNA-binding proteins affect translation, but their role in mRNA circularization has not been studied before. Here, we demonstrate that the major mRNA ribonucleoprotein YB-1 has a pivotal function in the regulation of eIF4F activity by PABP. In cell extracts, the addition of YB-1 exacerbated the inhibition of 80S ribosome initiation complex formation by PABP depletion. Rabbit reticulocyte lysate in which PABP weakly stimulates translation is rendered PABP-dependent after the addition of YB-1. In this system, eIF4E binding to the cap structure is inhibited by YB-1 and stimulated by a nonspecific RNA. Significantly, adding PABP back to the depleted lysate stimulated eIF4E binding to the cap structure more potently if this binding had been downregulated by YB-1. Conversely, adding nonspecific RNA abrogated PABP stimulation of eIF4E binding. These data strongly suggest that competition between YB-1 and eIF4G for mRNA binding is required for efficient stimulation of eIF4F activity by PABP.
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Control of the papillomavirus early-to-late switch by differentially expressed SRp20. J Virol 2008; 83:167-80. [PMID: 18945760 DOI: 10.1128/jvi.01719-08] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The viral early-to-late switch of papillomavirus infection is tightly linked to keratinocyte differentiation and is mediated in part by alternative mRNA splicing. Here, we report that SRp20, a cellular splicing factor, controls the early-to-late switch via interactions with A/C-rich RNA elements. An A/C-rich SE4 element regulates the selection of a bovine papillomavirus type 1 (BPV-1) late-specific splice site, and binding of SRp20 to SE4 suppresses this selection. Expression of late BPV-1 L1 or human papillomavirus (HPV) L1, the major capsid protein, inversely correlates with SRp20 levels in the terminally differentiated keratinocytes. In HPV type 16, a similar SRp20-interacting element also controls the viral early-to-late switch. Keratinocytes in raft cultures, which support L1 expression, make considerably less SRp20 than keratinocytes in monolayer cultures, which do not support L1 expression. Conversely, abundant SRp20 in cancer cells or undifferentiated keratinocytes is important for the expression of the viral early E6 and E7 by promoting the expression of cellular transcription factor SP1 for transactivation of viral early promoters.
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Chernov KG, Mechulam A, Popova NV, Pastre D, Nadezhdina ES, Skabkina OV, Shanina NA, Vasiliev VD, Tarrade A, Melki J, Joshi V, Baconnais S, Toma F, Ovchinnikov LP, Curmi PA. YB-1 promotes microtubule assembly in vitro through interaction with tubulin and microtubules. BMC BIOCHEMISTRY 2008; 9:23. [PMID: 18793384 PMCID: PMC2557009 DOI: 10.1186/1471-2091-9-23] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 09/15/2008] [Indexed: 11/16/2022]
Abstract
Background YB-1 is a major regulator of gene expression in eukaryotic cells. In addition to its role in transcription, YB-1 plays a key role in translation and stabilization of mRNAs. Results We show here that YB-1 interacts with tubulin and microtubules and stimulates microtubule assembly in vitro. High resolution imaging via electron and atomic force microscopy revealed that microtubules assembled in the presence of YB-1 exhibited a normal single wall ultrastructure and indicated that YB-1 most probably coats the outer microtubule wall. Furthermore, we found that YB-1 also promotes the assembly of MAPs-tubulin and subtilisin-treated tubulin. Finally, we demonstrated that tubulin interferes with RNA:YB-1 complexes. Conclusion These results suggest that YB-1 may regulate microtubule assembly in vivo and that its interaction with tubulin may contribute to the control of mRNA translation.
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Affiliation(s)
- Konstantin G Chernov
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM/UEVE U829 Evry, 91025 France.
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Hermsen JL, Gomez FE, Maeshima Y, Sano Y, Kang W, Kudsk KA. Decreased enteral stimulation alters mucosal immune chemokines. JPEN J Parenter Enteral Nutr 2008; 32:36-44. [PMID: 18165445 DOI: 10.1177/014860710803200136] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Migration of lymphocytes into and through the mucosal immune system depends upon adhesion molecules to attract circulating cells and chemokines to stimulate diapedesis into tissues. Decreased enteral stimulation significantly reduces mucosal addressin cellular adhesion molecule-1 (MAdCAM-1) levels, an adhesion molecule critical for homing of T and B cells to Peyer's patches (PP), which reduces PP and intestinal T and B cells. We studied the effect of type and route of nutrition on tissue specific chemokines in PP (CXCL-12, -13 and CCL-19, -20 and -21), small intestine (SI; CCL-20, -25 and -28) and lung (CXCL-12, CCL-28). METHODS Intravenously cannulated male Institute of Cancer Research (ICR) mice were randomized to chow or parenteral nutrition (PN) for 5 days. PP, SI, and lung chemokine mRNA levels were measured using real-time qRT-polymerase chain reaction, and analyzed semiquantitatively by the DeltaDeltaCt method. Protein levels were quantified using enzyme-linked immunosorbent assay (ELISA) techniques, and groups compared using Student's t-test. RESULTS PP CXCL13 protein significantly decreased, whereas CCL21 protein increased significantly in the parenterally fed group. Parenteral feeding significantly decreased SI CCL20 and CCL 25 protein levels. CCL28 decreased significantly in the SI and lung of intravenously fed animals. mRNA levels changed in the opposite direction (compared with protein) for all chemokines except CCL28. CONCLUSIONS Decreased enteral stimulation significantly alters key mucosal immune chemokine protein levels at multiple sites. In general, PN (and concomitant lack of enteral stimulation) results in decreased levels of chemokines that control lymphocyte migration within the mucosal immune system.
