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Smith S, Seth J, Midkiff A, Stahl R, Syu YC, Shkriabai N, Kvaratskhelia M, Musier-Forsyth K, Jain P, Green PL, Panfil AR. The Pleiotropic Effects of YBX1 on HTLV-1 Transcription. Int J Mol Sci 2023; 24:13119. [PMID: 37685922 PMCID: PMC10487795 DOI: 10.3390/ijms241713119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
HTLV-1 is an oncogenic human retrovirus and the etiologic agent of the highly aggressive ATL malignancy. Two viral genes, Tax and Hbz, are individually linked to oncogenic transformation and play an important role in the pathogenic process. Consequently, regulation of HTLV-1 gene expression is a central feature in the viral lifecycle and directly contributes to its pathogenic potential. Herein, we identified the cellular transcription factor YBX1 as a binding partner for HBZ. We found YBX1 activated transcription and enhanced Tax-mediated transcription from the viral 5' LTR promoter. Interestingly, YBX1 also interacted with Tax. shRNA-mediated loss of YBX1 decreased transcript and protein abundance of both Tax and HBZ in HTLV-1-transformed T-cell lines, as well as Tax association with the 5' LTR. Conversely, YBX1 transcriptional activation of the 5' LTR promoter was increased in the absence of HBZ. YBX1 was found to be associated with both the 5' and 3' LTRs in HTLV-1-transformed and ATL-derived T-cell lines. Together, these data suggest that YBX1 positively influences transcription from both the 5' and 3' promoter elements. YBX1 is able to interact with Tax and help recruit Tax to the 5' LTR. However, through interactions with HBZ, YBX1 transcriptional activation of the 5' LTR is repressed.
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Affiliation(s)
- Susan Smith
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Jaideep Seth
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Amanda Midkiff
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Rachel Stahl
- Center for Retrovirus Research, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (S.S.); (J.S.); (A.M.)
| | - Yu-Ci Syu
- Center for Retrovirus Research, Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; (Y.-C.S.); (K.M.-F.)
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.S.); (M.K.)
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.S.); (M.K.)
| | - Karin Musier-Forsyth
- Center for Retrovirus Research, Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; (Y.-C.S.); (K.M.-F.)
| | - Pooja Jain
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA;
| | - Patrick L. Green
- Center for Retrovirus Research, Comprehensive Cancer Center and Solove Research Institute, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Amanda R. Panfil
- Center for Retrovirus Research, Comprehensive Cancer Center and Solove Research Institute, Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
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Ma L, Singh J, Schekman R. Two RNA-binding proteins mediate the sorting of miR223 from mitochondria into exosomes. eLife 2023; 12:e85878. [PMID: 37489754 PMCID: PMC10403255 DOI: 10.7554/elife.85878] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Fusion of multivesicular bodies (MVBs) with the plasma membrane results in the secretion of intraluminal vesicles (ILVs), or exosomes. The sorting of one exosomal cargo RNA, miR223, is facilitated by the RNA-binding protein, YBX1 (Shurtleff et al., 2016). We found that miR223 specifically binds a 'cold shock' domain (CSD) of YBX1 through a 5' proximal sequence motif UCAGU that may represent a binding site or structural feature required for sorting. Prior to sorting into exosomes, most of the cytoplasmic miR223 resides in mitochondria. An RNA-binding protein localized to the mitochondrial matrix, YBAP1, appears to serve as a negative regulator of miR223 enrichment into exosomes. miR223 levels decreased in the mitochondria and increased in exosomes after loss of YBAP1. We observed YBX1 shuttle between mitochondria and endosomes in live cells. YBX1 also partitions into P body granules in the cytoplasm (Liu et al., 2021). We propose a model in which miR223 and likely other miRNAs are stored in mitochondria and are then mobilized by YBX1 to cytoplasmic phase condensate granules for capture into invaginations in the endosome that give rise to exosomes.
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Affiliation(s)
- Liang Ma
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Jasleen Singh
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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3
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Scully OJ, Shyamasundar S, Matsumoto K, Dheen ST, Yip GW, Bay BH. C1QBP Mediates Breast Cancer Cell Proliferation and Growth via Multiple Potential Signalling Pathways. Int J Mol Sci 2023; 24:ijms24021343. [PMID: 36674861 PMCID: PMC9864289 DOI: 10.3390/ijms24021343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Breast carcinoma is the most prevalent cancer in women globally, with complex genetic and molecular mechanisms that underlie its development and progression. Several challenges such as metastasis and drug resistance limit the prognosis of breast cancer, and hence a constant search for better treatment regimes, including novel molecular therapeutic targets is necessary. Complement component 1, q subcomponent binding protein (C1QBP), a promising molecular target, has been implicated in breast carcinogenesis. In this study, the role of C1QBP in breast cancer progression, in particular cancer cell growth, was determined in triple negative MDA-MB-231 breast cancer cells. Depletion of C1QBP decreased cell proliferation, whereas the opposite effect was observed when C1QBP was overexpressed in MDA-MB-231 cells. Furthermore, gene expression profiling and pathway analysis in C1QBP depleted cells revealed that C1QBP regulates several signaling pathways crucial for cell growth and survival. Taken together, these findings provide a deeper comprehension of the role of C1QBP in triple negative breast cancer, and could possibly pave the way for future advancement of C1QBP-targeted breast cancer therapy.
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Affiliation(s)
- Olivia J. Scully
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Sukanya Shyamasundar
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Ken Matsumoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource, 2-1 Hirosawa Wako-shi, Saitama 351-0198, Japan
| | - S. Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - George W. Yip
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
- Correspondence: (G.W.Y.); (B.H.B.)
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
- Correspondence: (G.W.Y.); (B.H.B.)
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4
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Barman B, Sung BH, Krystofiak E, Ping J, Ramirez M, Millis B, Allen R, Prasad N, Chetyrkin S, Calcutt MW, Vickers K, Patton JG, Liu Q, Weaver AM. VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites. Dev Cell 2022; 57:974-994.e8. [PMID: 35421371 PMCID: PMC9075344 DOI: 10.1016/j.devcel.2022.03.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCSs) as platforms for the generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes luminal filling of multivesicular bodies (MVBs), CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives the biogenesis of a select RNA-containing EV population.
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Affiliation(s)
- Bahnisikha Barman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bong Hwan Sung
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Evan Krystofiak
- Vanderbilt University Cell Imaging Shared Resource, Nashville, TN, USA
| | - Jie Ping
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol Ramirez
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bryan Millis
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt Biophotonics Center, Vanderbilt School of Engineering, Nashville, TN, USA
| | - Ryan Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sergei Chetyrkin
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Kasey Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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Wang S, Zeng F, Liang S, Wang Q, Wen Y, Wang Q, Zhang J, Li M, Fang S, Wei T, Li M, Manapov F, Zhang J, Guo L. WITHDRAWN: lncRNA Linc00173 modulates glucose metabolism and multidrug chemoresistance in SCLC: Potential molecular panel for targeted therapy. Mol Ther 2021:S1525-0016(21)00574-8. [PMID: 34763086 DOI: 10.1016/j.ymthe.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/05/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
This article has been withdrawn at the request of the editor-in-chief. Following publication of this article, the editor-in-chief discovered evidence of image duplication in Figures 1I, 1J, 3F, S5B, and S6B. Given the duplication of several western blots representing several gene products, the editor-in-chief has lost faith in the findings presented in this article. The authors maintain that these image duplications were the result of errors in file management and do not affect the conclusions of the study. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Shuyu Wang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China; Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Fanrui Zeng
- Department of Radiation Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, People's Republic of China
| | - Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Qiuping Wang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Yang Wen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Jiexia Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Shun Fang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China
| | - Minglun Li
- Department of Radiation Oncology, University Hospital, LMU Munich, Campus Grosshadern, Marchioninistr. 15, 81377 Munich, Germany
| | - Farkhad Manapov
- Department of Radiation Oncology, University Hospital, LMU Munich, Campus Grosshadern, Marchioninistr. 15, 81377 Munich, Germany
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China.
