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Multiple Criteria Optimization (MCO): A gene selection deterministic tool in RStudio. PLoS One 2022; 17:e0262890. [PMID: 35085348 PMCID: PMC8794188 DOI: 10.1371/journal.pone.0262890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/09/2022] [Indexed: 11/19/2022] Open
Abstract
Identifying genes with the largest expression changes (gene selection) to characterize a given condition is a popular first step to drive exploration into molecular mechanisms and is, therefore, paramount for therapeutic development. Reproducibility in the sciences makes it necessary to emphasize objectivity and systematic repeatability in biological and informatics analyses, including gene selection. With these two characteristics in mind, in previous works our research team has proposed using multiple criteria optimization (MCO) in gene selection to analyze microarray datasets. The result of this effort is the MCO algorithm, which selects genes with the largest expression changes without user manipulation of neither informatics nor statistical parameters. Furthermore, the user is not required to choose either a preference structure among multiple measures or a predetermined quantity of genes to be deemed significant a priori. This implies that using the same datasets and performance measures (PMs), the method will converge to the same set of selected differentially expressed genes (repeatability) despite who carries out the analysis (objectivity). The present work describes the development of an open-source tool in RStudio to enable both: (1) individual analysis of single datasets with two or three PMs and (2) meta-analysis with up to five microarray datasets, using one PM from each dataset. The capabilities afforded by the code include license-free portability and the possibility to carry out analyses via modest computer hardware, such as personal laptops. The code provides affordable, repeatable, and objective detection of differentially expressed genes from microarrays. It can be used to analyze other experiments with similar experimental comparative layouts, such as microRNA arrays and protein arrays, among others. As a demonstration of the capabilities of the code, the analysis of four publicly-available microarray datasets related to Parkinson´s Disease (PD) is presented here, treating each dataset individually or as a four-way meta-analysis. These MCO-supported analyses made it possible to identify MMP9 and TUBB2A as potential PD genetic biomarkers based on their persistent appearance across each of the case studies. A literature search confirmed the importance of these genes in PD and indeed as PD biomarkers, which evidences the code´s potential.
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Liebl MC, Moehlenbrink J, Becker H, Raddatz G, Abdeen SK, Aqeilan RI, Lyko F, Hofmann TG. DAZAP2 acts as specifier of the p53 response to DNA damage. Nucleic Acids Res 2021; 49:2759-2776. [PMID: 33591310 PMCID: PMC7969023 DOI: 10.1093/nar/gkab084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/13/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
The DNA damage-responsive tumor suppressors p53 and HIPK2 are well established regulators of cell fate decision-making and regulate the cellular sensitivity to DNA-damaging drugs. Here, we identify Deleted in Azoospermia-associated protein 2 (DAZAP2), a small adaptor protein, as a novel regulator of HIPK2 and specifier of the DNA damage-induced p53 response. Knock-down or genetic deletion of DAZAP2 strongly potentiates cancer cell chemosensitivity both in cells and in vivo using a mouse tumour xenograft model. In unstressed cells, DAZAP2 stimulates HIPK2 polyubiquitination and degradation through interplay with the ubiquitin ligase SIAH1. Upon DNA damage, HIPK2 site-specifically phosphorylates DAZAP2, which terminates its HIPK2-degrading function and triggers its re-localization to the cell nucleus. Interestingly, nuclear DAZAP2 interacts with p53 and specifies target gene expression through modulating a defined subset of p53 target genes. Furthermore, our results suggest that DAZAP2 co-occupies p53 response elements to specify target gene expression. Collectively, our findings propose DAZAP2 as novel regulator of the DNA damage-induced p53 response that controls cancer cell chemosensitivity.
