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Zhu B, Zhang Z, Pardeshi L, Chen Y, Ge W. Y box-binding protein 1 regulates zebrafish folliculogenesis partly through p21-mediated control of follicle cell proliferation. Development 2024; 151:dev202898. [PMID: 39470059 DOI: 10.1242/dev.202898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 10/04/2024] [Indexed: 10/30/2024]
Abstract
Y box-binding protein 1 (Ybx1/ybx1) regulates gene expression through DNA/RNA binding. In zebrafish, Ybx1 is highly abundant in primary growth (PG) follicles in the ovary, but decreases precipitously as the follicles enter the secondary growth (SG). To understand Ybx1 function in folliculogenesis, we created a ybx1 mutant using TALEN and observed disrupted folliculogenesis during the previtellogenic (PV) to early vitellogenic (EV) transition of SG, resulting in underdeveloped ovaries and infertility. Expression and western blot analyses revealed differential gene expression between ybx1-/- and control ovaries, with significantly increased expression of cdkn1a (p21), a cell cycle inhibitor, in ybx1-/- follicles. While cdkn1a knockout via CRISPR/Cas9 was embryonically lethal, the heterozygote (cdkn1a+/-) displayed advanced follicle activation and maturation, contrasting with the ybx1-/- phenotype. Partial loss of p21 alleviated the ybx1-/- phenotype, restoring folliculogenesis with normal PG-PV and PV-EV transitions in ybx1-/-;cdkn1a+/- mutants. While ybx1-/- mutant follicle cells displayed poor proliferation in vivo and in vitro, the cells from the ybx1-/-;cdkn1a+/- follicles resumed normal proliferation. In conclusion, Ybx1 is crucial for early folliculogenesis in zebrafish, potentially by repressing cdkn1a expression, either directly or indirectly.
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Affiliation(s)
- Bo Zhu
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), University of Macau, Taipa, Macau, China
| | - Zhiwei Zhang
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), University of Macau, Taipa, Macau, China
| | - Lakhansing Pardeshi
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Taipa, Macau, 999078, China
| | - Yingying Chen
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Taipa, Macau, 999078, China
| | - Wei Ge
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), University of Macau, Taipa, Macau, China
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2
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Yuan Z, Li B, Liao W, Kang D, Deng X, Tang H, Xie J, Hu D, Chen A. Comprehensive pan-cancer analysis of YBX family reveals YBX2 as a potential biomarker in liver cancer. Front Immunol 2024; 15:1382520. [PMID: 38698857 PMCID: PMC11063299 DOI: 10.3389/fimmu.2024.1382520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Background The Y-box-binding proteins (YBX) act as a multifunctional role in tumor progression, metastasis, drug resistance by regulating the transcription and translation process. Nevertheless, their functions in a pan-cancer setting remain unclear. Methods This study examined the clinical features expression, prognostic value, mutations, along with methylation patterns of three genes from the YBX family (YBX1, YBX2, and YBX3) in 28 different types of cancer. Data used for analysis were obtained from Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. A novel YBXs score was created using the ssGSEA algorithm for the single sample gene set enrichment analysis. Additionally, we explored the YBXs score's association with the tumor microenvironment (TME), response to various treatments, and drug resistance. Results Our analysis revealed that YBX family genes contribute to tumor progression and are indicative of prognosis in diverse cancer types. We determined that the YBXs score correlates significantly with numerous malignant pathways in pan-cancer. Moreover, this score is also linked with multiple immune-related characteristics. The YBXs score proved to be an effective predictor for the efficacy of a range of treatments in various cancers, particularly immunotherapy. To summarize, the involvement of YBX family genes is vital in pan-cancer and exhibits a significant association with TME. An elevated YBXs score indicates an immune-activated TME and responsiveness to diverse therapies, highlighting its potential as a biomarker in individuals with tumors. Finally, experimental validations were conducted to explore that YBX2 might be a potential biomarker in liver cancer. Conclusion The creation of YBXs score in our study offered new insights into further studies. Besides, YBX2 was found as a potential therapeutic target, significantly contributing to the improvement of HCC diagnosis and treatment strategies.
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Affiliation(s)
- Ze Yuan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Binbin Li
- Department of Medical Oncology, The Third People’s Hospital of Yongzhou, Yongzhou, China
| | - Wenmin Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Da Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dandan Hu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Aiqin Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Evdokimova V. Y-box Binding Protein 1: Looking Back to the Future. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S5-S145. [PMID: 35501983 DOI: 10.1134/s0006297922140024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.
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4
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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5
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Neil CR, Jeschonek SP, Cabral SE, O'Connell LC, Powrie EA, Otis JP, Wood TR, Mowry KL. L-bodies are RNA-protein condensates driving RNA localization in Xenopus oocytes. Mol Biol Cell 2021; 32:ar37. [PMID: 34613784 PMCID: PMC8694076 DOI: 10.1091/mbc.e21-03-0146-t] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule structure and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are localized as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here we demonstrate that RNPs containing vegetally localized RNAs represent a new class of cytoplasmic RNP granule, termed localization-bodies (L-bodies). We show that L-bodies contain a dynamic protein-containing phase surrounding a nondynamic RNA-containing phase. Our results support a role for RNA as a critical component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.
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Affiliation(s)
- Christopher R Neil
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Samantha P Jeschonek
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Sarah E Cabral
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Liam C O'Connell
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Erin A Powrie
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jessica P Otis
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Timothy R Wood
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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6
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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Specific activation of the hb4 gene in the Xenopus oocyte through a Nobox-binding element located at the proximal promoter sequence. ZYGOTE 2019; 27:195-202. [PMID: 31250783 DOI: 10.1017/s0967199419000017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We isolated and characterized Xenopus tropicalis hb4 flanking DNA and showed that the -3076/+29 sequence was able to drive stage-specific transcription in the developmental process. Transgenic reporter analysis indicated that green fluorescent protein was expressed in the ovaries of female frogs at 3 months of age and in both the ovaries and testis of frogs at 6 months of age. A series of experiments with deletion of the flanking sequence and a subsequent luciferase reporter assay revealed that there were two positive regulatory regions and that the most proximal sequence of the promoter region had a certain level of transcriptional activity in oocytes. Subsequently, we showed that a conserved sequence containing Nobox-binding element (NBE) was essential for transcriptional activation and that Nobox expressed in the ovary had a crucial role in hb4 transcription through the NBE sequence.
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8
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Han Y, Xu Z, Liu Y, Wei D, Zhang J, Xue L, Zhang X, Qin J, Deng H, Song L. Molecular cloning and characterization of a novel Y-box gene from planarian Dugesia japonica. Biochem Biophys Res Commun 2018; 505:1084-1089. [PMID: 30314702 DOI: 10.1016/j.bbrc.2018.09.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 11/28/2022]
Abstract
Y-box binding protein (YB protein) is an ancient conserved multifunctional DNA/RNA-binding protein. A novel YB protein DjY2 gene from planarian Dugesia japonica was cloned by RACE method and characterized. This cDNA contains 689 bp with a putative open reading frame of 197 amino acids. It has a predicted molecular mass of 22.14 kDa and an isoelectric point of 9.67. Whole-mount in situ hybridization and relative quantitative real-time PCR were used to study the spatial and temporal expression pattern of DjY2 in the process of planarian regeneration. Results showed that DjY2 was expressed in many parts of the body in intact planarian, but the expression level was low in head and pharynx. The transcripts of DjY2 was significantly increased both at the head parts and the tail parts after amputation, especially at the site of cutting. The spatial expression gradually recovered to the state of intact planarian with the time of regeneration. Our results indicated that DjY2 might participate in the process of regeneration in planarian.