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou 510282, People's Republic of China.
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6
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Meltendorf S, Fu H, Pierau M, Lindquist JA, Finzel S, Mertens PR, Gieseler-Halbach S, Ambach A, Thomas U, Lingel H, Voll RE, Brunner-Weinzierl MC. Cell Survival Failure in Effector T Cells From Patients With Systemic Lupus Erythematosus Following Insufficient Up-Regulation of Cold-Shock Y-Box Binding Protein 1. Arthritis Rheumatol 2020; 72:1721-1733. [PMID: 32475063 DOI: 10.1002/art.41382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 04/23/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The importance of cold-shock Y-box binding protein 1 (YB-1) for cell homeostasis is well-documented based on prior observations of its association with certain cancer entities. This study was undertaken to explore the role of YB-1 in T cell homeostasis and survival and the potential contribution of YB-1 to the pathogenesis of systemic lupus erythematosus (SLE). METHODS In the peripheral blood from 25 SLE patients and 25 healthy donors, the expression of YB-1 and frequency of T cell apoptosis was analyzed by quantitative polymerase chain reaction (qPCR) and fluorescence-activated cell sorting of CD4+ T cells ex vivo and also analyzed in T cells in vitro after 6 days of stimulation with anti-CD3-coupled or anti-CD3/anti-CD28-coupled microspheres. YB-1 was overexpressed using lentiviral transduction with wild-type green fluorescent protein (wtGFP) YB-1, and knockdown of YB-1 was achieved using specific short hairpin RNA (shRNA) (3-fold reduction; P < 0.0001). RESULTS YB-1 expression was significantly lower in apoptosis-prone T cells and in activated T cells from SLE patients compared to YB-1 expression in nonapoptotic T cells and activated T cells from healthy donors (P = 0.001). Knockdown of YB-1 in T cells consequently led to expression of proapoptotic molecules and caspase 3 activation (1.6-fold), and subsequently, to apoptosis. Furthermore, YB-1 promoted survival pathways involving enhanced protein expression of the kinase Akt (2-fold) and Bcl-2 (3-fold), even when Fas/CD95 was triggered. YB-1-mediated T cell survival was reversed by Akt and phosphatidylinositol 3-kinase (PI3K) inactivation. In SLE patients, rescue of YB-1 expression strongly promoted survival of T cells and even prevented cell death in T cells that were extremely apoptosis-prone. CONCLUSION Our data show that failure of YB-1 up-regulation in T cells from SLE patients led to enhanced apoptosis. These findings imply that YB-1 plays a crucial role in the disturbed homeostasis of activated T cells leading to hematopoietic alterations in SLE. These insights may help facilitate the development of new treatment strategies for SLE.
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Affiliation(s)
- Stefan Meltendorf
- Department of Experimental Pediatrics, Otto von uericke University, Magdeburg, Germany
| | - Hang Fu
- Department of Experimental Pediatrics, Otto von uericke University, Magdeburg, Germany
| | - Mandy Pierau
- Department of Experimental Pediatrics, Otto von uericke University, Magdeburg, Germany
| | - Jonathan A Lindquist
- Clinic of Nephrology, Hypertension, Diabetes, and Endocrinology, Otto von Guericke University, Magdeburg, Germany
| | - Stephanie Finzel
- Department of Rheumatology and Clinical Immunology, Albert Ludwig University of Freiburg, Freiburg, Germany
| | - Peter R Mertens
- Clinic of Nephrology, Hypertension, Diabetes, and Endocrinology, Otto von Guericke University, Magdeburg, Germany
| | | | - Andreas Ambach
- Department of Dermatology, Otto von Guericke University, Magdeburg, Germany
| | - Ulrich Thomas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Holger Lingel
- Department of Experimental Pediatrics, Otto von uericke University, Magdeburg, Germany
| | - Reinhard E Voll
- Department of Rheumatology and Clinical Immunology, Albert Ludwig University of Freiburg, Freiburg, Germany
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Yang HW, Kim HD, Kim TS, Kim J. Senescent Cells Differentially Translate Senescence-Related mRNAs Via Ribosome Heterogeneity. J Gerontol A Biol Sci Med Sci 2020; 74:1015-1024. [PMID: 30285098 DOI: 10.1093/gerona/gly228] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
The ribosome has a lateral stalk which consists of rpLP0, rpLP1, and rpLP2. One of these proteins, rpLP2, is decreased in translating ribosome when cellular senescence is induced. Y-box binding protein-1 (YB-1) is also reduced in polysomal fraction of senescent cells. We discovered that rpLP2 depletion in the ribosome can cause the detachment of YB-1 in polysomes and that it is linked to cellular senescence. Our results also revealed that a decrement of CK2α or GRK2 in senescent cells induced an increment of unphosphorylated rpLP2, resulting in release of YB-1 from polysomes. This heterogeneous senescent ribosome has different translational efficiencies for some senescence-related genes. We also showed that the decrease of rpLP1/rpLP2 and YB-1 in senescent ribosomes was not specific to cell type or stress type and the same phenomenon was also observed in aged mouse livers regardless of gender. Taken together, our results suggest that the senescent ribosome complex appears to have low levels of rpLP1/rpLP2 and YB-1, resulting in altered translational efficiency for senescence-related genes.
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Affiliation(s)
- Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
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8
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Suman, Chaudhary M, Nain V. In silico identification and evaluation of Bacillus subtilis cold shock protein B (cspB)-like plant RNA chaperones. J Biomol Struct Dyn 2020; 39:841-850. [PMID: 31959085 DOI: 10.1080/07391102.2020.1719198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cold shock domain (CSD) proteins with nucleic acid binding properties are well conserved from bacteria to higher organisms. In bacteria, the cold shock proteins (CSPs) are single domain RNA chaperones, whereas in animals and plants, CSDs are accompanied by additional domains with roles in transcription regulation. Bacterial CSPs (Escherischia coli-cspA and Bacilus subtilis-cspB) have successfully imparted drought tolerance in transgenic plants; however, these cannot be deployed in food crops due to their low public acceptance of transgenics with bacterial genes. Therefore, this study aimed to identify CSPB-like proteins from plants that can be used for developing drought tolerant transgenic crops. Twelve single domain plant CSPs presenting >40% sequence identity with CSPB were identified. All 12 plant CSPs were modeled by homology modeling and refined by molecular dynamics simulation for 10 ns. Selected plant CSPs and CSPB exhibited high structural similarity (Tm-score: 0.63-0.86). Structure based phylogenetic analysis revealed that Triticum aestivum-csp1 and Aegilops tauschii-cspE are structurally closer to CSPB compared to their orthologs and paralogs. Molecular docking with three RNA molecules (5U, UC3U, and C2UC) indicates that Ricinus communis-csd1 and T. aestivum-csp1 have a binding pattern and docking scores similar to those of CSPB. Furthermore, MD simulations for 20 ns and analysis of RMSD, RMSF, Rg as well as the number of hydrogen bonds in all the three complexes revealed that plant CSP-RNA complexes behave in a similar manner to that of the CSPB-RNA complex, making them highly potential candidate genes for developing drought tolerance in transgenic plants. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | | | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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9
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Amir M, Kumar V, Dohare R, Islam A, Ahmad F, Hassan MI. Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family. J Evol Biol 2018; 31:1903-1917. [PMID: 30267552 DOI: 10.1111/jeb.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/28/2022]
Abstract
The cold shock domain (CSD) belongs to the oligosaccharide/oligonucleotide-binding fold superfamily which is highly conserved from prokaryotes to higher eukaryotes, and appears to function as RNA chaperones. CSD is involved in diverse cellular processes, including adaptation to low temperatures, nutrient stress, cellular growth and developmental processes. Structural Classification of Proteins (SCOP) database broadly classifies OB fold proteins into 18 different superfamilies, including nucleic acid-binding superfamily (NAB). The NAB is further divided into 17 families together with cold shock DNA-binding protein family (CSDB). The CSDB have more than 240 000 sequences in UniProt database consisting of 32 domains including CSD. Among these domains, CSD is the second largest sequence contributor (> 40 398 sequences). Herein, we have systematically analysed the relative abundance and distribution of CSD proteins based on sequences, structures, repeats and gene ontology (GO) molecular functions in all domains of life. Analysis of sequence distribution suggesting that CSDs are largely found in bacteria (83-94%) with single CSD repeat. However, repeat distribution in eukaryota varies from 1 to 5 in combination with other auxiliary domain that makes CSD proteins functionally more diverse compared to the bacterial counterparts. Further, analysis of repeats distributions on evolutionary scale suggest that existence of CSD in multiple repeats is mainly driven through speciation, gene shuffling and gene duplication events.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Amity Institute of Neuropsychology & Neurosciences, Amity University Noida, UP, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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10