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Affiliation(s)
- Joshua L Hermsen
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792-7375, USA
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Fraser D, Phillips A, Zhang X, van Roeyen C, Muehlenberg P, En-Nia A, Mertens P. Y-box protein-1 controls transforming growth factor-β1 translation in proximal tubular cells. Kidney Int 2008; 73:724-32. [DOI: 10.1038/sj.ki.5002719] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Identification of internal ribosome entry segment (IRES)-trans-acting factors for the Myc family of IRESs. Mol Cell Biol 2007; 28:40-9. [PMID: 17967896 DOI: 10.1128/mcb.01298-07] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proto-oncogenes c-, L-, and N-myc can all be translated by the alternative method of internal ribosome entry whereby the ribosome is recruited to a complex structural element (an internal ribosome entry segment [IRES]). Ribosome recruitment is dependent upon the presence of IRES-trans-acting factors (ITAFs) that act as RNA chaperones and allow the mRNA to attain the correct conformation for the interaction of the 40S subunit. One of the major challenges for researchers in this area is to determine whether there are groups of ITAFs that regulate the IRES-mediated translation of subsets of mRNAs. We have identified four proteins, termed GRSF-1 (G-rich RNA sequence binding factor 1), YB-1 (Y-box binding protein 1), PSF (polypyrimidine tract binding protein-associated splicing factor), and its binding partner, p54nrb, that bind to the myc family of IRESs. We show that these proteins positively regulate the translation of the Myc family of oncoproteins (c-, L-, and N-Myc) in vivo and in vitro. Interestingly, synthesis from the unrelated IRESs, BAG-1 and Apaf-1, was not affected by YB-1, GRSF-1, or PSF levels in vivo, suggesting that these three ITAFs are specific to the myc IRESs. Myc proteins play a role in cell proliferation; therefore, these results have important implications regarding the control of tumorigenesis.
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Alekhina OM, Vassilenko KS, Spirin AS. Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation. Nucleic Acids Res 2007; 35:6547-59. [PMID: 17897963 PMCID: PMC2095793 DOI: 10.1093/nar/gkm725] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 08/28/2007] [Accepted: 08/31/2007] [Indexed: 11/14/2022] Open
Abstract
Real-time monitoring of the translation of non-capped luciferase mRNA in a wheat germ cell-free system has been performed by continuous in situ measurement of the luminescence increase in the translation mixture. The phenomenon of acceleration of translation has been revealed. It has been shown that the acceleration is accompanied by the loading of translating polysomes with additional ribosomes, and thus is caused mainly by a rise in the initiation rate, rather than the stimulation of elongation or the involvement of additional mRNA molecules in translation. The acceleration requires a sufficient concentration of mRNA and depends on the sequence of the 5' untranslated region (UTR). It can be abolished by the addition of excess cap analog (m(7)GpppGm). As the acceleration does not depend on the preliminary translation of other mRNAs in the same extract, the conclusion has been made that the effect is not due to activation of the ribosome population or other components of the system during translation, but rather it is the consequence of intra-polysomal events. The acceleration observed is discussed in terms of the model of two overlapping initiation pathways in eukaryotic polysomes: translation of non-capped mRNAs starts with eIF4F-independent initiation at 5' UTR, and after the formation of sufficiently loaded polysomes, they rearrange in such a way that a mechanism of re-initiation of terminating ribosomes switches on. The eIF4F-mediated circularization of polysomes may be considered as a possible event that leads to the re-initiation switch and the resultant acceleration effect.