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Affiliation(s)
- Yahong Han
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Zhenbiao Xu
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Yanan Liu
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Da Wei
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Jing Zhang
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Le Xue
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Xiangmin Zhang
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Jie Qin
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Hongkuan Deng
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China
| | - Linxia Song
- College of Life Science, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong, 255049, China.
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9
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Li G, Wang L, Wang Y, Li H, Liu Z, Wang H, Xu B, Guo X. Developmental characterization and environmental stress responses of Y-box binding protein 1 gene (AccYB-1) from Apis cerana cerana. Gene 2018; 674:37-48. [DOI: 10.1016/j.gene.2018.06.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 12/11/2022]
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10
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Characterization of Two Dinoflagellate Cold Shock Domain Proteins. mSphere 2016; 1:mSphere00034-15. [PMID: 27303711 PMCID: PMC4863620 DOI: 10.1128/msphere.00034-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/05/2015] [Indexed: 01/16/2023] Open
Abstract
Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists.
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11
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Schilling J, Loziuk PL, Muddiman DC, Daniels HV, Reading BJ. Mechanisms of Egg Yolk Formation and Implications on Early Life History of White Perch (Morone americana). PLoS One 2015; 10:e0143225. [PMID: 26580971 PMCID: PMC4651544 DOI: 10.1371/journal.pone.0143225] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/02/2015] [Indexed: 12/23/2022] Open
Abstract
The three white perch (Morone americana) vitellogenins (VtgAa, VtgAb, VtgC) were quantified accurately and precisely in the liver, plasma, and ovary during pre-, early-, mid-, and post-vitellogenic oocyte growth using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Western blotting generally mirrored the PC-IDMS results. By PC-IDMS, VtgC was quantifiable in pre-vitellogenic ovary tissues and VtgAb was quantifiable in pre-vitellogenic liver tissues however, neither protein was detected by western blotting in these respective tissues at this time point. Immunohistochemistry indicated that VtgC was present within pre-vitellogenic oocytes and localized to lipid droplets within vitellogenic oocytes. Affinity purification coupled to tandem mass spectrometry using highly purified VtgC as a bait protein revealed a single specific interacting protein (Y-box binding protein 2a-like [Ybx2a-like]) that eluted with suramin buffer and confirmed that VtgC does not bind the ovary vitellogenin receptors (LR8 and Lrp13). Western blotting for LR8 and Lrp13 showed that both receptors were expressed during vitellogenesis with LR8 and Lrp13 expression highest in early- and mid-vitellogenesis, respectively. The VtgAa within the ovary peaked during post-vitellogenesis, while VtgAb peaked during early-vitellogenesis in both white perch and the closely related striped bass (M. saxatilis). The VtgC was steadily accumulated by oocytes beginning during pre-vitellogenesis and continued until post-vitellogenesis and its composition varies widely between striped bass and white perch. In striped bass, the VtgC accounted for 26% of the vitellogenin-derived egg yolk, however in the white perch it comprised only 4%. Striped bass larvae have an extended developmental window and these larvae have yolk stores that may enable them to survive in the absence of food for twice as long as white perch after hatch. Thus, the VtgC may play an integral role in providing nutrients to late stage fish larvae prior to the onset of exogenous feeding and its composition in the egg yolk may relate to different early life histories among this diverse group of animals.
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Affiliation(s)
- Justin Schilling
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Philip L. Loziuk
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David C. Muddiman
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Harry V. Daniels
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Benjamin J. Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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12
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Dolfini D, Mantovani R. Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y? Cell Death Differ 2013; 20:676-85. [PMID: 23449390 PMCID: PMC3619239 DOI: 10.1038/cdd.2013.13] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/11/2013] [Accepted: 01/18/2013] [Indexed: 01/14/2023] Open
Abstract
The Y box is an important sequence motif found in promoters and enhancers containing a CCAAT box - one of the few elements enriched in promoters of large sets of genes overexpressed in cancer. The search for the transcription factor(s) acting on it led to the biochemical purification of the nuclear factor Y (NF-Y) heterotrimer, and to the cloning - through the screening of expression libraries - of Y box-binding protein 1 (YB-1), an oncogene, overexpressed in aggressive tumors and associated with drug resistance. These two factors have been associated with Y/CCAAT-dependent activation of numerous growth-related genes, notably multidrug resistance protein 1. We review two decades of data indicating that NF-Y ultimately acts on Y/CCAAT in cancer cells, a notion recently confirmed by genome-wide data. Other features of YB-1, such as post-transcriptional control of mRNA biology, render it important in cancer biology.
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Affiliation(s)
- D Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milan 20133, Italy
| | - R Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milan 20133, Italy
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13
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Wang XL, Zhang YX, Yang CG, Zhang B, Chen SL. Cloning, characterization and expression analysis of a cold shock domain family member YB-1 in turbot Scophthalmus maximus. FISH & SHELLFISH IMMUNOLOGY 2012; 33:1215-1221. [PMID: 22982328 DOI: 10.1016/j.fsi.2012.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 08/11/2012] [Accepted: 09/03/2012] [Indexed: 06/01/2023]
Abstract
The Y-box proteins are a family of highly conserved nucleic acid binding proteins. In this report we have identified a new member, YB-1 from turbot (Scophthalmus maximus) spleen cDNA library. The full-length cDNA sequence of turbot YB-1 was obtained and then the expression at transcriptional level was researched by qRT-PCR. In normal organs, the expression of YB-1 was higher in liver, brain, gill and heart, respectively. YB-1 had the highest expression level at gastrula stage during the early stages of embryo development. In the liver, kidney and spleen, the turbot YB-1 expression level was the highest at 72 h after challenge with lymphocystis disease virus (LCDV) and the highest at 12 h after challenge with Vibrio anguillarum (V. anguillarum). Furthermore, the expression of turbot YB-1 also distinctly increased in turbot kidney cells (TK) at 24 h after challenge with V. anguillarum and LCDV. These results indicated that the turbot YB-1 protein may play a significant role in the immune response of turbot.
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Affiliation(s)
- Xian-Li Wang
- Translational Center for Stem Cell Research, Tongji Hospital, Stem Cell Research Center, Tongji University School of Medicine, Shanghai 200065, China
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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: 252] [Impact Index Per Article: 19.4] [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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15
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Nakamura Y, Tanaka KJ, Miyauchi M, Huang L, Tsujimoto M, Matsumoto K. Translational repression by the oocyte-specific protein P100 in Xenopus. Dev Biol 2010; 344:272-83. [PMID: 20471969 DOI: 10.1016/j.ydbio.2010.05.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 04/09/2010] [Accepted: 05/07/2010] [Indexed: 01/10/2023]
Abstract
The translational regulation of maternal mRNAs is one of the most important steps in the control of temporal-spatial gene expression during oocyte maturation and early embryogenesis in various species. Recently, it has become clear that protein components of mRNPs play essential roles in the translational regulation of maternal mRNAs. In the present study, we investigated the function of P100 in Xenopus oocytes. P100 exhibits sequence conservation with budding yeast Pat1 and is likely the orthologue of human Pat1a (also called PatL2). P100 is maternally expressed in immature oocytes, but disappears during oocyte maturation. In oocytes, P100 is an RNA binding component of ribosome-free mRNPs, associating with other mRNP components such as Xp54, xRAP55 and CPEB. Translational repression by overexpression of P100 occurred when reporter mRNAs were injected into oocytes. Intriguingly, we found that when P100 was overexpressed in the oocytes, the kinetics of oocyte maturation was considerably retarded. In addition, overexpression of P100 in oocytes significantly affected the accumulation of c-Mos and cyclin B1 during oocyte maturation. These results suggest that P100 plays a role in regulating the translation of specific maternal mRNAs required for the progression of Xenopus oocyte maturation.