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Matsumoto K, Kose S, Kuwahara I, Yoshimura M, Imamoto N, Yoshida M. Y-box protein-associated acidic protein (YBAP1/C1QBP) affects the localization and cytoplasmic functions of YB-1. Sci Rep 2018; 8:6198. [PMID: 29670170 PMCID: PMC5906478 DOI: 10.1038/s41598-018-24401-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
The Y-box proteins are multifunctional nucleic acid-binding proteins involved in various aspects of gene regulation. The founding member of the Y-box protein family, YB-1, functions as a transcription factor as well as a principal component of messenger ribonucleoprotein particles (mRNPs) in somatic cells. The nuclear level of YB-1 is well correlated with poor prognosis in many human cancers. Previously, we showed that a Y-box protein–associated acidic protein, YBAP1, which is identical to complement component 1, q subcomponent-binding protein (C1QBP, also called gC1qR, hyaluronan-binding protein 1 [HABP1] or ASF/SF2-associated protein p32), relieves translational repression by YB-1. Here we show that the nuclear localization of YB-1 harboring a point mutation in the cold shock domain was inhibited when co-expressed with YBAP1, whereas cytoplasmic accumulation of the wild-type YB-1 was not affected. We showed that YBAP1 inhibited the interaction between YB-1 and transportin 1. In the cytoplasm, YBAP1 affected the accumulation of YB-1 to processing bodies (P-bodies) and partially abrogated the mRNA stabilization by YB-1. Our results, indicating that YBAP1/C1QBP regulates the nucleo-cytoplasmic distribution of YB-1 and its cytoplasmic functions, are consistent with a model that YBAP1/C1QBP acts as an mRNP remodeling factor.
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Affiliation(s)
- Ken Matsumoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan. .,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan. .,Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan.
| | - Shingo Kose
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Wako, Saitama, Japan
| | - Iku Kuwahara
- Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan
| | - Mami Yoshimura
- Molecular Entomology Laboratory, RIKEN, Wako, Saitama, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Wako, Saitama, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan
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11
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Geng Q, Xhabija B, Knuckle C, Bonham CA, Vacratsis PO. The Atypical Dual Specificity Phosphatase hYVH1 Associates with Multiple Ribonucleoprotein Particles. J Biol Chem 2016; 292:539-550. [PMID: 27856639 DOI: 10.1074/jbc.m116.715607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/03/2016] [Indexed: 12/30/2022] Open
Abstract
Human YVH1 (hYVH1), also known as dual specificity phosphatase 12 (DUSP12), is a poorly characterized atypical dual specificity phosphatase widely conserved throughout evolution. Recent findings have demonstrated that hYVH1 expression affects cellular DNA content and is a novel cell survival phosphatase preventing both thermal and oxidative stress-induced cell death, whereas studies in yeast have established YVH1 as a novel 60S ribosome biogenesis factor. In this study, we have isolated novel hYVH1-associating proteins from human U2OS osteosarcoma cells using affinity chromatography coupled to mass spectrometry employing ion mobility separation. Numerous ribosomal proteins were identified, confirming the work done in yeast. Furthermore, proteins known to be present on additional RNP particles were identified, including Y box-binding protein 1 (YB-1) and fragile X mental retardation protein, proteins that function in translational repression and stress granule regulation. Follow-up studies demonstrated that hYVH1 co-localizes with YB-1 and fragile X mental retardation protein on stress granules in response to arsenic treatment. Interestingly, hYVH1-positive stress granules were significantly smaller, whereas knocking down hYVH1 expression attenuated stress granule breakdown during recovery from arsenite stress, indicating a possible role for hYVH1 in stress granule disassembly. These results propagate a role for dual specificity phosphatases at RNP particles and suggest that hYVH1 may affect a variety of fundamental cellular processes by regulating messenger ribonucleoprotein (mRNP) dynamics.
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Affiliation(s)
- Qiudi Geng
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Besa Xhabija
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Colleen Knuckle
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Christopher A Bonham
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Panayiotis O Vacratsis
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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12
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Kleene KC. Position-dependent interactions of Y-box protein 2 (YBX2) with mRNA enable mRNA storage in round spermatids by repressing mRNA translation and blocking translation-dependent mRNA decay. Mol Reprod Dev 2016; 83:190-207. [PMID: 26773323 DOI: 10.1002/mrd.22616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022]
Abstract
Many mRNAs encoding proteins needed for the construction of the specialized organelles of spermatozoa are stored as translationally repressed, free messenger ribonucleoproteins in round spermatids, to be actively translated in elongating and elongated spermatids. The factors that repress translation in round spermatids, however, have been elusive. Two lines of evidence implicate the highly abundant and well-known translational repressor, Y-box protein 2 (YBX2), as a critical factor: First, protamine 1 (Prm1) and sperm-mitochondria cysteine-rich protein (Smcp) mRNAs are prematurely recruited onto polysomes in Ybx2-knockout mouse round spermatids. Second, mutations in 3' untranslated region (3'UTR) cis-elements that abrogate YBX2 binding activate translation of Prm1 and Smcp mRNAs in round spermatids of transgenic mice. The abundance of YBX2 and its affinity for variable sequences, however, raise questions of how YBX2 targets specific mRNAs for repression. Mutations to the Prm1 and Smcp mRNAs in transgenic mice reveal that strong repression in round spermatids requires YBX2 binding sites located near the 3' ends of their 3'UTRs as locating the same sites in upstream positions produce negligible repression. This location-dependence implies that the assembly of repressive complexes is nucleated by adjacent cis-elements that enable cooperative interactions of YBX2 with co-factors. The available data suggest that, in vertebrates, YBX2 has the important role of coordinating the storage of translationally repressed mRNAs in round spermatids by inhibiting translational activity and the degradation of transcripts via translation-dependent deadenylation. These insights should facilitiate future experiments designed to unravel how YBX2 targets mRNAs for repression in round spermatids and how mutations in the YBX2 gene cause infertility in humans. Mol. Reprod. Dev. 83: 190-207, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kenneth C Kleene
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts
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13
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Scully OJ, Yu Y, Salim A, Thike AA, Yip GWC, Baeg GH, Tan PH, Matsumoto K, Bay BH. Complement component 1, q subcomponent binding protein is a marker for proliferation in breast cancer. Exp Biol Med (Maywood) 2015; 240:846-53. [PMID: 25573962 DOI: 10.1177/1535370214565075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/10/2014] [Indexed: 12/29/2022] Open
Abstract
Complement component 1, q subcomponent binding protein (C1QBP), is a multi-compartmental protein with higher mRNA expression reported in breast cancer tissues. This study evaluated the association between immunohistochemical expression of the C1QBP protein in breast cancer tissue microarrays (TMAs) and clinicopathological parameters, in particular tumor size. In addition, an in vitro study was conducted to substantiate the breast cancer TMA findings. Breast cancer TMAs were constructed from pathological specimens of patients diagnosed with invasive ductal carcinoma. C1QBP protein and proliferating cell nuclear antigen (PCNA) immunohistochemical analyses were subsequently performed in the TMAs. C1QBP immunostaining was detected in 131 out of 132 samples examined. The C1QBP protein was predominantly localized in the cytoplasm of the breast cancer cells. Univariate analysis revealed that a higher C1QBP protein expression was significantly associated with older patients (P = 0.001) and increased tumor size (P = 0.002). Multivariate analysis showed that C1QBP is an independent predictor of tumor size in progesterone-positive tumors. Furthermore, C1QBP was also significantly correlated with expression of PCNA, a known marker of proliferation. Inhibition of C1QBP expression was performed by transfecting C1QBP siRNA into T47D breast cancer cells, a progesterone receptor-positive breast cancer cell line. C1QBP gene expression was analyzed by real-time RT-PCR, and protein expression by Western blot. Cell proliferation assays were also performed by commercially available assays. Down-regulation of C1QBP expression significantly decreased cell proliferation and growth in T47D cells. Taken together, our findings suggest that the C1QBP protein could be a potential proliferative marker in breast cancer.