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Affiliation(s)
- Magdalena C Liebl
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
| | - Jutta Moehlenbrink
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
| | - Huong Becker
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
| | - Günter Raddatz
- Division of Epigenetics, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Suhaib K Abdeen
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Frank Lyko
- Division of Epigenetics, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
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3
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Epigenome-wide association study of depression symptomatology in elderly monozygotic twins. Transl Psychiatry 2019; 9:214. [PMID: 31477683 PMCID: PMC6718679 DOI: 10.1038/s41398-019-0548-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/15/2019] [Accepted: 06/20/2019] [Indexed: 12/11/2022] Open
Abstract
Depression is a severe and debilitating mental disorder diagnosed by evaluation of affective, cognitive and physical depression symptoms. Severity of these symptoms strongly impacts individual's quality of life and is influenced by a combination of genetic and environmental factors. One of the molecular mechanisms allowing for an interplay between these factors is DNA methylation, an epigenetic modification playing a pivotal role in regulation of brain functioning across lifespan. The aim of this study was to investigate if there are DNA methylation signatures associated with depression symptomatology in order to identify molecular mechanisms contributing to pathophysiology of depression. We performed an epigenome-wide association study (EWAS) of continuous depression symptomatology score measured in a cohort of 724 monozygotic Danish twins (346 males, 378 females). Through EWAS analyses adjusted for sex, age, flow-cytometry based blood cell composition, and twin relatedness structure in the data we identified depression symptomatology score to be associated with blood DNA methylation levels in promoter regions of neuropsin (KLK8, p-value = 4.7 × 10-7) and DAZ associated protein 2 (DAZAP2, p-value = 3.13 × 10-8) genes. Other top associated probes were located in gene bodies of MAD1L1 (p-value = 5.16 × 10-6), SLC29A2 (p-value = 6.15 × 10-6) and AKT1 (p-value = 4.47 × 10-6), all genes associated before with development of depression. Additionally, the following three measures (a) DNAmAge (calculated with Horvath and Hannum epigenetic clock estimators) adjusted for chronological age, (b) difference between DNAmAge and chronological age, and (c) DNAmAge acceleration were not associated with depression symptomatology score in our cohort. In conclusion, our data suggests that depression symptomatology score is associated with DNA methylation levels of genes implicated in response to stress, depressive-like behaviors, and recurrent depression in patients, but not with global DNA methylation changes across the genome.
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Yang L, Li X, Qin X, Wang Q, Zhou K, Li H, Zhang X, Wang Q, Li W. Deleted in azoospermia-associated protein 2 regulates innate immunity by stimulating Hippo signaling in crab. J Biol Chem 2019; 294:14704-14716. [PMID: 31395655 DOI: 10.1074/jbc.ra119.009559] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/23/2019] [Indexed: 11/06/2022] Open
Abstract
The Hippo-signaling pathway plays a critical role in both normal animal physiology and pathogenesis. Because pharmacological interventions targeting this pathway have diverse clinical implications, a better understanding of its regulation in various conditions and organisms is crucial. Here, we identified deleted in azoospermia-associated protein 2 (DAZAP2) in the Chinese mitten crab (Eriocheir sinensis), designated EsDAZAP2, as a Hippo-regulatory protein highly similar to proteins in various species of insects, fish, and mammals. We found that a bacterial infection significantly induces EsDAZAP2 expression, and an EsDAZAP2 knockdown both suppresses antimicrobial peptide (AMP) expression in vitro and results in increased viable bacterial counts and mortality in vivo, suggesting that EsDAZAP2 plays a critical role in innate immunity. Using yeast two-hybrid screening and co-immunoprecipitation assays, we found that EsDAZAP2 regulates the Toll pathway rather than the immune deficiency and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathways. Our findings also demonstrate that EsDAZAP2 binds to the Hippo protein, Salvador (Sav). Moreover, by examining the regulation of Dorsal, a transcription factor that regulates AMP expression in E. sinensis, we provide experimental evidence indicating that EsDAZAP2 promotes Hippo pathway activation in innate immunity, with EsDAZAP2 and Hippo binding to different Sav domains. To the best of our knowledge, this is the first report of a DAZAP2-regulated Hippo-signaling pathway operating in animal innate immunity.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuejie Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Xiang Qin
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qiying Wang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kaimin Zhou
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Hao Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xin Zhang
- Laboratory of Cellular Immunity, Shuguang Hospital, affiliated with Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qun Wang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiwei Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
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5
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An SWA, Choi E, Hwang W, Son HG, Yang J, Seo K, Nam H, Nguyen NTH, Kim EJE, Suh BK, Kim Y, Nakano S, Ryu Y, Man Ha C, Mori I, Park SK, Yoo J, Kim S, Lee SV. KIN-4/MAST kinase promotes PTEN-mediated longevity of Caenorhabditis elegans via binding through a PDZ domain. Aging Cell 2019; 18:e12906. [PMID: 30773781 PMCID: PMC6516182 DOI: 10.1111/acel.12906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/16/2018] [Accepted: 12/02/2018] [Indexed: 01/09/2023] Open
Abstract
PDZ domain‐containing proteins (PDZ proteins) act as scaffolds for protein–protein interactions and are crucial for a variety of signal transduction processes. However, the role of PDZ proteins in organismal lifespan and aging remains poorly understood. Here, we demonstrate that KIN‐4, a PDZ domain‐containing microtubule‐associated serine‐threonine (MAST) protein kinase, is a key longevity factor acting through binding PTEN phosphatase in Caenorhabditis elegans. Through a targeted genetic screen for PDZ proteins, we find that kin‐4 is required for the long lifespan of daf‐2/insulin/IGF‐1 receptor mutants. We then show that neurons are crucial tissues for the longevity‐promoting role of kin‐4. We find that the PDZ domain of KIN‐4 binds PTEN, a key factor for the longevity of daf‐2 mutants. Moreover, the interaction between KIN‐4 and PTEN is essential for the extended lifespan of daf‐2 mutants. As many aspects of lifespan regulation in C. elegans are evolutionarily conserved, MAST family kinases may regulate aging and/or age‐related diseases in mammals through their interaction with PTEN.