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Affiliation(s)
- Yoriko Nakamura
- Laboratory of Cellular Biochemistry, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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16
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Golam Mostafa M, Sugimoto T, Hiyoshi M, Kawasaki H, Kubo H, Matsumoto K, Abe SI, Takamune K. Xtr, a plural tudor domain-containing protein, coexists with FRGY2 both in cytoplasmic mRNP particle and germ plasm in Xenopus embryo: Its possible role in translational regulation of maternal mRNAs. Dev Growth Differ 2009; 51:595-605. [DOI: 10.1111/j.1440-169x.2009.01121.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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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: 51] [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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18
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Medvedev S, Yang J, Hecht NB, Schultz RM. CDC2A (CDK1)-mediated phosphorylation of MSY2 triggers maternal mRNA degradation during mouse oocyte maturation. Dev Biol 2008; 321:205-15. [PMID: 18606161 PMCID: PMC2593896 DOI: 10.1016/j.ydbio.2008.06.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 05/22/2008] [Accepted: 06/10/2008] [Indexed: 12/16/2022]
Abstract
Degradation of maternal mRNA is thought to be essential to undergo the maternal-to-embryonic transition. Messenger RNA is extremely stable during oocyte growth in mouse and MSY2, an abundant germ cell-specific RNA-binding protein, likely serves as a mediator of global mRNA stability. Oocyte maturation, however, triggers an abrupt transition in which most mRNAs are significantly degraded. We report that CDC2A (CDK1)-mediated phosphorylation of MSY2 triggers this transition. Injecting Cdc2a mRNA, which activates CDC2A, overcomes milrinone-mediated inhibition of oocyte maturation, induces MSY2 phosphorylation and the maturation-associated degradation of mRNAs. Inhibiting CDC2A following its activation with roscovitine inhibits MSY2 phosphorylation and prevents mRNA degradation. Expressing non-phosphorylatable dominant-negative forms of MSY2 inhibits the maturation-associated decrease in mRNAs, whereas expressing constitutively active forms induces mRNA degradation in the absence of maturation and phosphorylation of endogenous MSY2. A positive-feedback loop of CDK1-mediated phosphorylation of MSY2 that leads to degradation of Msy2 mRNA that in turn leads to a decrease in MSY2 protein may ensure that the transition is irreversible.
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Affiliation(s)
- Sergey Medvedev
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Juxiang Yang
- Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104
| | - Norman B. Hecht
- Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104
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19
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Marracci S, Casola C, Bucci S, Mancino G, Ragghianti M. Isolation and expression ofRlYB2, a germ cell‐specificY‐boxgene inRana. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/11250000701690616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Mtango NR, Potireddy S, Latham KE. Oocyte quality and maternal control of development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 268:223-90. [PMID: 18703408 DOI: 10.1016/s1937-6448(08)00807-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The oocyte is a unique and highly specialized cell responsible for creating, activating, and controlling the embryonic genome, as well as supporting basic processes such as cellular homeostasis, metabolism, and cell cycle progression in the early embryo. During oogenesis, the oocyte accumulates a myriad of factors to execute these processes. Oogenesis is critically dependent upon correct oocyte-follicle cell interactions. Disruptions in oogenesis through environmental factors and changes in maternal health and physiology can compromise oocyte quality, leading to arrested development, reduced fertility, and epigenetic defects that affect long-term health of the offspring. Our expanding understanding of the molecular determinants of oocyte quality and how these determinants can be disrupted has revealed exciting new insights into the role of oocyte functions in development and evolution.
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Affiliation(s)
- Namdori R Mtango
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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21
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Tanaka KJ, Ogawa K, Takagi M, Imamoto N, Matsumoto K, Tsujimoto M. RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. J Biol Chem 2006; 281:40096-106. [PMID: 17074753 DOI: 10.1074/jbc.m609059200] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mRNAs in eukaryotic cells are presumed to always associate with a set of proteins to form mRNPs. In Xenopus oocytes, a large pool of maternal mRNAs is masked from the translational apparatus as storage mRNPs. Here we identified Xenopus RAP55 (xRAP55) as a component of RNPs that associate with FRGY2, the principal component of maternal mRNPs. RAP55 is a member of the Scd6 or Lsm14 family. RAP55 localized to cytoplasmic foci in Xenopus oocytes and the processing bodies (P-bodies) in cultured human cells: in the latter cells, RAP55 is an essential constituent of the P-bodies. We isolated xRAP55-containing complexes from Xenopus oocytes and identified xRAP55-associated proteins, including a DEAD-box protein, Xp54, and a protein arginine methyltransferase, PRMT1. Recombinant xRAP55 repressed translation, together with Xp54, in an in vitro translation system. In addition, xRAP55 repressed translation in oocytes when tethered with a reporter mRNA. Domain analyses revealed that the N-terminal region of RAP55, including the Lsm domain, is important for the localization to P-bodies and translational repression. Taken together, our results suggest that xRAP55 is involved in translational repression of mRNA as a component of storage mRNPs.
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Affiliation(s)
- Kimio J Tanaka
- Laboratory of Cellular Biochemistry, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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22
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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: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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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: 23] [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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24
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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: 216] [Impact Index Per Article: 11.4] [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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25
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Gonda K, Wudel J, Nelson D, Katoku-Kikyo N, Reed P, Tamada H, Kikyo N. Requirement of the protein B23 for nucleolar disassembly induced by the FRGY2a family proteins. J Biol Chem 2006; 281:8153-60. [PMID: 16415342 PMCID: PMC2222668 DOI: 10.1074/jbc.m512890200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Xenopus somatic cell nuclear cloning, the nucleoli of donor nuclei rapidly and almost completely disappear in egg cytoplasm. We previously showed that the germ cell-specific proteins FRGY2a and FRGY2b were responsible for this unusually drastic nucleolar disassembly. The nucleolar disassembly occurs without inhibition of pre-rRNA transcription, a well known trigger for nucleolar segregation, and the mechanism for the nucleolar disassembly by FRGY2a and FRGY2b remains largely unknown. In this study, we searched for FRGY2a-interacting proteins and investigated the functional consequences of their interactions through a series of experiments. We showed that during the nucleolar disassembly, FRGY2a localized to the nucleoli of isolated nuclei and was capable of disassembling purified nucleoli, suggesting a direct interaction between FRGY2a and nucleolar components. Using a His tag pulldown approach, we identified the abundant and multifunctional nucleolar protein B23 as a potential target of FRGY2a and its related human protein YB1. A specific interaction between FRGY2a/YB1 and B23 was confirmed by co-immunoprecipitation. Finally, B23 knockdown using short interfering RNA and a subsequent add-back experiment confirmed that B23 was necessary for nucleolar disassembly by YB1. We propose that FRGY2a and YB1 disassemble nucleoli by sequestering B23, which is associated with pre-ribosomes and other structurally important nucleolar components.