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Affiliation(s)
- Olivia Jane Scully
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Yingnan Yu
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Aye Aye Thike
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - George Wai-Cheong Yip
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Gyeong Hun Baeg
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Puay-Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Ken Matsumoto
- Chemical Genetics Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
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14
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Cullinane DL, Chowdhury TA, Kleene KC. Mechanisms of translational repression of the Smcp mRNA in round spermatids. Reproduction 2014; 149:43-54. [PMID: 25336347 DOI: 10.1530/rep-14-0394] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The protamine 1 (Prm1) and sperm mitochondria-associated, cysteine-rich protein (Smcp) mRNAs exemplify a widespread pattern of mRNA-specific regulation of mRNA translation in post-meiotic spermatogenic cells, spermatids. Both mRNAs are transcribed and initially stored in free-mRNPs in early spermatids, and translated on polysomes in late spermatids. In this study, we demonstrate that the 5' and 3'-UTRs and the 3' terminus of the Smcp 3'-UTR are required for normal repression of the Smcp mRNA in transgenic mice. RNA affinity chromatography and mass spectrometry sequencing identified Y-box protein 2 (YBX2/MSY2) as the major protein that interacts with the 3' terminus of the Smcp 3'-UTR and a Y-box recognition sequence, GCCACCU, in the translation control element that is necessary for Prm1 mRNA repression. Depletion of YBX2 in Ybx2-null mice prematurely activates Prm1 and Smcp mRNA translation in early spermatids. Fluorescent in situ hybridization reveals that the Smcp intron, the Smcp mRNA, and both Smcp-Gfp transgenic mRNAs are strongly concentrated in the chromatoid body, and that theYbx2-null mutation does not eliminate the Smcp mRNA from the chromatoid body. This and previous findings suggest that the Smcp pre-mRNA is spliced and associates with YBX2 in the chromatoid body, and that repressed free-mRNPs are stored in the general cytoplasm. As YBX2 is the predominant protein in testis free-mRNPs, it likely represses many mRNAs in early spermatids. The mechanisms by which YBX2 represses the Smcp and Prm1 mRNAs are relevant to reproductive medicine because mutations in the human YBX2 gene correlate with abnormal protamine expression and male infertility.
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Affiliation(s)
- Danielle L Cullinane
- Department of BiologyUniversity of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125-3393, USA
| | - Tamjid A Chowdhury
- Department of BiologyUniversity of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125-3393, USA
| | - Kenneth C Kleene
- Department of BiologyUniversity of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125-3393, USA
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15
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Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 protein: functions and regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:95-110. [PMID: 24217978 DOI: 10.1002/wrna.1200] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/23/2013] [Accepted: 09/27/2013] [Indexed: 12/15/2022]
Abstract
The Y-box binding protein 1 (YB-1, YBX1) is a member of the family of DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. It falls into a group of intrinsically disordered proteins that do not follow the classical rule 'one protein-one function' but introduce a novel principle stating that a disordered structure suggests many functions. YB-1 participates in a wide variety of DNA/RNA-dependent events, including DNA reparation, pre-mRNA transcription and splicing, mRNA packaging, and regulation of mRNA stability and translation. At the cell level, the multiple activities of YB-1 are manifested as its involvement in cell proliferation and differentiation, stress response, and malignant cell transformation. WIREs RNA 2014, 5:95-110. doi: 10.1002/wrna.1200 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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16
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Sasaki K, Kim MH, Imai R. Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 is a negative regulator of cold acclimation. THE NEW PHYTOLOGIST 2013; 198:95-102. [PMID: 23323758 DOI: 10.1111/nph.12118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/27/2012] [Indexed: 06/01/2023]
Abstract
Bacterial cold shock proteins (CSPs) act as RNA chaperones that destabilize mRNA secondary structures at low temperatures. Bacterial CSPs are composed solely of a nucleic acid-binding domain termed the cold shock domain (CSD). Plant CSD proteins contain an auxiliary domain in addition to the CSD but also show RNA chaperone activity. However, their biological functions are poorly understood. We examined Arabidopsis COLD SHOCK DOMAIN PROTEIN 2 (AtCSP2) using overexpressing and mutant lines. A double mutant, with reduced AtCSP2 and no AtCSP4, showed higher freezing tolerance than the wild-type when cold-acclimated. The increase in freezing tolerance was associated with up-regulation of CBF transcription factors and their downstream genes. By contrast, overexpression of AtCSP2 resulted in decreased freezing tolerance when cold-acclimated. In addition, late flowering and shorter siliques were observed in the overexpressing lines. AtCSP2 negatively regulates freezing tolerance and is partially redundant with its closest paralog, AtCSP4.
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Affiliation(s)
- Kentaro Sasaki
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Myung-Hee Kim
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
| | - Ryozo Imai
- Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo, 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
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17
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The major mRNP protein YB-1: structural and association properties in solution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:559-67. [PMID: 23220387 DOI: 10.1016/j.bbapap.2012.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/07/2012] [Accepted: 11/27/2012] [Indexed: 02/04/2023]
Abstract
YB-1 is a major mRNP protein participating in the regulation of transcription and translation of a wide range of eukaryotic genes in many organisms probably due to its influence on mRNA packing into mRNPs. While the functional properties of YB-1 are extensively studied, little is known about its structural properties. In the present work we focused on studying its secondary structure, rigidity of its tertiary structure, compactness, and oligomerization in vitro by using far UV-CD, DSC, one-dimensional (1)H NMR, SAXS, sedimentation and FPLC. It was shown that only the cold shock domain within the entire YB-1 chain has a well-packed tertiary structure undergoing cooperative heat and cold denaturation transitions. In contrast, the rest of the YB-1 molecule is not rigidly packed and consists of PP II-like helical secondary structure elements and coil-like regions. At the same time, the overall dimension of the protein molecule is unexpectedly small. The polypeptide chains of YB-1 have a high tendency to form oligomers at neutral pH, while the extent and structural organization of the oligomers depend on protein concentration and ionic strength varying from compact monomeric units up to high molecular weight oligomers. These oligomers in solution are unstable and dissociate upon protein concentration decrease.