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Affiliation(s)
- Seon Woo A. An
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Eun‐Seok Choi
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Wooseon Hwang
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Heehwa G. Son
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Jae‐Seong Yang
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Keunhee Seo
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Hyun‐Jun Nam
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Nhung T. H. Nguyen
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Eun Ji E. Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Bo Kyoung Suh
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Youngran Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Shunji Nakano
- Neuroscience Institute, Graduate School of Science Nagoya University Nagoya Japan
| | - Youngjae Ryu
- Research Division Korea Brain Research Institute Daegu South Korea
| | - Chang Man Ha
- Research Division Korea Brain Research Institute Daegu South Korea
| | - Ikue Mori
- Neuroscience Institute, Graduate School of Science Nagoya University Nagoya Japan
| | - Sang Ki Park
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Joo‐Yeon Yoo
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Sanguk Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
| | - Seung‐Jae V. Lee
- Department of Life Sciences Pohang University of Science and Technology Pohang Gyeongbuk South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang Gyeongbuk South Korea
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6
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Son HG, Seo K, Seo M, Park S, Ham S, An SWA, Choi ES, Lee Y, Baek H, Kim E, Ryu Y, Ha CM, Hsu AL, Roh TY, Jang SK, Lee SJV. Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C. elegans. Genes Dev 2018; 32:1562-1575. [PMID: 30478249 PMCID: PMC6295163 DOI: 10.1101/gad.317362.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. In Caenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.
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Affiliation(s)
- Heehwa G Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Center for plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea.,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea
| | - Sangsoon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seon Woo A An
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eun-Seok Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Yujin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Haeshim Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eunju Kim
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Ao-Lin Hsu
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Research Center for Healthy Aging, China Medical University, Taichung 404, Taiwan.,Institute of New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seung-Jae V Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
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7
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Poblete-Durán N, Prades-Pérez Y, Vera-Otarola J, Soto-Rifo R, Valiente-Echeverría F. Who Regulates Whom? An Overview of RNA Granules and Viral Infections. Viruses 2016; 8:v8070180. [PMID: 27367717 PMCID: PMC4974515 DOI: 10.3390/v8070180] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022] Open
Abstract
After viral infection, host cells respond by mounting an anti-viral stress response in order to create a hostile atmosphere for viral replication, leading to the shut-off of mRNA translation (protein synthesis) and the assembly of RNA granules. Two of these RNA granules have been well characterized in yeast and mammalian cells, stress granules (SGs), which are translationally silent sites of RNA triage and processing bodies (PBs), which are involved in mRNA degradation. This review discusses the role of these RNA granules in the evasion of anti-viral stress responses through virus-induced remodeling of cellular ribonucleoproteins (RNPs).
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Affiliation(s)
- Natalia Poblete-Durán
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Yara Prades-Pérez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago 8330024, Chile.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
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Kuchta K, Muszewska A, Knizewski L, Steczkiewicz K, Wyrwicz LS, Pawlowski K, Rychlewski L, Ginalski K. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. Nucleic Acids Res 2016; 44:3534-48. [PMID: 27060136 PMCID: PMC4857005 DOI: 10.1093/nar/gkw222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are thought to be involved in several diseases, with FAM46C reported as a causal driver of multiple myeloma; however, their exact functions remain unknown. By using a combination of various bioinformatics analyses (e.g. domain architecture, cellular localization) and exhaustive literature and database searches (e.g. expression profiles, protein interactors), we classified FAM46 proteins as active non-canonical poly(A) polymerases, which modify cytosolic and/or nuclear RNA 3′ ends. These proteins may thus regulate gene expression and probably play a critical role during cell differentiation. A detailed analysis of sequence and structure diversity of known NTases possessing PAP/OAS1 SBD domain, combined with state-of-the-art comparative modelling, allowed us to identify potential active site residues responsible for catalysis and substrate binding. We also explored the role of single point mutations found in human cancers and propose that FAM46 genes may be involved in the development of other major malignancies including lung, colorectal, hepatocellular, head and neck, urothelial, endometrial and renal papillary carcinomas and melanoma. Identification of these novel enzymes taking part in RNA metabolism in eukaryotes may guide their further functional studies.