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Affiliation(s)
| | | | | | - Nobuko Katoku-Kikyo
- From the Stem Cell Institute, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455
| | - Peter Reed
- From the Stem Cell Institute, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455
| | - Hiroshi Tamada
- From the Stem Cell Institute, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455
| | - Nobuaki Kikyo
- From the Stem Cell Institute, Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455
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26
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Matsumoto K, Tanaka KJ, Tsujimoto M. An acidic protein, YBAP1, mediates the release of YB-1 from mRNA and relieves the translational repression activity of YB-1. Mol Cell Biol 2005; 25:1779-92. [PMID: 15713634 PMCID: PMC549371 DOI: 10.1128/mcb.25.5.1779-1792.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Eukaryotic Y-box proteins are nucleic acid-binding proteins implicated in a wide range of gene regulatory mechanisms. They contain the cold shock domain, which is a nucleic acid-binding structure also found in bacterial cold shock proteins. The Y-box protein YB-1 is known to be a core component of messenger ribonucleoprotein particles (mRNPs) in the cytoplasm. Here we disrupted the YB-1 gene in chicken DT40 cells. Through the immunoprecipitation of an epitope-tagged YB-1 protein, which complemented the slow-growth phenotype of YB-1-depleted cells, we isolated YB-1-associated complexes that likely represented general mRNPs in somatic cells. RNase treatment prior to immunoprecipitation led to the identification of a Y-box protein-associated acidic protein (YBAP1). The specific association of YB-1 with YBAP1 resulted in the release of YB-1 from reconstituted YB-1-mRNA complexes, thereby reducing the translational repression caused by YB-1 in the in vitro system. Our data suggest that YBAP1 induces the remodeling of YB-1-mRNA complexes.
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Affiliation(s)
- Ken Matsumoto
- Laboratory of Cellular Biochemistry, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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27
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Tanaka KJ, Matsumoto K, Tsujimoto M, Nishikata T. CiYB1 is a major component of storage mRNPs in ascidian oocytes: implications in translational regulation of localized mRNAs. Dev Biol 2004; 272:217-30. [PMID: 15242802 DOI: 10.1016/j.ydbio.2004.04.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Revised: 04/19/2004] [Accepted: 04/20/2004] [Indexed: 11/21/2022]
Abstract
In ascidian eggs, the existence of several localized maternal cytoplasmic determinants has been proposed and the importance of localized mRNAs for tissue differentiation has been demonstrated. We previously identified the ascidian Y-box proteins (CiYB1, 2 and 3), homologues of which are known to be involved in the storage of maternal mRNA in oocytes of other organisms. In this study, we found that CiYB1 protein is abundant in the gonad, egg, and embryo. Purification of messenger ribonucleoprotein (mRNP) particles from the gonad revealed that CiYB1 was one of their major components. A significant change in the distribution of CiYB1 protein from stored mRNP particles in the gonad to the ribosome fraction in eggs and embryos was observed. This change correlates most likely with the shift of stored maternal mRNAs to polyribosomes. Moreover, we found that CiYB1 colocalized with Cipem and Ci-macho1 mRNAs, which are localized at the posterior end of the embryo at the cleavage stage. Cipem and Ci-macho1 mRNAs were co-immunoprecipitated with CiYB1 in the oocyte and embryo lysates. The formation of a complex between Cipem mRNA and CiYB1 protein resulted in translational repression in the in vitro translation system. Our results indicate that associating with CiYB1 protein contributes to the translational control of the localized mRNA in eggs and embryos.
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Affiliation(s)
- Kimio J Tanaka
- Laboratory of Cellular Biochemistry, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan
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28
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Ohba H, Chiyoda T, Endo E, Yano M, Hayakawa Y, Sakaguchi M, Darnell RB, Okano HJ, Okano H. Sox21 is a repressor of neuronal differentiation and is antagonized by YB-1. Neurosci Lett 2004; 358:157-60. [PMID: 15039105 DOI: 10.1016/j.neulet.2004.01.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 01/08/2004] [Accepted: 01/09/2004] [Indexed: 10/26/2022]
Abstract
Sox21, a high-mobility group box transcription factor, is expressed throughout the immature neural stem/progenitor population in ventricular zone but not in the cortical plate in embryonic mouse brain and its expression is restricted to the subventricular zone in the adult brain. In undifferentiated PC12 cells, endogenous Sox21 expression is detected but its expression ceases during the nerve growth factor (NGF)-induced neuronal differentiation. Overexpression of Sox21 results in a substantial repression of NGF-induced neurite outgrowth in PC12 cells. Further, we biochemically identified a Sox21-associating protein, Y-box binding protein 1 which not only binds to Sox21 but also partially restores NGF-induced neurite outgrowth of PC12 cells inhibited by Sox21. These results suggest that Sox21 is a repressor of neuronal differentiation in the developing nervous system.
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Affiliation(s)
- Hiroyuki Ohba
- CREST-JST and Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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29
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Jurchott K, Bergmann S, Stein U, Walther W, Janz M, Manni I, Piaggio G, Fietze E, Dietel M, Royer HD. YB-1 as a cell cycle-regulated transcription factor facilitating cyclin A and cyclin B1 gene expression. J Biol Chem 2003; 278:27988-96. [PMID: 12695516 DOI: 10.1074/jbc.m212966200] [Citation(s) in RCA: 172] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the Y-box protein YB-1 is increased in proliferating normal and cancer cells, but its role in cell proliferation and cell cycle progression is unclear. We have identified a cell cycle-dependent relocalization of YB-1 from the cytoplasm to the nucleus at the G1/S phase transition and demonstrate that both the charged zipper and the cold shock domain are involved in regulating this process. Using cell lines that constitutively overexpress YB-1, we show that nuclear accumulation of YB-1 is associated with increased cyclin A and cyclin B1 mRNA and protein expression. We provide evidence that deregulated YB-1 expression is linked to adhesion-independent cell proliferation through the induction of cyclin A. Thus, we have identified YB-1 as a cell cycle stage-specific transcription factor important for cell proliferation.
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Affiliation(s)
- Karsten Jurchott
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.
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30
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Zasedateleva OA, Krylov AS, Prokopenko DV, Skabkin MA, Ovchinnikov LP, Kolchinsky A, Mirzabekov AD. Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip. J Mol Biol 2002; 324:73-87. [PMID: 12421560 DOI: 10.1016/s0022-2836(02)00937-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. The oligonucleotides were chemically immobilized within polyacrylamide gel pads fixed on a glass slide. The binding of p50 to the generic microchip was shown to be the most specific to ss GGGG motif and then to ss CACC and CATC motifs. GC-rich ds oligonucleotides of the generic microchip, and particularly those containing GGTG/CACC, GATG/CATC, and GTGG/CCAC heterogeneous motifs, were most efficiently destabilized due to interaction with p50. Gel-shift electrophoresis has shown that the protein exhibits much higher binding specificity to 24-mer oligoA-TGGGGG-oligoA containing G-rich 6-mer, in comparison with 24-mer oligoA-AAATAT-oligoA carrying A,T-rich 6-mer in full correspondence with the data obtained with the microchip. Studies of DNA-binding proteins using gel-immobilized ss and ds DNA fragments provide a unique possibility to detect low-affinity complexes of these proteins with short sequence motifs and assess the role of these motifs in sequence-specific interactions with long recognition sites.
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Affiliation(s)
- O A Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russian Federation
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31
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Valadão AF, Fantappie MR, LoVerde PT, Pena SDJ, Rumjanek FD, Franco GR. Y-box binding protein from Schistosoma mansoni: interaction with DNA and RNA. Mol Biochem Parasitol 2002; 125:47-57. [PMID: 12467973 DOI: 10.1016/s0166-6851(02)00210-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A Schistosoma mansoni homologue of the human Y-box binding protein (SMYB1), as well as truncated proteins containing its N-terminal Cold Shock Domain (CSD) or its C-terminal domain (TAIL) were cloned into the p-MAL-c2 expression vector and produced in Escherichia coli. In order to characterize the interactions of these proteins to an inverted CCAAT motif present in a number of gene promoters, their binding to DNA was measured by Electrophoretic Mobility Shift Assays. SMYB1 bound to single- and double-stranded DNA containing the CCAAT motif and could bind also to RNA. The truncated CSD and TAIL domain proteins bound to dsDNA and RNA, but exhibited distinct binding patterns. Protein-DNA interaction was also investigated in vivo, using the Yeast One-Hybrid System. The plasmid constructs were GSTTRI, a DNA fragment composed of three copies of the CCAAT motif of the S. mansoni glutathione S-transferase gene promoter and four oligonucleotides spanning different regions of the S. mansoni p14 gene promoter. None of the yeast clones transformed with the above plasmids was able to grow in selective medium or to activate the transcription of the HIS3 reporter gene, suggesting that SMYB1 could not interact with these promoters in vivo.