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18
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Tanaka T, Ohashi S, Moue M, Kobayashi S. Mechanism of YB-1-mediated translational induction of GluR2 mRNA in response to neural activity through nAChR. Biochim Biophys Acta Gen Subj 2012; 1820:1035-42. [DOI: 10.1016/j.bbagen.2012.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/27/2012] [Accepted: 04/09/2012] [Indexed: 01/09/2023]
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19
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Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. Y-box-binding protein 1 (YB-1) and its functions. BIOCHEMISTRY (MOSCOW) 2012; 76:1402-33. [PMID: 22339596 DOI: 10.1134/s0006297911130049] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the structure and functions of Y-box binding protein 1 (YB-1) and its homologs. Interactions of YB-1 with DNA, mRNAs, and proteins are considered. Data on the participation of YB-1 in DNA reparation and transcription, mRNA splicing and translation are systematized. Results on interactions of YB-1 with cytoskeleton components and its possible role in mRNA localization are discussed. Data on intracellular distribution of YB-1, its redistribution between the nucleus and the cytoplasm, and its secretion and extracellular functions are summarized. The effect of YB-1 on cell differentiation, its involvement in extra- and intracellular signaling pathways, and its role in early embryogenesis are described. The mechanisms of regulation of YB-1 expression in the cell are presented. Special attention is paid to the involvement of YB-1 in oncogenic cell transformation, multiple drug resistance, and dissemination of tumors. Both the oncogenic and antioncogenic activities of YB-1 are reviewed. The potential use of YB-1 in diagnostics and therapy as an early cancer marker and a molecular target is discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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20
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Matsumoto K, Nakayama H, Yoshimura M, Masuda A, Dohmae N, Matsumoto S, Tsujimoto M. PRMT1 is required for RAP55 to localize to processing bodies. RNA Biol 2012; 9:610-23. [PMID: 22614839 DOI: 10.4161/rna.19527] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In eukaryotic cells, components of messenger ribonucleoproteins (mRNPs) are often detected in cytoplasmic granules, such as processing bodies (P-bodies) and stress granules (SGs) where translationally repressed mRNAs accumulate. RAP55A, which is an RNA binding component of mRNPs, acts as a translational repressor and localizes to P-bodies and SGs. We found here that a homologous protein RAP55B also localized to P-bodies when expressed in human cultured cells. When RAP55A or RAP55B was highly expressed in the cells, they induced the formation of SG-like large cytoplasmic mRNP granules that contained both P-body and SG components, indicating that RAP55 is important for the assembly of cytoplasmic mRNP granules. In addition, we found that RAP55A associated with protein arginine methyltransferases PRMT1 and PRMT5. Multiple arginine residues of RAP55A were indeed asymmetrically dimethylated in the cell and PRMT1 was shown to be a component of large mRNP granules induced by RAP55A overexpression. Although PRMT1 did not accumulate in P-bodies, siRNA-mediated knockdown of PRMT1 impaired the localization of RAP55A to P-bodies, while other components were still retained in these structures. Thus, our data indicate that RAP55 is important for the assembly of cytoplasmic mRNP granules and that PRMT1 is required for RAP55A to localize to P-bodies.
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Affiliation(s)
- Ken Matsumoto
- Molecular Entomology Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan.
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21
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Ohashi S, Moue M, Tanaka T, Kobayashi S. Translational level of acetylcholine receptor α mRNA in mouse skeletal muscle is regulated by YB-1 in response to neural activity. Biochem Biophys Res Commun 2011; 414:647-52. [DOI: 10.1016/j.bbrc.2011.09.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 09/15/2011] [Indexed: 12/17/2022]
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22
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Sasaki K, Imai R. Pleiotropic roles of cold shock domain proteins in plants. FRONTIERS IN PLANT SCIENCE 2011; 2:116. [PMID: 22639630 PMCID: PMC3355641 DOI: 10.3389/fpls.2011.00116] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 05/21/2023]
Abstract
The cold shock domain (CSD) is a nucleic acid binding domain that is widely conserved from bacteria to higher plants and animals. In Escherichia coli, cold shock proteins (CSPs) are composed solely of a CSD and function as RNA chaperones that destabilize RNA secondary structures. Cellular RNAs tend to be folded into unfavorable structures under low temperature conditions, and RNA chaperones resolve these structures, recovering functionality of the RNAs. CSP functions are associated mainly with cold adaptation, but they are also involved in other biological processes under normal growth conditions. Eukaryotic CSD proteins contain auxiliary domains in addition to the CSD and regulate many biological processes such as development and stress tolerance. In plants, it has been demonstrated that CSD proteins play essential roles in acquiring freezing tolerance. In addition, it has been suggested that some plant CSD proteins regulate embryo development, flowering time, and fruit development. In this review, we summarize the pleiotropic biological functions of CSP proteins in plants and discuss possible mechanisms by which plant CSD proteins regulate the functions of RNA molecules.
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Affiliation(s)
- Kentaro Sasaki
- Hokkaido Agriculture Research Center, National Agriculture and Food Research OrganizationSapporo, Japan
- Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
| | - Ryozo Imai
- Hokkaido Agriculture Research Center, National Agriculture and Food Research OrganizationSapporo, Japan
- Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- *Correspondence: Ryozo Imai, Hokkaido Agriculture Research Center, National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan. e-mail:
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Higashi K, Tomigahara Y, Shiraki H, Miyata K, Mikami T, Kimura T, Moro T, Inagaki Y, Kaneko H. A novel small compound that promotes nuclear translocation of YB-1 ameliorates experimental hepatic fibrosis in mice. J Biol Chem 2010; 286:4485-92. [PMID: 21115500 DOI: 10.1074/jbc.m110.151936] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transforming growth factor-β (TGF-β) is considered to be a major factor contributing to liver fibrosis. We have previously shown that nuclear translocation of YB-1 antagonizes the TGF-β/Smad3 signaling in regulating collagen gene expression. More recently, we have demonstrated that the novel small compound HSc025 promotes nuclear translocation of YB-1, resulting in the improvement of skin and pulmonary fibrosis. Here, we presented evidence as to the mechanism by which HSc025 stimulates nuclear translocation of YB-1 and the pharmacological effects of HSc025 on a murine model of hepatic fibrosis. A proteomics approach and binding assays using HSc025-immobilized resin showed that HSc025 binds to the amino acid sequence within the C-tail region of YB-1. In addition, immunoprecipitation experiments and glutathione S-transferase pulldown assays identified poly(A)-binding protein (PABP) as one of the cytoplasmic anchor proteins of YB-1. HSc025 directly binds to YB-1 and interrupts its interaction with PABP, resulting in accelerated nuclear translocation of YB-1. Transfection of cells with PABP siRNA promoted nuclear translocation of YB-1 and subsequently inhibited basal and TGF-β-stimulated collagen gene expression. Moreover, HSc025 significantly suppressed collagen gene expression in cultured activated hepatic stellate cells. Oral administration of HSc025 to mice with carbon tetrachloride-induced hepatic fibrosis improved liver injury as well as the degree of hepatic fibrosis. Altogether, the results provide a novel insight into therapy for organ fibrosis using YB-1 modulators.
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Affiliation(s)
- Kiyoshi Higashi
- Environmental Health Science Laboratory, Sumitomo Chemical Company Limited, Osaka 554-8558, Japan
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Tanaka T, Ohashi S, Funakoshi T, Kobayashi S. YB-1 binds to GluR2 mRNA and CaM1 mRNA in the brain and regulates their translational levels in an activity-dependent manner. Cell Mol Neurobiol 2010; 30:1089-100. [PMID: 20614234 DOI: 10.1007/s10571-010-9541-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/23/2010] [Indexed: 12/11/2022]
Abstract
The translational regulator YB-1 binds to mRNAs. In the brain, YB-1 is prominently expressed from the prenatal stage until the first week after birth, being associated with polysomes and distributed in neuronal dendrites, but its expression declines to a much lower level thereafter. It is therefore of interest to identify the mRNAs whose translation is controlled by YB-1 in the postnatal growing brain. In this study we found that YB-1 interacted with the mRNAs for glutamate receptor subunit 2 (GluR2) and calmodulin1 (CaM1) in both brain and NG108-15 cells. Overexpression or knockdown of YB-1 altered the levels of these proteins significantly in cultured cells without any change in their mRNA levels. When the cells were treated with neurotransmitters, translation of these proteins was induced within a short time, and a change in the amount of YB-1 on its target mRNAs was observed in the heavy-sedimenting polysome fractions on a sucrose gradient. Depletion of YB-1 expression by siRNA abrogated the translational activation. Furthermore, in the brain of kainic acid-treated mice, the distribution of YB-1 was shifted to much heavier fractions associated with polysomes within 30 min to 1 h after the treatment, and the distribution returned to lighter fractions within the following 2 h. The protein levels of GluR2 and CaM1 were also increased transiently when the distribution of YB-1 on the gradient changed. These results suggest that in the brain of growing mice, YB-1 binds to GluR2 and CaM1 mRNAs and regulates their translation in an activity-dependent manner.