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Affiliation(s)
| | | | - Alexander S. Spirin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Nashchekin D, Masich S, Soop T, Kukalev A, Kovrigina E, Nashchekina O, Daneholt B. Two splicing isoforms of the Y-box protein ctYB-1 appear on the same mRNA molecule. FEBS J 2007; 274:202-11. [PMID: 17222182 DOI: 10.1111/j.1742-4658.2006.05576.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Y-box proteins constitute an evolutionarily conserved family of DNA- and RNA-binding proteins involved in the regulation of transcription and translation. In the dipteran Chironomus tentans, a homologue to the vertebrate Y-box protein YB-1 was recently characterized and designated ctYB-1. It is transferred from nucleus to cytoplasm bound to mRNA and is likely to affect translation. It appears in two size variants, p40 and p50. We further analysed the two size variants and their interaction with mRNA. Southern blot analysis, in situ hybridization and RT-PCR analysis suggested that there is just one YB-1 gene, and that the two size variants represent splicing isoforms. In a C. tentans epithelial cell line, only p40 is present, whereas both variants appear together in eight tissues from fourth-instar larvae, although in somewhat different proportions. Furthermore, the appearance of the two isoforms was studied in relation to a specific 35-40 kb mRNA transcript in the salivary glands, the Balbiani ring mRNA. Because of their exceptional size, Balbiani ring messenger ribonucleoprotein particles in nucleoplasm and Balbiani ring polysomes in cytoplasm could be identified and selectively studied. We were able to establish that both isoforms are associated with both nuclear and cytoplasmic Balbiani ring mRNA. In addition, a p50-specific antibody coimmunoprecipitated p40 from Balbiani ring polysomes, suggesting that the two splicing isoforms are located along the same Balbiani ring mRNA molecule. The functional significance of the two isoforms is being discussed.
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Affiliation(s)
- Dmitry Nashchekin
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, Stockholm, Sweden
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82
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Bilanges B, Stokoe D. Mechanisms of translational deregulation in human tumors and therapeutic intervention strategies. Oncogene 2007; 26:5973-90. [PMID: 17404576 DOI: 10.1038/sj.onc.1210431] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Analysis of the recurrent genetic aberrations present in human tumors provides insight into how normal cells escape appropriate proliferation and survival cues. Commonly mutated genes encode proteins that monitor DNA damage (e.g., p53), proteins that regulate the cell cycle (such as Rb), and proteins that regulate signal transduction pathways (such as APC, PTEN and Ras). Analysis of the relevant targets and downstream events of these genes in normal and tumor cells will clearly highlight important pathways for tumorigenesis. However, more infrequent mutations are also informative in defining events critical for the process of tumorigenesis, and often delineate important pathways lying downstream of commonly mutated oncogenes and tumor suppressors. Together, these studies have led to the conclusion that deregulated protein synthesis plays an important role in human cancer. This review will discuss the evidence implicating mRNA translation as an important downstream consequence of signal transduction pathways initiated by mutated oncogenes and tumor suppressors, as well as additional genetic findings implicating the importance of global and specific translational control in human cancer. It will also discuss therapeutic strategies that take advantage of differences in translational regulation between normal and tumor cells.
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Affiliation(s)
- B Bilanges
- UCSF Cancer Research Institute, San Francisco, CA 94115, USA.
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83
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Esnault S, Fang Y, Kelly EAB, Sedgwick JB, Fine J, Malter JS, Jarjour NN. Circadian changes in granulocyte-macrophage colony-stimulating factor message in circulating eosinophils. Ann Allergy Asthma Immunol 2007; 98:75-82. [PMID: 17225724 DOI: 10.1016/s1081-1206(10)60863-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Granulocyte-macrophage colony-stimulating factor (GM-CSF), which stimulates eosinophil recruitment, activation, and survival, is expressed by activated eosinophils. Although eosinophil recruitment and enhanced survival have been associated with nocturnal asthma (NA), the contribution of GM-CSF to NA is unknown. OBJECTIVE To determine whether circulating eosinophil GM-CSF expression correlates with the symptoms of NA. METHODS The GM-CSF messenger RNA (mRNA) expression at 4 PM and 4 AM was determined by reverse-transcriptase polymerase chain reaction with Southern blot analysis in subjects with and without NA and in controls. RESULTS A total of 142 asthma subjects were screened for nocturnal asthma with 1-week home peak expiratory flow rate (PEFR) monitoring. Eleven subjects had NA (>20% diurnal variation in PEFR on 4 of 7 days), and 6 met the criteria for non-NA (<10% diurnal variation in PEFR on 7 of 7 days); 8 controls were studied. In subjects with NA, GM-CSF mRNA expression in circulating eosinophils increased 3-fold at 4 AM compared with 4 PM. Diurnal changes in GM-CSF mRNA expression were not detected in the non-NA and control groups. CONCLUSIONS Day-night variation in eosinophil GM-CSF expression is associated with circadian variation in airway function in asthma, a key manifestation of asthma severity.