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Affiliation(s)
- A F Valadão
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-010, Brazil
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32
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Yu J, Hecht NB, Schultz RM. RNA-Binding Properties and Translation Repression In Vitro by Germ Cell-Specific MSY2 Protein1. Biol Reprod 2002; 67:1093-8. [PMID: 12297523 DOI: 10.1095/biolreprod67.4.1093] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The large amount of MSY2 protein, a mouse germ cell-specific Y-box protein, in oocytes and its degradation by the late two-cell stage suggest that MSY2 may stabilize and/or regulate the translation of maternal mRNAs. We report here the ability of bacterially expressed recombinant MSY2 protein to bind to mRNA and repress translation in vitro. Although MSY2 displays some sequence specificity in binding to short RNA sequences derived from the 3' untranslated region (UTR) of the protamine 1 (Prm1) mRNA, as determined by both gel shift and filter binding assays, essentially no sequence specificity is observed when full-length Prm1 mRNA is used. The binding of MSY2 is approximately 10-fold greater to the full-length Prm1 mRNA than to a 37-nucleotide sequence derived from the 3' UTR, and gel shift assays indicate that multiple MSY2 molecules bind to a single Prm1 mRNA. MSY2 binding to luciferase mRNA at ratios of protein to mRNA that are likely to exist in the oocyte also leads to a moderate inhibition of protein synthesis in vitro. Given the abundance of MSY2 in mouse oocytes (2% of total oocyte protein), these data suggest that MSY2 packages mRNAs in vivo with relatively little sequence specificity, which may lead to both stabilization and translation repression of maternal mRNAs.
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Affiliation(s)
- Junying Yu
- Department of Biology and Center for Research on Reproduction. Women's Health, University of Pennsylvania, Philadelphia 19104-6018, USA
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33
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Cheng S, Alfonso-Jaume MA, Mertens PR, Lovett DH. Tumour metastasis suppressor, nm23-beta, inhibits gelatinase A transcription by interference with transactivator Y-box protein-1 (YB-1). Biochem J 2002; 366:807-16. [PMID: 12010125 PMCID: PMC1222814 DOI: 10.1042/bj20020202] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2002] [Revised: 04/23/2002] [Accepted: 05/15/2002] [Indexed: 11/17/2022]
Abstract
Gelatinase A transcriptional regulation is the consequence of combinatorial interactions with key promoter and enhancer elements identified within this gene. A potent 40 bp enhancer response element, RE-1, located in the near 5' flanking regions of the rat and human gelatinase A genes drives high-level expression in glomerular mesangial cells (MCs). Southwestern-blot analysis of MC nuclear extracts revealed specific interactions of RE-1 with at least four proteins, of which three have been identified as p53, activator protein 2 and the single-stranded DNA-binding factor Y-box protein-1 (YB-1). In the present study, we report the identification of a fourth 17 kDa RE-1-binding protein as the rat homologue (nm23-beta) of the human nm23-H1 metastasis suppressor gene. Recombinant nm23-beta protein bound only the single-stranded forms of the RE-1 sequence. Mutagenesis revealed direct interaction of nm23-beta with a repeat sequence, 5'-GGGTTT-3', shown previously to specifically interact with YB-1 [Mertens, Harendza, Pollock and Lovett (1997) J. Biol. Chem. 272, 22905-22912], and recombinant nm23-beta protein competed for single-stranded YB-1 binding. Transient transfection of MC with an nm23-beta expression plasmid within the context of a RE-1/simian virus 40 promoter/luciferase reporter yielded a concentration-dependent repression (80-90%) of luciferase activity in MC and Rat1 fibroblasts. A similar pattern of nm23-beta repression was demonstrated within the context of the RE-1/homologous gelatinase A promoter. Co-transfection of nm23-beta blocked YB-1-mediated activation of transcription and expression of gelatinase A. Nm23-beta may be an important physiological regulator of gelatinase A transcription that acts by competitive interference with the single-stranded transactivator YB-1. Gelatinase A is a key mediator of tumour metastasis, suggesting that competitive suppression of transcription by nm23-beta (or the human nm23-H1) may be a component of the reduced metastatic capabilities of cells expressing high levels of this protein.
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MESH Headings
- Animals
- Binding, Competitive
- Blotting, Southern
- Blotting, Western
- CCAAT-Enhancer-Binding Proteins/metabolism
- Cell Division
- Cell Nucleus/metabolism
- Cloning, Molecular
- DNA, Complementary/metabolism
- DNA-Binding Proteins
- Fibroblasts/metabolism
- Genes, Reporter
- Humans
- Luciferases/metabolism
- Matrix Metalloproteinase 2/metabolism
- Monomeric GTP-Binding Proteins/metabolism
- Mutagenesis, Site-Directed
- Mutation
- NFI Transcription Factors
- NM23 Nucleoside Diphosphate Kinases
- Neoplasm Metastasis
- Nuclear Proteins
- Nucleoside-Diphosphate Kinase/metabolism
- Oligonucleotides/metabolism
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
- Rats
- Recombinant Proteins/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
- Y-Box-Binding Protein 1
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Affiliation(s)
- Sunfa Cheng
- Department of Medicine, San Francisco Veterans Affair Medical Center, University of California, San Francisco 94121, USA
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34
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Zend-Ajusch E, Hornung U, Burgtorf C, Lütjens G, Shan Z, Schartl M, Haaf T. Isolation and characterization of cold-shock domain protein genes, Oryzias latipes Y-box protein 2 (OlaYP2) and Fugu rubripes Y-box protein 1 (FruYP1), in medakafish and pufferfish. Gene 2002; 296:111-9. [PMID: 12383508 DOI: 10.1016/s0378-1119(02)00838-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Y-box protein (YP) family shares a nucleic acid binding domain, called cold-shock domain, that has been evolutionarily highly conserved from bacteria to human. The different YPs identified so far in vertebrates are thought to function as transcriptional activators, transcriptional repressors and/or translational repressors. Medakafish and pufferfish are very suitable vertebrate models for the study of developmental genetics and comparative genomics, respectively. Here we report the isolation of two teleost YP genes, medakafish Oryzias latipes (Ola)YP2 and Fugu rubripes (Fru)YP1, which are expressed in multiple tissues. Phylogenetic analysis demonstrated that OlaYP2 and FruYP1 belong to different subclasses of the cold-shock domain protein genes. Future studies in suitable model systems, like the medaka for developmental biology and Fugu for evolutionary genomics, are expected to contribute to our understanding of YPs.