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Affiliation(s)
- Toru Tanaka
- Research Unit of Biochemistry, School of Pharmacy, Nihon University, Funabashi, Chiba, Japan
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25
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The N-terminal domain of y-box binding protein-1 induces cell cycle arrest in g2/m phase by binding to cyclin d1. Int J Cell Biol 2010; 2009:243532. [PMID: 20414334 PMCID: PMC2855077 DOI: 10.1155/2009/243532] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 12/31/2009] [Indexed: 12/11/2022] Open
Abstract
Y-box binding protein YB-1 is a multifunctional protein involved in cell proliferation, regulation of transcription and translation. Our previous study indicated that disruption of one allele of Chk-YB-1b gene in DT-40 cells resulted in major defects in the cell cycle. The abnormalities seen in heterozygous mutants could be attributed to a dominant negative effect exerted by the disrupted YB-1 allele product. To test this hypothesis the N-terminal sequence of the YB-1 was fused with the third helix of antennapedia and the green fluorescent protein. These purified fusion proteins were introduced into rat hepatoma cells and their effect on cell proliferation was studied. Results indicate that the N-terminal 77 amino acid domain of the YB-1 protein induced the cells to arrest in G2/M phase of the cell cycle and undergo apoptosis. Additional deletion analysis indicated that as few as 26 amino acids of the N-terminus of YB-1 can cause these phenotypic changes. We further demonstrated that this N-terminal 77 amino acid domain of YB-1 sequesters cyclin D1 in the cytoplasm of cells at G2/M phase of cell cycle. We conclude that the N-terminal domain of YB-1 plays a major role in cell cycle progression through G2/M phase of cell cycle.
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26
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Chaikam V, Karlson DT. Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins. BMB Rep 2010; 43:1-8. [DOI: 10.5483/bmbrep.2010.43.1.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ohashi S, Atsumi M, Kobayashi S. HSP60 interacts with YB-1 and affects its polysome association and subcellular localization. Biochem Biophys Res Commun 2009; 385:545-50. [PMID: 19470374 DOI: 10.1016/j.bbrc.2009.05.094] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 05/21/2009] [Indexed: 11/16/2022]
Abstract
YB-1 is a DNA/RNA-binding protein which, in the cytoplasm, associates with polysomes and regulates translation. However, YB-1 has a novel nuclear localization signal, and its nuclear accumulation is correlated with cancer induction. Here we designated the amino-acid sequence as YB-NLS and demonstrated that YB-NLS is necessary for the nuclear translocation of overexpressed YB-1 in NG108-15 cells. In addition, we found that a heat shock protein, HSP60, binds to YB-NLS in the cytoplasm. Interestingly, when HSP60 expression was repressed, an increase of polysome-associated YB-1 was observed in heavy-sedimenting fractions on a sucrose gradient. Overexpression of HSP60 resulted in a decrease of YB-1 in the heavy-sedimenting fractions and suppression of YB-NLS activity. Furthermore, the NLS-deleted YB-1 was apparently associated with the heavy-sedimenting polysomes. These results suggest that HSP60 interacts with YB-1 at the YB-NLS region and acts as a regulator of polysome association and the subcellular distribution of YB-1.
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Affiliation(s)
- Sachiyo Ohashi
- Research Unit of Biochemistry, College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba 274-8555, Japan
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28
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Affinity chromatography using 2' fluoro-substituted RNAs for detection of RNA-protein interactions in RNase-rich or RNase-treated extracts. Biotechniques 2009; 46:95-8. [PMID: 19317654 DOI: 10.2144/000113067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Use of RNA affinity chromatography is commonly used to identify RNA binding proteins that interact with specific RNA cis-elements that function in post-transcriptional gene regulation. These purifications can be complicated by residual RNase activity in cellular extracts that can degrade the RNAs on these affinity columns. Furthermore, some proteins may associate indirectly with the column as a component of multi-protein complexes that are "tethered" through the binding of cellular RNAs. We present a protocol for an RNA affinity procedure that can be used in conjunction with RNase-rich or RNase-treated extracts by using RNAs synthesized with 2' fluoro-substituted cytidine triphosphate (CTP) and uridine triphosphate (UTP). The resulting RNAs are shown to be RNase A-resistant and capable of direct coupling to adipic acid dihydrazide agarose beads. Using an RNA cis-element previously shown to bind hnRNP M, we demonstrated that the substituted RNAs preserve binding capability by a common class of RNA binding proteins. Our results provide a method that may be used more generally for RNA affinity purification or as a validation step to verify more direct binding of a given RNA binding protein to a target RNA.
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29
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General RNA-binding proteins have a function in poly(A)-binding protein-dependent translation. EMBO J 2008; 28:58-68. [PMID: 19078965 DOI: 10.1038/emboj.2008.259] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 11/12/2008] [Indexed: 12/29/2022] Open
Abstract
The interaction between the poly(A)-binding protein (PABP) and eukaryotic translational initiation factor 4G (eIF4G), which brings about circularization of the mRNA, stimulates translation. General RNA-binding proteins affect translation, but their role in mRNA circularization has not been studied before. Here, we demonstrate that the major mRNA ribonucleoprotein YB-1 has a pivotal function in the regulation of eIF4F activity by PABP. In cell extracts, the addition of YB-1 exacerbated the inhibition of 80S ribosome initiation complex formation by PABP depletion. Rabbit reticulocyte lysate in which PABP weakly stimulates translation is rendered PABP-dependent after the addition of YB-1. In this system, eIF4E binding to the cap structure is inhibited by YB-1 and stimulated by a nonspecific RNA. Significantly, adding PABP back to the depleted lysate stimulated eIF4E binding to the cap structure more potently if this binding had been downregulated by YB-1. Conversely, adding nonspecific RNA abrogated PABP stimulation of eIF4E binding. These data strongly suggest that competition between YB-1 and eIF4G for mRNA binding is required for efficient stimulation of eIF4F activity by PABP.
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Chaikam V, Karlson D. Functional characterization of two cold shock domain proteins from Oryza sativa. PLANT, CELL & ENVIRONMENT 2008; 31:995-1006. [PMID: 18397370 DOI: 10.1111/j.1365-3040.2008.01811.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Two novel rice cold shock domain (CSD) proteins were cloned and characterized under different stress treatments and during various stages of development. OsCSP1 and OsCSP2 (Oryza sativa CSD protein) encode putative proteins consisting of an N-terminal CSD and glycine-rich regions that are interspersed by 4 and 2 CX(2)CX(4)HX(4)C (CCHC) retroviral-like zinc fingers, respectively. In vivo functional analysis confirmed that OsCSPs can complement a cold-sensitive bacterial strain which lacks four endogenous cold shock proteins. In vitro ssDNA binding assays determined that recombinant OsCSPs are capable of functioning as nucleic acid-binding proteins. Both OsCSP transcripts are transiently up-regulated in response to low-temperature stress and rapidly return to a basal level of gene expression. Protein blot analysis determined that OsCSPs are maintained at a constant level subsequent to a cold treatment lasting over a period of several days. Both the transcript and protein data are in sharp contrast to those previously obtained for winter wheat WCSP1. A time-coursed study through various stages of rice development confirmed that both OsCSP proteins and transcripts are highly accumulated in reproductive tissues and tissues which exhibit meristematic activity.
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Affiliation(s)
- Vijay Chaikam
- West Virginia University, Division of Plant & Soil Sciences, 1090 Agricultural Sciences, Morgantown, WV 26506-6108, USA
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31
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Allemand E, Hastings ML, Murray MV, Myers MP, Krainer AR. Alternative splicing regulation by interaction of phosphatase PP2Cgamma with nucleic acid-binding protein YB-1. Nat Struct Mol Biol 2007; 14:630-8. [PMID: 17572683 DOI: 10.1038/nsmb1257] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 05/02/2007] [Indexed: 01/29/2023]
Abstract
Kinases and phosphatases participate in precursor messenger RNA (pre-mRNA) splicing regulation, but their precise roles and the identities of their cofactors and substrates remain poorly understood. The human Ser/Thr phosphatase PP2Cgamma promotes spliceosome assembly. We show that PP2Cgamma's distinctive acidic domain is essential for its activity in splicing and interacts with YB-1, a spliceosome-associated factor. Moreover, PP2Cgamma is a phosphoprotein in vivo, and its acidic domain is phosphorylated under splicing conditions in vitro. PP2Cgamma phosphorylation enhances its interaction with YB-1 and is reversed by the phosphatase in cis. PP2Cgamma knockdown leaves constitutive splicing unaffected but inhibits cell proliferation and affects alternative splicing of CD44, a YB-1 target. This effect on splicing regulation is mediated by PP2Cgamma's acidic domain, which is essential to promote inclusion of CD44 exons v4 and v5 in vivo. We propose that PP2Cgamma modulates alternative splicing of specific pre-mRNAs coregulated by YB-1.