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Affiliation(s)
- Stéphane Esnault
- Waisman Center for Developmental Disabilities, Madison, Wisconsin, USA
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84
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Schittek B, Psenner K, Sauer B, Meier F, Iftner T, Garbe C. The increased expression of Y box-binding protein 1 in melanoma stimulates proliferation and tumor invasion, antagonizes apoptosis and enhances chemoresistance. Int J Cancer 2007; 120:2110-8. [PMID: 17266041 DOI: 10.1002/ijc.22512] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In previous studies we identified the transcription/translation factor Y-box-binding protein (YB-1) as a gene that is upregulated in primary melanoma and melanoma metastases when compared to benign melanocytic nevi. To analyze whether YB-1 expression correlates with melanoma progression in vitro and in vivo, we performed expression analysis on melanoma cell lines representing different stages of melanoma progression and on tissues of melanocytic nevi, primary melanoma and melanoma metastases. Our data indicate that compared to benign melanocytes YB-1 expression is increased in melanoma cells in vitro and in vivo and that YB-1 is translocated into the nucleus in invasive and metastatic melanoma cells. To reveal the functional role of YB-1 in melanoma progression we achieved a stable downregulation of YB-1 using shRNA in metastatic melanoma cells. Interestingly, YB-1 downregulation resulted in a pronounced reduced rate of proliferation and an increased rate of apoptotic cell death. In addition, migration and invasion of melanoma cells in monolayer and in a three-dimensional skin reconstruct in vitro was significantly reduced. These effects were accompanied by downregulation of genes involved in proliferation, survival and migration/invasion of melanoma cells such as MMP-2, bcl-2, Cyclin D1, p53 and p16INK4A. Furthermore, melanoma cells with a reduced YB-1 expression showed a decreased resistance to the chemotherapeutic agents cisplatin and etoposide. These data suggest that YB-1 is involved in malignant transformation of melanocytes and contributes to the stimulation of proliferation, tumor invasion, survival and chemoresistance. Thus, YB-1 may be a promising molecular target in melanoma therapy.
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Affiliation(s)
- Birgit Schittek
- Division of Dermatologic Oncology, Department of Dermatology, University of Tübingen, Liebermeisterstrasse 25, D-72076 Tübingen, Germany.
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85
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Gallois-Montbrun S, Kramer B, Swanson CM, Byers H, Lynham S, Ward M, Malim MH. Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and stress granules. J Virol 2006; 81:2165-78. [PMID: 17166910 PMCID: PMC1865933 DOI: 10.1128/jvi.02287-06] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Members of the APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide 1-like) family of cytidine deaminases inhibit host cell genome invasion by exogenous retroviruses and endogenous retrotransposons. Because these enzymes can edit DNA or RNA and potentially mutate cellular targets, their activities are presumably regulated; for instance, APOBEC3G (A3G) recruitment into high-molecular-weight ribonucleoprotein (RNP) complexes has been shown to suppress its enzymatic activity. We used tandem affinity purification together with mass spectrometry (MS) to identify protein components within A3G-containing RNPs. We report that numerous cellular RNA-binding proteins with diverse roles in RNA function, metabolism, and fate determination are present in A3G RNPs but that most interactions with A3G are mediated via binding to shared RNAs. Confocal microscopy demonstrated that substantial quantities of A3G localize to cytoplasmic microdomains that are known as P bodies and stress granules (SGs) and are established sites of RNA storage and metabolism. Indeed, subjecting cells to stress induces the rapid redistribution of A3G and a number of P-body proteins to SGs. Among these proteins are Argonaute 1 (Ago1) and Argonaute 2 (Ago2), factors that are important for RNA silencing and whose interactions with A3G are resistant to RNase treatment. Together, these findings reveal that A3G associates with RNPs that are found throughout the cytosol as well as in discrete microdomains. We also speculate that the interplay between A3G, RNA-silencing pathways, and cellular sites of RNA metabolism may contribute to A3G's role as an inhibitor of retroelement mobility and as a possible regulator of cellular RNA function.
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Affiliation(s)
- Sarah Gallois-Montbrun
- Department of Infectious Diseases, King's College London School of Medicine, 2nd floor, New Guy's House, Guy's Hospital, London Bridge, London SE1 9RT, United Kingdom
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86
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Anderson EC, Lever AML. Human immunodeficiency virus type 1 Gag polyprotein modulates its own translation. J Virol 2006; 80:10478-86. [PMID: 17041220 PMCID: PMC1641787 DOI: 10.1128/jvi.02596-05] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The full-length viral RNA of human immunodeficiency virus type 1 (HIV-1) functions both as the mRNA for the viral structural proteins Gag and Gag/Pol and as the genomic RNA packaged within viral particles. The packaging signal which Gag recognizes to initiate genome encapsidation is in the 5' untranslated region (UTR) of the HIV-1 RNA, which is also the location of translation initiation complex formation. Hence, it is likely that there is competition between the translation and packaging processes. We studied the ability of Gag to regulate translation of its own mRNA. Gag had a bimodal effect on translation from the HIV-1 5' UTR, stimulating translation at low concentrations and inhibiting translation at high concentrations in vitro and in vivo. The inhibition was dependent upon the ability of Gag to bind the packaging signal through its nucleocapsid domain. The stimulatory activity was shown to depend on the matrix domain of Gag. These results suggest that Gag controls the equilibrium between translation and packaging, ensuring production of enough molecules of Gag to make viral particles before encapsidating its genome.