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Affiliation(s)
- Enchshargal Zend-Ajusch
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2601, Australia
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35
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Hönig A, Auboeuf D, Parker MM, O'Malley BW, Berget SM. Regulation of alternative splicing by the ATP-dependent DEAD-box RNA helicase p72. Mol Cell Biol 2002; 22:5698-707. [PMID: 12138182 PMCID: PMC133985 DOI: 10.1128/mcb.22.16.5698-5707.2002] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although a number of ATP-dependent RNA helicases are important for constitutive RNA splicing, no helicases have been implicated in alternative RNA splicing. Here, we show that the abundant DEAD-box RNA helicase p72, but not its close relative p68, affects the splicing of alternative exons containing AC-rich exon enhancer elements. The effect of p72 was tested by using mini-genes that undergo different types of alternative splicing. When the concentration of p72 was increased in transient transfections, the inclusion of enhancer-containing CD44 alternative exons v4 and v5 increased using a mini-gene that contained these exons and their flanking introns inserted into a beta-globin gene. Other types of alternative splicing were not impacted by altering p72 concentrations. Mutation of the p72 helicase ATP-binding site or deletion of the carboxy-terminal region of the protein reduced the ability of the transfected protein to affect CD44 variable exon splicing. Use of in vitro extracts overexpressing p72 indicated that p72 becomes associated with complexes containing precursor RNA. Helicases have been implicated both in altering RNA-RNA interactions and in remodeling RNA-protein complexes. CD44 exon v4 contains a potential internal secondary structure element that base pairs the 5' splice site with a region inside the exon located between enhancer elements. Mutations that destroyed this complementarity modestly increased inclusion in the absence of p72 but still responded to increasing p72 concentration like the wild-type exon, suggesting that p72 might have effects on protein-RNA interactions. In agreement with this hypothesis, p72 was not able to restore the inclusion of an exon mutated for its major enhancer element. Our results suggest that RNA helicases may be important alternative splicing regulatory factors.
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Affiliation(s)
- Arnd Hönig
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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36
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Shao L, Sperber K. Impaired regulation of HLA-DR expression in human immunodeficiency virus-infected monocytes. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2002; 9:739-46. [PMID: 12093667 PMCID: PMC120040 DOI: 10.1128/cdli.9.4.739-746.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ling Shao
- Division of Clinical Immunology, Mount Sinai School of Medicine, New York, New York 10029, USA
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37
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Ficzycz A, Ovsenek N. The Yin Yang 1 transcription factor associates with ribonucleoprotein (mRNP) complexes in the cytoplasm of Xenopus oocytes. J Biol Chem 2002; 277:8382-7. [PMID: 11734562 DOI: 10.1074/jbc.m110304200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yin Yang 1 (YY1) is a multifunctional transcription factor that activates, represses, or initiates transcription of a diverse assortment of genes. Previous studies suggest a role for YY1 in cellular growth and differentiation, but its biological function during development of the vertebrate oocyte or embryo remains to be determined. We recently showed that YY1 is abundantly expressed throughout oogenesis and early embryonic stages of Xenopus, but it is sequestered in the cytoplasm and does not function directly in transcriptional regulation. In the present study we used a series of biochemical analyses to explore the potential function of YY1 in the oocyte cytoplasm. YY1 was isolated from oocyte lysates by oligo(dT)-cellulose chromatography, suggesting that it associates with maternally expressed mRNA in vivo. RNA mobility shift assays demonstrate that endogenous YY1 binds to labeled histone mRNA. Size exclusion chromatography of oocyte lysates revealed that YY1 exists in high molecular mass complexes in the range of 480 kDa. Destruction of endogenous RNA by RNase treatment of lysates, abolished the binding of YY1 to oligo(dT)-cellulose and resulted in redistribution from 480-kDa complexes to the monomeric form. Microinjection of RNase directly into the cytoplasm released YY1 from 480-kDa complexes and unmasked its DNA-binding activity, but did not promote translocation to the nucleus. These results provide evidence that YY1 is a component of ribonucleoprotein (mRNP) complexes in the Xenopus oocyte, indicating a novel function for YY1 in the storage or metabolism of maternal transcripts.
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Affiliation(s)
- Andrew Ficzycz
- Department of Anatomy and Cell Biology, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
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38
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Smillie DA, Sommerville J. RNA helicase p54 (DDX6) is a shuttling protein involved in nuclear assembly of stored mRNP particles. J Cell Sci 2002; 115:395-407. [PMID: 11839790 DOI: 10.1242/jcs.115.2.395] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we showed that an integral component of stored mRNP particles in Xenopus oocytes, Xp54, is a DEAD-box RNA helicase with ATP-dependent RNA-unwinding activity. Xp54 belongs to small family of helicases (DDX6) that associate with mRNA molecules encoding proteins required for progress through meiosis. Here we describe the nucleocytoplasmic translocation of recombinant Xp54 in microinjected oocytes and in transfected culture cells. We demonstrate that Xp54 is present in oocyte nuclei, its occurrence in both soluble and particle-bound forms and its ability to shuttle between nucleus and cytoplasm. Translocation of Xp54 from the nucleus to the cytoplasm appears to be dependent on the presence of a leucine-rich nuclear export signal (NES) and is blocked by leptomycin B, a specific inhibitor of the CRM1 receptor pathway. However, the C-terminal region of Xp54 can act to retain the protein in the cytoplasm of full-grown oocytes and culture cells. Cytoplasmic retention of Xp54 is overcome by activation of transcription. That Xp54 interacts directly with nascent transcripts is shown by immunostaining of the RNP matrix of lampbrush chromosome loops and co-immunoprecipitation with de novo-synthesized RNA. However, we are unable to show that nuclear export of this RNA is affected by either treatment with leptomycin B or mutation of the NES. We propose that newly synthesized Xp54 is regulated in its nucleocytoplasmic distribution: in transcriptionally quiescent oocytes it is largely restricted to the cytoplasm and, if imported into the nucleus, it is rapidly exported again by the CRM1 pathway. In transcriptionally active oocytes, it binds to a major set of nascent transcripts, accompanies mRNA sequences to the cytoplasm by an alternative export pathway and remains associated with masked mRNA until the time of translation activation at meiotic maturation and early embryonic cell division.
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Affiliation(s)
- David A Smillie
- Division of Cell and Molecular Biology, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TS, Scotland
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39
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Abstract
Translational control plays a central role during oocyte maturation and early embryogenesis, as these processes occur in the absence of transcription. MSY2, a member of a multifunctional Y-box protein family, is implicated in repressing the translation of paternal mRNAs. Here, we characterize MSY2 expression in mouse oocytes and preimplantation embryos. Northern blot analysis indicates that MSY2 expression is highly restricted and essentially confined to the oocyte in the female mouse. MSY2 transcript and protein, as assessed by reverse transcription-polymerase chain reaction and immunoblotting, respectively, are expressed in growing oocytes, metaphase II-arrested eggs, and 1-cell embryos, but then are degraded by the late 2-cell stage; no expression is detectable in the blastocysts. During oocyte maturation, MSY2 is phosphorylated and following fertilization it is dephosphorylated. Quantification of the mass amount of MSY2 reveals that it represents 2% of the total protein in the fully grown oocyte, i.e., it is a very abundant protein. Both endogenous MSY2 and MSY2-enhanced green fluorescent protein (EGFP), which is synthesized following microinjection of an mRNA encoding MSY2-EGFP, are primarily localized in the cytoplasm, and about 75% of the MSY2 remains associated with oocyte cytoskeletal preparations. Results of these studies are consistent with the proposal that MSY2 functions by stabilizing and/or repressing the translation of maternal mRNAs.