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Affiliation(s)
- Eric Allemand
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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32
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Max KEA, Zeeb M, Bienert R, Balbach J, Heinemann U. Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus. FEBS J 2007; 274:1265-79. [PMID: 17266726 DOI: 10.1111/j.1742-4658.2007.05672.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP (Bc-Csp) in complex with hexathymidine (dT(6)) at a resolution of 1.29 A. Bound to dT(6), crystalline Bc-Csp forms a domain-swapped dimer in which beta strands 1-3 associate with strands 4 and 5 from the other subunit to form a closed beta barrel and vice versa. The globular units of dimeric Bc-Csp closely resemble the well-known structure of monomeric CSP. Structural reorganization from the monomer to the domain-swapped dimer involves a strictly localized change in the peptide bond linking Glu36 and Gly37 of Bc-Csp. Similar structural reorganizations have not been found in any other CSP or oligonucleotide/oligosaccharide-binding fold structures. Each dT(6) ligand is bound to one globular unit of Bc-Csp via an amphipathic protein surface. Individual binding subsites interact with the DNA bases through stacking and hydrogen bonding. The sugar-phosphate backbone remains solvent exposed. Based on crystallographic and biochemical studies of deoxyoligonucleotide binding to CSP, we suggest a common mode of binding of single-stranded heptanucleotide motifs to proteins containing cold shock domains, including the eukaryotic Y-box factors.
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Affiliation(s)
- Klaas E A Max
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany
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Uchiumi T, Fotovati A, Sasaguri T, Shibahara K, Shimada T, Fukuda T, Nakamura T, Izumi H, Tsuzuki T, Kuwano M, Kohno K. YB-1 Is Important for an Early Stage Embryonic Development. J Biol Chem 2006; 281:40440-9. [PMID: 17082189 DOI: 10.1074/jbc.m605948200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic Y-box-binding protein-1 (YB-1) is involved in the transcriptional and translational control of many biological processes, including cell proliferation. In clinical studies, the cellular level of YB-1 closely correlates with tumor growth and prognosis. To understand the role of YB-1 in vivo, especially in the developmental process, we generated YB-1 knock-out mice, which are embryonic lethal and exhibit exencephaly associated with abnormal patterns of cell proliferation within the neuroepithelium. beta-Actin expression and F-actin formation were reduced in the YB-1 null embryo and YB-1(-/-) mouse embryonic fibroblasts, suggesting that the neural tube defect is caused by abnormal cell morphology and actin assembly within the neuroepithelium. Fibroblasts derived from YB-1(-/-) embryos demonstrated reduced growth and cell density. A colony formation assay showed that YB-1(-/-) mouse embryonic fibroblasts failed to undergo morphological transformation and remained contact-inhibited in culture. These results demonstrate that YB-1 is involved in early mouse development, including neural tube closure and cell proliferation.
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Affiliation(s)
- Takeshi Uchiumi
- Department of Molecular Biology, University of Occupational and Environmental Health, School of Medicine, Yahatanishi-ku, Kitakyushu 807-8555, Japan.
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34
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Miwa A, Higuchi T, Kobayashi S. Expression and polysome association of YB-1 in various tissues at different stages in the lifespan of mice. Biochim Biophys Acta Gen Subj 2006; 1760:1675-81. [PMID: 17045744 DOI: 10.1016/j.bbagen.2006.08.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/29/2006] [Accepted: 08/28/2006] [Indexed: 11/29/2022]
Abstract
Tissue-specific translational regulation is important for gene expression. YB-1 binds to mRNAs to form mRNPs and affects translation. In this study we investigated expression and polysome association of YB-1 in various tissues at different stages in the lifespan of mice. YB-1 levels decreased markedly with growth in brain, heart and muscle, but increased in the spleen. In lung, kidney and testis, the levels of YB-1 diminished with aging. In liver, no significant change in the level of YB-1 was observed throughout life. We further showed that the distribution pattern of YB-1 on a sucrose gradient differed according to tissue. Moreover, the distribution pattern of YB-1 changed drastically with growth in the liver. In 5-day-old liver, YB-1 was distributed almost exclusively in nonpolysomal fractions, whereas in 4-week-old liver, it was associated with heavy-sedimenting polysomes, as was the case in 5-day-old brain. Immunohistochemical analysis revealed that YB-1 is mainly a cytoplasmic protein in these tissues. Our results indicate that the expression and polysome association of YB-1 are regulated with growth or aging in a tissue-specific manner, presumably to control gene expression at the translational level in each tissue.
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Affiliation(s)
- Arisa Miwa
- Department of Biochemistry, College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba 274-8555, Japan
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35
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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: 92] [Impact Index Per Article: 5.1] [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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36
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Skabkin MA, Lyabin DN, Ovchinnikov LP. Nonspecific and specific interactions of Y-box-binding protein 1 (YB-1) with mRNA and posttranscriptional regulation of protein synthesis in animal cells. Mol Biol 2006. [DOI: 10.1134/s0026893306040078] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Shinozaki F, Minami M, Chiba T, Suzuki M, Yoshimatsu K, Ichikawa Y, Terasawa K, Emori Y, Matsumoto K, Kurosaki T, Nakai A, Tanaka K, Minami Y. Depletion of hsp90beta induces multiple defects in B cell receptor signaling. J Biol Chem 2006; 281:16361-9. [PMID: 16617057 DOI: 10.1074/jbc.m600891200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hsp90 participates in many distinct aspects of cellular functions and accomplishes these roles by interacting with multiple client proteins. To gain insight into the interactions between Hsp90 and its clients, here we have reduced the protein level of Hsp90 in avian cells by gene targeting in an attempt to elicit the otherwise undetectable (because of the vast amount of cellular Hsp90) Hsp90-interacting proteins. Hsp90beta-deficient cells can grow, albeit more slowly than wild-type cells. B cell antigen receptor signaling is multiply impaired in these mutant cells; in particular, the amount of immunoglobulin M heavy chain protein is markedly reduced. Furthermore, serum activation does not promote ERK phosphorylation in Hsp90beta-deficient cells. These multifaceted depressive effects seem to be provoked independently of each other and possibly recapitulate the proteome-wide in vivo functions of Hsp90. Reintroduction of the Hsp90beta gene efficiently restores all of the defects. Unexpectedly, however, introducing the Hsp90alpha gene is also effective in restoration; thus, these defects might be caused by a reduction in the total expression of Hsp90 rather than by loss of Hsp90beta-specific function.
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Affiliation(s)
- Fumika Shinozaki
- Department of Biophysics and Biochemistry, and Undergraduate Program for Bioinformatics and Systems Biology, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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38
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Kohno Y, Matsuki Y, Tanimoto A, Izumi H, Uchiumi T, Kohno K, Shimajiri S, Sasaguri Y. Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen. Br J Cancer 2006; 94:710-6. [PMID: 16479255 PMCID: PMC2361212 DOI: 10.1038/sj.bjc.6602987] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Y-box-binding proteins are members of the human cold-shock domain protein superfamily, which includes dbpA, dbpB/YB-1, and dbpC/contrin. dbpC/contrin is a germ cell-specific Y-box-binding protein and is suggested to function as a nuclear transcription factor and RNA-binding protein in the cytoplasm. Whereas ubiquitous dbpB/YB-1 expression has been well studied in various types of human carcinomas as a prognostic or predictive marker, the dbpC/contrin expression in human tumour cells has not been reported. In this report, we provide the first evidence showing that dbpC was highly expressed in human testicular seminoma and ovarian dysgerminomas, and in carcinomas in other tissues and that its expression in normal tissues is nearly restricted to germ cells and placental trophoblasts. These results indicate that dbpC/contrin would be a potentially novel cancer/testis antigen.