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MESH Headings
- 5' Untranslated Regions
- Animals
- Base Sequence
- COS Cells
- Chlorocebus aethiops
- DNA, Viral/genetics
- Gene Products, gag/biosynthesis
- Gene Products, gag/genetics
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Models, Biological
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Transfection
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Affiliation(s)
- Emma C Anderson
- Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom
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87
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Uchiumi T, Fotovati A, Sasaguri T, Shibahara K, Shimada T, Fukuda T, Nakamura T, Izumi H, Tsuzuki T, Kuwano M, Kohno K. YB-1 Is Important for an Early Stage Embryonic Development. J Biol Chem 2006; 281:40440-9. [PMID: 17082189 DOI: 10.1074/jbc.m605948200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic Y-box-binding protein-1 (YB-1) is involved in the transcriptional and translational control of many biological processes, including cell proliferation. In clinical studies, the cellular level of YB-1 closely correlates with tumor growth and prognosis. To understand the role of YB-1 in vivo, especially in the developmental process, we generated YB-1 knock-out mice, which are embryonic lethal and exhibit exencephaly associated with abnormal patterns of cell proliferation within the neuroepithelium. beta-Actin expression and F-actin formation were reduced in the YB-1 null embryo and YB-1(-/-) mouse embryonic fibroblasts, suggesting that the neural tube defect is caused by abnormal cell morphology and actin assembly within the neuroepithelium. Fibroblasts derived from YB-1(-/-) embryos demonstrated reduced growth and cell density. A colony formation assay showed that YB-1(-/-) mouse embryonic fibroblasts failed to undergo morphological transformation and remained contact-inhibited in culture. These results demonstrate that YB-1 is involved in early mouse development, including neural tube closure and cell proliferation.
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Affiliation(s)
- Takeshi Uchiumi
- Department of Molecular Biology, University of Occupational and Environmental Health, School of Medicine, Yahatanishi-ku, Kitakyushu 807-8555, Japan.
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88
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Miwa A, Higuchi T, Kobayashi S. Expression and polysome association of YB-1 in various tissues at different stages in the lifespan of mice. Biochim Biophys Acta Gen Subj 2006; 1760:1675-81. [PMID: 17045744 DOI: 10.1016/j.bbagen.2006.08.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/29/2006] [Accepted: 08/28/2006] [Indexed: 11/29/2022]
Abstract
Tissue-specific translational regulation is important for gene expression. YB-1 binds to mRNAs to form mRNPs and affects translation. In this study we investigated expression and polysome association of YB-1 in various tissues at different stages in the lifespan of mice. YB-1 levels decreased markedly with growth in brain, heart and muscle, but increased in the spleen. In lung, kidney and testis, the levels of YB-1 diminished with aging. In liver, no significant change in the level of YB-1 was observed throughout life. We further showed that the distribution pattern of YB-1 on a sucrose gradient differed according to tissue. Moreover, the distribution pattern of YB-1 changed drastically with growth in the liver. In 5-day-old liver, YB-1 was distributed almost exclusively in nonpolysomal fractions, whereas in 4-week-old liver, it was associated with heavy-sedimenting polysomes, as was the case in 5-day-old brain. Immunohistochemical analysis revealed that YB-1 is mainly a cytoplasmic protein in these tissues. Our results indicate that the expression and polysome association of YB-1 are regulated with growth or aging in a tissue-specific manner, presumably to control gene expression at the translational level in each tissue.
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Affiliation(s)
- Arisa Miwa
- Department of Biochemistry, College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba 274-8555, Japan
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89
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Skabkin MA, Lyabin DN, Ovchinnikov LP. Nonspecific and specific interactions of Y-box-binding protein 1 (YB-1) with mRNA and posttranscriptional regulation of protein synthesis in animal cells. Mol Biol 2006. [DOI: 10.1134/s0026893306040078] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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90
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Svitkin YV, Sonenberg N. Translational control by the poly(A) binding protein: A check for mRNA integrity. Mol Biol 2006. [DOI: 10.1134/s0026893306040133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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91
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Nashchekin D, Zhao J, Visa N, Daneholt B. A Novel Ded1-like RNA Helicase Interacts with the Y-box Protein ctYB-1 in Nuclear mRNP Particles and in Polysomes. J Biol Chem 2006; 281:14263-72. [PMID: 16556597 DOI: 10.1074/jbc.m600262200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have characterized a novel mRNA-binding protein, designated hrp84, in the dipteran Chironomus tentans and identified it as a DEAD-box RNA helicase. The protein contains the typical helicase core domain, a glycine-rich C-terminal part and a putative nuclear export signal in the N terminus. The protein belongs to the Ded1 subgroup of DEAD-box helicases, which is highly conserved from yeast (Ded1p) to mammals (DDX3). In tissue culture cells, hrp84 is present both in the nucleus and cytoplasm and, as shown by in vivo UV cross-linking, is bound to mRNA in both compartments. Immunoprecipitation experiments revealed that hpr84 is associated with the C. tentans homologue (ctYB-1) of the vertebrate Y-box protein YB-1 both in the nucleus and cytoplasm, and the two proteins also appear together in polysomes. The interaction is likely to be direct as shown by in vitro binding of purified components. We conclude that the mRNA-bound hrp84.ctYB-1 complex is formed in the nucleus and is translocated with mRNA into the cytoplasm and further into polysomes. As both Ded1 and YB-1 are known to regulate the initiation of translation, we propose that the RNA helicase-Y-box protein complex affects the efficiency of mRNA translation, presumably by modulating the conformation of the mRNP template.