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Affiliation(s)
- J Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018, USA
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40
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Giorgini F, Davies HG, Braun RE. MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of protamine 1 mRNA in vitro and in vivo. Mol Cell Biol 2001; 21:7010-9. [PMID: 11564883 PMCID: PMC99876 DOI: 10.1128/mcb.21.20.7010-7019.2001] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Y-box proteins are major constituents of ribonucleoprotein particles (RNPs) which contain translationally silent mRNAs in gametic cells. We have recently shown that a sequence-specific RNA binding activity present in spermatogenic cells contains the two Y-box proteins MSY2 and MSY4. We show here that MSY2 and MSY4 bind a sequence, 5'-UCCAUCA-3', present in the 3' untranslated region of the translationally repressed protamine 1 (Prm1) mRNA. Using pre- and post-RNase T1-digested substrate RNAs, it was determined that MSY2 and MSY4 can bind an RNA of eight nucleotides containing the MSY2 and MSY4 binding site. Single nucleotide mutations in the sequence eliminated the binding of MSY2 and MSY4 in an electrophoretic mobility shift assay, and the resulting mutants failed to compete for binding in a competition assay. A consensus site of U(AC)C(A)CAU(C)CA(CU) (subscripts indicate nucleotides which do not disrupt YRS binding by MSY2 and MSY4), denoted the Y-box recognition site (YRS), was defined from this mutational analysis. These mutations in the YRS were further characterized in vivo using a novel application of the yeast three-hybrid system. Experiments with transgenic mice show that disruption of the YRS in vivo relieves Prm1-like repression of a reporter gene. The conservation of the RNA binding motifs among Y-box protein family members raises the possibility that other Y-box proteins may have previously unrecognized sequence-specific RNA binding activities.
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Affiliation(s)
- F Giorgini
- Department of Genetics, University of Washington, Seattle, Washington 98195, USA.
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41
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Rakoff-Nahoum S, Chen H, Kraus T, George I, Oei E, Tyorkin M, Salik E, Beuria P, Sperber K. Regulation of class II expression in monocytic cells after HIV-1 infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:2331-42. [PMID: 11490022 DOI: 10.4049/jimmunol.167.4.2331] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Human macrophage hybridoma cells were used to study HLA-DR expression after HIV-1 infection. HLA-DR surface expression was lost 2 wk after infection that was associated with decreased mRNA transcription. Transfecting HLA-DR-alpha and HLA-DR-beta cDNA driven by a nonphysiological CMV promoter restored expression, suggesting that regulatory DNA-binding proteins may be affected by HIV-1 infection. There was no protein binding to conserved class II DNA elements (W/Z/S box, X-1 and X-2 boxes, and Y box) in a HIV-1-infected human macrophage hybridoma cell line, 43(HIV), and in primary monocytes that lost HLA-DR expression after HIV-1(BaL) infection. PCR analysis of the HIV-1-infected cells that lost HLA-DR expression revealed mRNA for W/Z/S (RFX-5), X-1 (RFX-5), X-2 (hX-2BP), and one Y box DNA-binding protein (NF-YB), and CIITA, a non-DNA-binding protein necessary for class II transcription. There was no mRNA for the Y box-binding protein, NF-YA. However, HLA-DR expression could be restored by transfection with NF-YA driven by a CMV promoter, although HLA-DR failed to localize in either the late endosomes, lysosomes, or acidic compartments. This was associated with a loss of class II-associated invariant chain peptide and leupeptin-induced protein in the 43(HIV) cells. To address this further, non-HIV-1-infected 43 cells were infected with vaccinia virus containing HIV-1 gag, nef, pol, and env proteins. HLA-DR failed to localize in neither the late endosomes, lysosomes, or acidic compartments in the vaccinia-infected cells containing HIV-1 env protein. HIV-1 appears to have multiple effects on class II expression in monocytic cells that may contribute to the immune defects seen in HIV-1-infected patients.
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Affiliation(s)
- S Rakoff-Nahoum
- Division of Clinical Immunology, Mount Sinai School of Medicine, New York, NY 10029, USA
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42
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Stickeler E, Fraser SD, Honig A, Chen AL, Berget SM, Cooper TA. The RNA binding protein YB-1 binds A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4. EMBO J 2001; 20:3821-30. [PMID: 11447123 PMCID: PMC125550 DOI: 10.1093/emboj/20.14.3821] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Exon enhancers are accessory pre-mRNA splicing signals that stimulate exon splicing. One class of proteins, the serine-arginine-rich (SR) proteins, have been demonstrated to bind enhancers and activate splicing. Here we report that A/C-rich exon enhancers (ACE elements) are recognized by the human YB-1 protein, a non-SR protein. Sequence-specific binding of YB-1 was observed both to an ACE derived from an in vivo iterative selection protocol and to ACE elements in an alternative exon (v4) from the human CD44 gene. The ACE element that was the predominant YB-1 binding site in CD44 exon v4 was required for maximal in vivo splicing and in vitro spliceosome assembly. Expression of wild-type YB-1 increased inclusion of exon v4, whereas a truncated form of YB-1 did not. Stimulation of exon v4 inclusion by wild-type YB-1 required the ACE necessary for YB-1 binding in vitro, suggesting that YB-1 stimulated exon inclusion in vivo by binding to an exonic ACE element. These observations identify a protein in addition to SR proteins that participates in the recognition of exon enhancers.
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Affiliation(s)
- Elmar Stickeler
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
| | - Sherri D. Fraser
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
| | - Arnd Honig
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
| | - Andy L. Chen
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
| | - Susan M. Berget
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
| | - Thomas A. Cooper
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetterstrasse 55, D-79106 Freiburg, Germany, Department of Biochemistry and Molecular Biology and Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA Corresponding author e-mail:
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Karmirantzou M, Hamodrakas SJ. A Web-based classification system of DNA-binding protein families. PROTEIN ENGINEERING 2001; 14:465-72. [PMID: 11522919 DOI: 10.1093/protein/14.7.465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The family of DNA-binding proteins is one of the most populated and studied amongst the various genomes of bacteria, archaea and eukaryotes and the Web-based system presented here is an approach to their classification. The DnaProt resource is an annotated and searchable collection of protein sequences for the families of DNA-binding proteins. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes. The database is freely available for online search of a library containing specific patterns of the identified DNA-binding protein classes and retrieval of individual entries from our WWW server (http://kronos.biol.uoa.gr/~mariak/dbDNA.html).
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Affiliation(s)
- M Karmirantzou
- Faculty of Biology, Department of Cell Biology and Biophysics, University of Athens, Panepistimiopolis, Athens 157 01, Greece
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44
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Manival X, Ghisolfi-Nieto L, Joseph G, Bouvet P, Erard M. RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins. Nucleic Acids Res 2001; 29:2223-33. [PMID: 11376140 PMCID: PMC55715 DOI: 10.1093/nar/29.11.2223] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2001] [Revised: 04/17/2001] [Accepted: 04/17/2001] [Indexed: 11/13/2022] Open
Abstract
Numerous RNA-binding proteins have modular structures, comprising one or several copies of a selective RNA-binding domain generally coupled to an auxiliary domain that binds RNA non-specifically. We have built and compared homology-based models of the cold-shock domain (CSD) of the Xenopus protein, FRGY2, and of the third RNA recognition motif (RRM) of the ubiquitous nucleolar protein, nucleolin. Our model of the CSD(FRG)-RNA complex constitutes the first prediction of the three-dimensional structure of a CSD-RNA complex and is consistent with the hypothesis of a convergent evolution of CSD and RRM towards a related single-stranded RNA-binding surface. Circular dichroism spectroscopy studies have revealed that these RNA-binding domains are capable of orchestrating similar types of RNA conformational change. Our results further show that the respective auxiliary domains, despite their lack of sequence homology, are functionally equivalent and indispensable for modulating the properties of the specific RNA-binding domains. A comparative analysis of FRGY2 and nucleolin C-terminal domains has revealed common structural features representing the signature of a particular type of auxiliary domain, which has co-evolved with the CSD and the RRM.