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Affiliation(s)
- Y Kohno
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Department of Ophthalmology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Y Matsuki
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - A Tanimoto
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan; E-mail:
| | - H Izumi
- Department of Molecular Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - T Uchiumi
- Department of Molecular Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - K Kohno
- Department of Molecular Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - S Shimajiri
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Department of Surgical Pathology, Kyushu Koseinenkin Hospital, Kitakyushu, Japan
| | - Y Sasaguri
- Department of Pathology and Cell Biology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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39
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Evdokimova V, Ruzanov P, Anglesio MS, Sorokin AV, Ovchinnikov LP, Buckley J, Triche TJ, Sonenberg N, Sorensen PHB. Akt-mediated YB-1 phosphorylation activates translation of silent mRNA species. Mol Cell Biol 2006; 26:277-92. [PMID: 16354698 PMCID: PMC1317623 DOI: 10.1128/mcb.26.1.277-292.2006] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
YB-1 is a broad-specificity RNA-binding protein that is involved in regulation of mRNA transcription, splicing, translation, and stability. In both germinal and somatic cells, YB-1 and related proteins are major components of translationally inactive messenger ribonucleoprotein particles (mRNPs) and are mainly responsible for storage of mRNAs in a silent state. However, mechanisms regulating the repressor activity of YB-1 are not well understood. Here we demonstrate that association of YB-1 with the capped 5' terminus of the mRNA is regulated via phosphorylation by the serine/threonine protein kinase Akt. In contrast to its nonphosphorylated form, phosphorylated YB-1 fails to inhibit cap-dependent but not internal ribosome entry site-dependent translation of a reporter mRNA in vitro. We also show that similar to YB-1, Akt is associated with inactive mRNPs and that activated Akt may relieve translational repression of the YB-1-bound mRNAs. Using Affymetrix microarrays, we found that many of the YB-1-associated messages encode stress- and growth-related proteins, raising the intriguing possibility that Akt-mediated YB-1 phosphorylation could, in part, increase production of proteins regulating cell proliferation, oncogenic transformation, and stress response.
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Affiliation(s)
- Valentina Evdokimova
- Department of Pathology, British Columbia Research Institute for Children's and Women's Health, Vancouver, BC, Canada V5Z 163.
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40
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Vaiman AV, Stromskaya TP, Rybalkina EY, Sorokin AV, Guryanov SG, Zabotina TN, Mechetner EB, Ovchinnikov LP, Stavrovskaya AA. Intracellular localization and content of YB-1 protein in multidrug resistant tumor cells. BIOCHEMISTRY (MOSCOW) 2006; 71:146-54. [PMID: 16489918 DOI: 10.1134/s0006297906020052] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The multifunctional mammalian protein YB-1 is a member of the large DNA- and RNA-binding protein family with an evolutionarily ancient cold-shock domain. YB-1 is involved in multiple DNA- and mRNA-dependent events and regulates gene expression at various levels. It can be found both in the nucleus and the cytoplasm. Bound to DNA in the cell nucleus, YB-1 functions as a transcription factor interacting with inverted CCAAT-box (Y-box) in promoters and enhancers of multiple genes. In particular, YB-1 regulates activity of the multidrug resistance (MDR) genes MDR1 and LRP. In tumors, YB-1 has been suggested to be an early and global marker of MDR. In this study, we compared amounts of YB-1 mRNAs and intracellular localization of YB-1 protein in six pairs of drug sensitive and drug resistant sublines of diverse tumors. We have shown that neither great increase in the level of YB-1 mRNA nor substantial increase in the number of cells with nuclear localization of YB-1 are obligatory traits of drug resistant tumor cell populations. However, the cells with highest amounts of YB-1 mRNA also demonstrated increased quantities of MDR1, MRP1, BCRP, and LRP mRNAs encoding different MDR proteins. Transfection of two different populations of drug-sensitive cells with YB-1 cDNA led to increase in the amount of YB-1 mRNA. The quantities of MRP1 and LRP mRNAs increased in both populations. Introduction of YB-1 small hairpin RNA (shRNA) resulted in decreased amounts of YB-1 mRNA, as well as MRP1, LRP, and MDR1 mRNAs (in three different cell lines). Our data suggest that although YB-1 regulates several MDR genes, it could not be regarded as a global marker of already formed drug resistant tumor cell populations. It is most likely that at the first steps of MDR development YB-1 activity is necessary for propagation of resistant cell populations rather than for maintenance of drug resistance.
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Affiliation(s)
- A V Vaiman
- Institute of Carcinogenesis, Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, 115478 Moscow, Russia.
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41
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Zhang A, Liu X, Cogan JG, Fuerst MD, Polikandriotis JA, Kelm RJ, Strauch AR. YB-1 coordinates vascular smooth muscle alpha-actin gene activation by transforming growth factor beta1 and thrombin during differentiation of human pulmonary myofibroblasts. Mol Biol Cell 2005; 16:4931-40. [PMID: 16093352 PMCID: PMC1243245 DOI: 10.1091/mbc.e05-03-0216] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Profibrotic regulatory mechanisms for tissue repair after traumatic injury have developed under strong evolutionary pressure to rapidly stanch blood loss and close open wounds. We have examined the roles played by two profibrotic mediators, transforming growth factor beta1 (TGFbeta1) and thrombin, in directing expression of the vascular smooth muscle alpha-actin (SMalphaA) gene, an important determinant of myofibroblast differentiation and early protein marker for stromal cell response to tissue injury. TGFbeta1 is a well known transcriptional activator of the SMalphaA gene in myofibroblasts. In contrast, thrombin independently elevates SMalphaA expression in human pulmonary myofibroblasts at the posttranscriptional level. A common feature of SMalphaA up-regulation mediated by thrombin and TGFbeta1 is the involvement of the cold shock domain protein YB-1, a potent repressor of SMalphaA gene transcription in human fibroblasts that also binds mRNA and regulates translational efficiency. YB-1 dissociates from SMalphaA enhancer DNA in the presence of TGFbeta1 or its Smad 2, 3, and 4 coregulatory mediators. Thrombin does not effect SMalphaA gene transcription but rather displaces YB-1 from SMalphaA exon 3 coding sequences previously shown to be required for mRNA translational silencing. The release of YB-1 from promoter DNA coupled with its ability to bind RNA and shuttle between the nucleus and cytoplasm is suggestive of a regulatory loop for coordinating SMalphaA gene output in human pulmonary myofibroblasts at both the transcriptional and translational levels. This loop may help restrict organ-destructive remodeling due to excessive myofibroblast differentiation.
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Affiliation(s)
- Aiwen Zhang
- Department of Physiology and Cell Biology, The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine and Public Health, Columbus, OH 43210, USA
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Matsumoto K, Bay BH. Significance of the Y-box proteins in human cancers. J Mol Genet Med 2005; 1:11-7. [PMID: 19565008 PMCID: PMC2702063 DOI: 10.4172/1747-0862.1000005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/01/2005] [Accepted: 08/01/2005] [Indexed: 11/22/2022] Open
Abstract
Y-box proteins belong to the cold shock domain family of proteins that are known to be involved in both transcriptional and translational control. Here, we give a brief overview of the structure, regulation and physiological functions of the Y-box proteins. This is followed by examining the role of Y-box protein 1 (YB-1), the most extensively studied of the Y-box protein in tumorigenesis, and its clinicopathological significance. YB-1 has the potential to be a prognostic marker and predictor of chemoresistance in human cancers.
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Affiliation(s)
- Ken Matsumoto
- Laboratory of Cellular Biochemistry, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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