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Affiliation(s)
- Dmitri Nashchekin
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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92
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Evdokimova V, Ruzanov P, Anglesio MS, Sorokin AV, Ovchinnikov LP, Buckley J, Triche TJ, Sonenberg N, Sorensen PHB. Akt-mediated YB-1 phosphorylation activates translation of silent mRNA species. Mol Cell Biol 2006; 26:277-92. [PMID: 16354698 PMCID: PMC1317623 DOI: 10.1128/mcb.26.1.277-292.2006] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
YB-1 is a broad-specificity RNA-binding protein that is involved in regulation of mRNA transcription, splicing, translation, and stability. In both germinal and somatic cells, YB-1 and related proteins are major components of translationally inactive messenger ribonucleoprotein particles (mRNPs) and are mainly responsible for storage of mRNAs in a silent state. However, mechanisms regulating the repressor activity of YB-1 are not well understood. Here we demonstrate that association of YB-1 with the capped 5' terminus of the mRNA is regulated via phosphorylation by the serine/threonine protein kinase Akt. In contrast to its nonphosphorylated form, phosphorylated YB-1 fails to inhibit cap-dependent but not internal ribosome entry site-dependent translation of a reporter mRNA in vitro. We also show that similar to YB-1, Akt is associated with inactive mRNPs and that activated Akt may relieve translational repression of the YB-1-bound mRNAs. Using Affymetrix microarrays, we found that many of the YB-1-associated messages encode stress- and growth-related proteins, raising the intriguing possibility that Akt-mediated YB-1 phosphorylation could, in part, increase production of proteins regulating cell proliferation, oncogenic transformation, and stress response.
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Affiliation(s)
- Valentina Evdokimova
- Department of Pathology, British Columbia Research Institute for Children's and Women's Health, Vancouver, BC, Canada V5Z 163.
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93
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Vaiman AV, Stromskaya TP, Rybalkina EY, Sorokin AV, Guryanov SG, Zabotina TN, Mechetner EB, Ovchinnikov LP, Stavrovskaya AA. Intracellular localization and content of YB-1 protein in multidrug resistant tumor cells. BIOCHEMISTRY (MOSCOW) 2006; 71:146-54. [PMID: 16489918 DOI: 10.1134/s0006297906020052] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The multifunctional mammalian protein YB-1 is a member of the large DNA- and RNA-binding protein family with an evolutionarily ancient cold-shock domain. YB-1 is involved in multiple DNA- and mRNA-dependent events and regulates gene expression at various levels. It can be found both in the nucleus and the cytoplasm. Bound to DNA in the cell nucleus, YB-1 functions as a transcription factor interacting with inverted CCAAT-box (Y-box) in promoters and enhancers of multiple genes. In particular, YB-1 regulates activity of the multidrug resistance (MDR) genes MDR1 and LRP. In tumors, YB-1 has been suggested to be an early and global marker of MDR. In this study, we compared amounts of YB-1 mRNAs and intracellular localization of YB-1 protein in six pairs of drug sensitive and drug resistant sublines of diverse tumors. We have shown that neither great increase in the level of YB-1 mRNA nor substantial increase in the number of cells with nuclear localization of YB-1 are obligatory traits of drug resistant tumor cell populations. However, the cells with highest amounts of YB-1 mRNA also demonstrated increased quantities of MDR1, MRP1, BCRP, and LRP mRNAs encoding different MDR proteins. Transfection of two different populations of drug-sensitive cells with YB-1 cDNA led to increase in the amount of YB-1 mRNA. The quantities of MRP1 and LRP mRNAs increased in both populations. Introduction of YB-1 small hairpin RNA (shRNA) resulted in decreased amounts of YB-1 mRNA, as well as MRP1, LRP, and MDR1 mRNAs (in three different cell lines). Our data suggest that although YB-1 regulates several MDR genes, it could not be regarded as a global marker of already formed drug resistant tumor cell populations. It is most likely that at the first steps of MDR development YB-1 activity is necessary for propagation of resistant cell populations rather than for maintenance of drug resistance.
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Affiliation(s)
- A V Vaiman
- Institute of Carcinogenesis, Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, 115478 Moscow, Russia.