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Affiliation(s)
- X Manival
- Institut de Pharmacologie et de Biologie Structurale, CNRS, 205 route de Narbonne, F-31077 Toulouse Cedex, France
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45
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46
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Ceman S, Nelson R, Warren ST. Identification of mouse YB1/p50 as a component of the FMRP-associated mRNP particle. Biochem Biophys Res Commun 2000; 279:904-8. [PMID: 11162447 DOI: 10.1006/bbrc.2000.4035] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fragile X mental retardation is caused by the absence of FMRP, an RNA-binding protein found in a large mRNP complex. Although there is evidence that FMRP exists as a homo-multimer, additional proteins have been identified that associate with FMRP in the mRNP. The autosomal paralogs of FMRP, FXR1P, and FXR2P, associate with FMRP, as do nucleolin and NUFIP1, all RNA binding proteins. Using cell lines that were stably transfected with Flag-Fmr1, we identified an additional protein that coimmunoprecipitates with FMRP. The approximately 50 kDa protein was identified by mass spectrometry as mouse Y box-binding protein 1 (YB1), which is 97% identical to the core mRNP protein p50, an RNA-binding protein. An anti-p50 antiserum recognized the 50 kDa protein, confirming the identification. The association of the FMRP-mRNP with a Y box protein, the latter commonly found in mRNPs, further suggests the involvement of FMRP in translation modulation.
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Affiliation(s)
- S Ceman
- Department of Biochemistry, Howard Hughes Medical Institute, Atlanta, Georgia 30322, USA
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47
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Matsumoto K, Aoki K, Dohmae N, Takio K, Tsujimoto M. CIRP2, a major cytoplasmic RNA-binding protein in Xenopus oocytes. Nucleic Acids Res 2000; 28:4689-97. [PMID: 11095679 PMCID: PMC115157 DOI: 10.1093/nar/28.23.4689] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In an attempt to isolate mRNA-binding proteins we fractionated Xenopus oocyte lysate by oligo(dT)-cellulose chromatography. A 20 kDa protein was the major component of the eluate. cDNA cloning revealed that this protein is a Xenopus homolog of the cold-inducible RNA-binding protein (CIRP) which was originally identified in mammalian cells as a protein that is overexpressed upon a temperature downshift. This Xenopus protein, termed here xCIRP2, is highly expressed in ovary, testis and brain in adult Xenopus tissues. In oocytes it is predominantly localized in the cytoplasm. By biochemical fractionation we provide evidence that xCIRP2 is associated with ribosomes, suggesting that it participates in translational regulation in oocytes. Microinjection of labeled mRNA into oocytes followed by UV cross-linking of the oocyte lysate led to identification of two major RNA-binding activities. Immunoprecipitation of the RNA-binding proteins demonstrated that one is xCIRP2 and that the other contains FRGY2. FRGY2, which is one of the principal constituents of mRNA storage particles involved in translational masking of maternal mRNA, has an RNA-binding domain conserved to those of bacterial cold shock proteins. Possible implications of the highly abundant expression in oocytes of cold shock RNA-binding proteins of both eukaryotic and prokaryotic types are discussed.
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Affiliation(s)
- K Matsumoto
- RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan.
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Soyal SM, Amleh A, Dean J. FIGalpha, a germ cell-specific transcription factor required for ovarian follicle formation. Development 2000; 127:4645-54. [PMID: 11023867 DOI: 10.1242/dev.127.21.4645] [Citation(s) in RCA: 323] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Primordial follicles are formed perinatally in mammalian ovaries and at birth represent the lifetime complement of germ cells. With cyclic periodicity, cohorts enter into a growth phase that culminates in ovulation of mature eggs, but little is known about the regulatory cascades that govern these events. FIGalpha, a transcription factor implicated in postnatal oocyte-specific gene expression, is detected as early as embryonic day 13. Mouse lines lacking FIGalpha were established by targeted mutagenesis in embryonic stem cells. Although embryonic gonadogenesis appeared normal, primordial follicles were not formed at birth, and massive depletion of oocytes resulted in shrunken ovaries and female sterility. Fig(α) (the gene for FIGalpha null males have normal fertility. The additional observation that null females do not express Zp1, Zp2 or Zp3 indicates that FIGalpha plays a key regulatory role in the expression of multiple oocyte-specific genes, including those that initiate folliculogenesis and those that encode the zona pellucida required for fertilization and early embryonic survival. The persistence of FIGalpha in adult females suggests that it may regulate additional pathways that are essential for normal ovarian development.
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Affiliation(s)
- S M Soyal
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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Ladomery M, Marshall R, Arif L, Sommerville J. 4SR, a novel zinc-finger protein with SR-repeats, is expressed during early development of Xenopus. Gene 2000; 256:293-302. [PMID: 11054559 DOI: 10.1016/s0378-1119(00)00375-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The protein C4SR contains two cysteine(4) (C(4)) zinc-finger motifs at its amino terminus, a stretch of acidic residues in the middle and a series of serine-arginine (SR) repeats at its carboxyl terminus. A cDNA clone encoding the zinc-finger domain was first selected from a Xenopus laevis oocyte expression library on the basis of the ability of the fusion protein to stably bind an RNA probe. The mRNA encoding C4SR is expressed during oogenesis, and the protein is present at a constant level in oocytes and early embryos. The C4SR protein is expressed in transcriptionally active erythroblasts but not in transcriptionally inert mature erythrocytes. An epitope-tagged C4SR protein, expressed in oocytes, associates with nascent transcripts at many loci in lampbrush chromosomes and is absent from storage particles (snurposomes) containing the normally recognized complement of RNA splicing components. It is likely that C4SR is involved in pre-mRNA transcription/packaging rather than in exon splicing. The zinc-finger motif, present as two copies in C4SR, is also present in a range of transcription-associated proteins. We suggest the descriptor (DW)C(4), in which DW refers to the invariant aspartic acid (D)/tryptophan (W) dipeptide that precedes the first cysteine residue, for this distinctive zinc-finger structure.
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Affiliation(s)
- M Ladomery
- Division of Cell and Molecular Biology, University of St Andrews, School of Biological and Medical Sciences, Westburn Lane, Bute Medical Buildings C17, KY16 9TS, Fife, UK
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Lasham A, Lindridge E, Rudert F, Onrust R, Watson J. Regulation of the human fas promoter by YB-1, Puralpha and AP-1 transcription factors. Gene 2000; 252:1-13. [PMID: 10903433 DOI: 10.1016/s0378-1119(00)00220-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fas (CD95/Apo-1) gene expression is dysregulated in a number of diseased states. Towards understanding the regulation of fas gene expression, we previously identified activator and repressor elements within the human fas promoter. Using a combination of expression screening and reporter gene assays, we have identified transcription factors which bind to these elements and thereby regulate transcription of the fas promoter. These are three single-stranded DNA binding proteins, YB-1, Puralpha and Purbeta and two components of the AP-1 complex, c-Fos and c-Jun. c-Jun is a potent transcriptional activator of fas and stimulated expression levels up to 184-fold in reporter gene assays. Co-expression with c-Fos abrogated c-Jun-mediated activation. YB-1 and Puralpha are transcriptional repressors of fas and decreased basal transcription by 60-fold in reporter gene assays. Purbeta was predominantly an antagonist of YB-1/Puralpha-mediated repression. Overexpression of YB-1 and Puralpha in Jurkat cells was shown to reduce the level of cell surface Fas staining, providing further evidence that these proteins regulate the fas promoter. It has been suggested that YB-1 plays a role in cell proliferation as an activator of growth-associated gene expression. We have shown that YB-1 is a repressor of a cell death-associated gene fas. These results suggest that YB-1 may play an important role in controlling cell survival by co-ordinately regulating the expression of cell growth-associated and death-associated genes.
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Affiliation(s)
- A Lasham
- Genesis Research and Development Corporation Limited, Auckland, New Zealand.
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