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94
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Abstract
There have long been indications of a role for PI3K (phosphatidylinositol 3-kinase) in cancer pathogenesis. Experimental data document a requirement for deregulation of both transcription and translation in PI3K-mediated oncogenic transformation. The recent discoveries of cancer-specific mutations in PIK3CA, the gene that encodes the catalytic subunit p110alpha of PI3K, have heightened the interest in the oncogenic potential of this lipid kinase and have made p110alpha an ideal drug target.
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Affiliation(s)
- Andreas G Bader
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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95
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Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY. Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci U S A 2005; 102:17551-8. [PMID: 16251272 PMCID: PMC1266160 DOI: 10.1073/pnas.0507856102] [Citation(s) in RCA: 342] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rett syndrome (RTT) is a postnatal neurodevelopmental disorder characterized by the loss of acquired motor and language skills, autistic features, and unusual stereotyped movements. RTT is caused by mutations in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Mutations in MECP2 cause a variety of neurodevelopmental disorders including X-linked mental retardation, psychiatric disorders, and some cases of autism. Although MeCP2 was identified as a methylation-dependent transcriptional repressor, transcriptional profiling of RNAs from mice lacking MeCP2 did not reveal significant gene expression changes, suggesting that MeCP2 does not simply function as a global repressor. Changes in expression of a few genes have been observed, but these alterations do not explain the full spectrum of Rett-like phenotypes, raising the possibility that additional MeCP2 functions play a role in pathogenesis. In this study, we show that MeCP2 interacts with the RNA-binding protein Y box-binding protein 1 and regulates splicing of reporter minigenes. Importantly, we found aberrant alternative splicing patterns in a mouse model of RTT. Thus, we uncovered a previously uncharacterized function of MeCP2 that involves regulation of splicing, in addition to its role as a transcriptional repressor.
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Affiliation(s)
- Juan I Young
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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96
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Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005; 361:13-37. [PMID: 16213112 DOI: 10.1016/j.gene.2005.06.037] [Citation(s) in RCA: 527] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 05/31/2005] [Accepted: 06/27/2005] [Indexed: 01/19/2023]
Abstract
The mechanism of initiation of translation differs between prokaryotes and eukaryotes, and the strategies used for regulation differ accordingly. Translation in prokaryotes is usually regulated by blocking access to the initiation site. This is accomplished via base-paired structures (within the mRNA itself, or between the mRNA and a small trans-acting RNA) or via mRNA-binding proteins. Classic examples of each mechanism are described. The polycistronic structure of mRNAs is an important aspect of translational control in prokaryotes, but polycistronic mRNAs are not usable (and usually not produced) in eukaryotes. Four structural elements in eukaryotic mRNAs are important for regulating translation: (i) the m7G cap; (ii) sequences flanking the AUG start codon; (iii) the position of the AUG codon relative to the 5' end of the mRNA; and (iv) secondary structure within the mRNA leader sequence. The scanning model provides a framework for understanding these effects. The scanning mechanism also explains how small open reading frames near the 5' end of the mRNA can down-regulate translation. This constraint is sometimes abrogated by changing the structure of the mRNA, sometimes with clinical consequences. Examples are described. Some mistaken ideas about regulation of translation that have found their way into textbooks are pointed out and corrected.
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Affiliation(s)
- Marilyn Kozak
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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97
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Abstract
RNA-binding proteins play a major part in the control of gene expression during early development. At this stage, the majority of regulation occurs at the levels of translation and RNA localization. These processes are, in general, mediated by RNA-binding proteins interacting with specific sequence motifs in the 3'-untranslated regions of their target RNAs. Although initial work concentrated on the analysis of these sequences and their trans-acting factors, we are now beginning to gain an understanding of the mechanisms by which some of these proteins function. In this review, we will describe a number of different families of RNA-binding proteins, grouping them together on the basis of common regulatory strategies, and emphasizing the recurrent themes that occur, both across different species and as a response to different biological problems.
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98
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Bagni C, Greenough WT. From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome. Nat Rev Neurosci 2005; 6:376-87. [PMID: 15861180 DOI: 10.1038/nrn1667] [Citation(s) in RCA: 368] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mental retardation protein FMRP is involved in the transport of mRNAs and their translation at synapses. Patients with fragile X syndrome, in whom FMRP is absent or mutated, show deficits in learning and memory that might reflect impairments in the translational regulation of a subset of neuronal mRNAs. The study of FMRP provides important insights into the regulation and functions of local protein synthesis in the neuronal periphery, and increases our understanding of how these functions can produce specific effects at individual synapses.
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Affiliation(s)
- Claudia Bagni
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, Roma, Italy.
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Skabkina OV, Lyabin DN, Skabkin MA, Ovchinnikov LP. YB-1 autoregulates translation of its own mRNA at or prior to the step of 40S ribosomal subunit joining. Mol Cell Biol 2005; 25:3317-23. [PMID: 15798215 PMCID: PMC1069629 DOI: 10.1128/mcb.25.8.3317-3323.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YB-1 is a member of the numerous families of proteins with an evolutionary ancient cold-shock domain. It is involved in many DNA- and RNA-dependent events and regulates gene expression at different levels. Previously, we found a regulatory element within the 3' untranslated region (UTR) of YB-1 mRNA that specifically interacted with YB-1 and poly(A)-binding protein (PABP); we also showed that PABP positively affected YB-1 mRNA translation in a poly(A) tail-independent manner (O. V. Skabkina, M. A. Skabkin, N. V. Popova, D. N. Lyabin, L. O. Penalva, and L. P. Ovchinnikov, J. Biol. Chem. 278:18191-18198, 2003). Here, YB-1 is shown to strongly and specifically inhibit its own synthesis at the stage of initiation, with accumulation of its mRNA in the form of free mRNPs. YB-1 and PABP binding sites have been mapped on the YB-1 mRNA regulatory element. These were UCCAG/ACAA for YB-1 and a approximately 50-nucleotide A-rich sequence for PABP that overlapped each other. PABP competes with YB-1 for binding to the YB-1 mRNA regulatory element and restores translational activity of YB-1 mRNA that has been inhibited by YB-1. Thus, YB-1 negatively regulates its own synthesis, presumably by specific interaction with the 3'UTR regulatory element, whereas PABP restores translational activity of YB-1 mRNA by displacing YB-1 from this element.
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Affiliation(s)
- Olga V Skabkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
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Meng Z, King PH, Nabors LB, Jackson NL, Chen CY, Emanuel PD, Blume SW. The ELAV RNA-stability factor HuR binds the 5'-untranslated region of the human IGF-IR transcript and differentially represses cap-dependent and IRES-mediated translation. Nucleic Acids Res 2005; 33:2962-79. [PMID: 15914670 PMCID: PMC1140080 DOI: 10.1093/nar/gki603] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The type I insulin-like growth factor receptor (IGF-IR) is an integral component in the control of cell proliferation, differentiation and apoptosis. The IGF-IR mRNA contains an extraordinarily long (1038 nt) 5'-untranslated region (5'-UTR), and we have characterized a diverse series of proteins interacting with this RNA sequence which may provide for intricate regulation of IGF-IR gene expression at the translational level. Here, we report the purification and identification of one of these IGF-IR 5'-UTR-binding proteins as HuR, using a novel RNA crosslinking/RNase elution strategy. Because HuR has been predominantly characterized as a 3'-UTR-binding protein, enhancing mRNA stability and generally increasing gene expression, we sought to determine whether HuR might serve a different function in the context of its binding the IGF-IR 5'-UTR. We found that HuR consistently repressed translation initiation through the IGF-IR 5'-UTR. The inhibition of translation by HuR was concentration dependent, and could be reversed in trans by addition of a fragment of the IGF-IR 5'-UTR containing the HuR binding sites as a specific competitor, or abrogated by deletion of the third RNA recognition motif of HuR. We determined that HuR repressed translation initiation through the IGF-IR 5'-UTR in cells as well, and that siRNA knockdown of HuR markedly increased IGF-IR protein levels. Interestingly, we also found that HuR potently inhibited IGF-IR translation mediated through internal ribosome entry. Kinetic assays were performed to investigate the mechanism of translation repression by HuR and the dynamic interplay between HuR and the translation apparatus. We found that HuR, occupying a cap-distal position, significantly delayed translation initiation mediated by cap-dependent scanning, but was eventually displaced from its binding site, directly or indirectly, as a consequence of ribosomal scanning. However, HuR perpetually blocked the activity of the IGF-IR IRES, apparently arresting the IRES-associated translation pre-initiation complex in an inactive state. This function of HuR as a 5'-UTR-binding protein and dual-purpose translation repressor may be critical for the precise regulation of IGF-IR expression essential to normal cellular homeostasis.
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Affiliation(s)
- Zheng Meng
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirmingham, AL, USA
| | - Peter H. King
- Department of Neurology, University of Alabama at BirminghamBirmingham, AL, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35294, USA
| | - L. Burt Nabors
- Department of Neurology, University of Alabama at BirminghamBirmingham, AL, USA
| | - Nateka L. Jackson
- Department of Medicine, University of Alabama at BirminghamBirmingham, AL, USA
| | - Ching-Yi Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirmingham, AL, USA
| | - Peter D. Emanuel
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirmingham, AL, USA
- Department of Medicine, University of Alabama at BirminghamBirmingham, AL, USA
- Comprehensive Cancer Center, University of Alabama at BirminghamBirmingham, AL, USA
| | - Scott W. Blume
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirmingham, AL, USA
- Department of Medicine, University of Alabama at BirminghamBirmingham, AL, USA
- Comprehensive Cancer Center, University of Alabama at BirminghamBirmingham, AL, USA
- To whom correspondence should be addressed at 1824 6th Avenue South, Wallace Tumor Institute, Room 508, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Tel: +1 205 975 2409; Fax: +1 205 975 6911;
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