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Affiliation(s)
- Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Anna Muszewska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Lukasz Knizewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Lucjan S Wyrwicz
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
| | - Krzysztof Pawlowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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9
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Chen L, Jiang X, Feng H, Shi H, Sun L, Tao W, Xi Q, Wang D. Simultaneous exposure to estrogen and androgen resulted in feminization and endocrine disruption. J Endocrinol 2016; 228:205-18. [PMID: 26759274 DOI: 10.1530/joe-15-0432] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2016] [Indexed: 01/05/2023]
Abstract
Estrogen, which is synthesized earlier in females than androgen in males, is critical for sex determination in non-mammalian vertebrates. However, it remains unknown that what would happen to the gonadal phenotype if estrogen and androgen were administrated simultaneously. In this study, XY and XX tilapia fry were treated with the same dose of 17α-methyltestosterone (MT) and 17β-estradiol (E2) alone and in combination from 0 to 30 days after hatching. Treatment of XY fish with E2 resulted in male to female sex reversal, while treatment of XX fish with MT resulted in female to male sex reversal. In contrast, simultaneous treatment of XX and XY fish with MT and E2 resulted in female, but with cyp11b2 and cyp19a1a co-expressed in the ovary. Serum 11-ketotestosteron level of the MT and E2 simultaneously treated XX and XY female was similar to that of the XY control, while serum E2 level of these two groups was similar to that of the XX control. Transcriptomic cluster analysis revealed that the MT and E2 treated XX and XY gonads clustered into the same branch with the XX control. However a small fraction of genes, which showed disordered expression, may be associated with stress response. These results demonstrated that estrogen could maintain the female phenotype of XX fish and feminize XY fish even in the presence of androgen. Simultaneous treatment with estrogen and androgen up-regulated the endogenous estrogen and androgen synthesis, and resulted in disordered gene expression and endocrine disruption in tilapia.
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Affiliation(s)
- Lili Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaolong Jiang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haiwei Feng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongjuan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qingping Xi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
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10
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Maternal dazap2 Regulates Germ Granules by Counteracting Dynein in Zebrafish Primordial Germ Cells. Cell Rep 2015; 12:49-57. [PMID: 26119733 DOI: 10.1016/j.celrep.2015.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/03/2015] [Accepted: 06/02/2015] [Indexed: 11/24/2022] Open
Abstract
Primordial germ cells (PGCs) are the stem cells of the germline. Generally, germline induction occurs via zygotic factors or the inheritance of maternal determinants called germ plasm (GP). GP is packaged into ribonucleoprotein complexes within oocytes and later promotes the germline fate in embryos. Once PGCs are specified by either mechanism, GP components localize to perinuclear granular-like structures. Although components of zebrafish PGC germ granules have been studied, the maternal factors regulating their assembly and contribution to germ cell development are unknown. Here, we show that the scaffold protein Dazap2 binds to Bucky ball, an essential regulator of oocyte polarity and GP assembly, and colocalizes with the GP in oocytes and in PGCs. Mutational analysis revealed a requirement for maternal Dazap2 (MDazap2) in germ-granule maintenance. Through molecular epistasis analyses, we show that MDazap2 is epistatic to Tdrd7 and maintains germ granules in the embryonic germline by counteracting Dynein activity.
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11
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Aulas A, Caron G, Gkogkas CG, Mohamed NV, Destroismaisons L, Sonenberg N, Leclerc N, Parker JA, Vande Velde C. G3BP1 promotes stress-induced RNA granule interactions to preserve polyadenylated mRNA. ACTA ACUST UNITED AC 2015; 209:73-84. [PMID: 25847539 PMCID: PMC4395486 DOI: 10.1083/jcb.201408092] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 03/04/2015] [Indexed: 12/03/2022]
Abstract
The TDP-43 target G3BP1 is essential for a functional interaction between stress granules and processing bodies. G3BP1, a target of TDP-43, is required for normal stress granule (SG) assembly, but the functional consequences of failed SG assembly remain unknown. Here, using both transformed cell lines and primary neurons, we investigated the functional impact of this disruption in SG dynamics. While stress-induced translational repression and recruitment of key SG proteins was undisturbed, depletion of G3BP1 or its upstream regulator TDP-43 disturbed normal interactions between SGs and processing bodies (PBs). This was concomitant with decreased SG size, reduced SG–PB docking, and impaired preservation of polyadenylated mRNA. Reintroduction of G3BP1 alone was sufficient to rescue all of these phenotypes, indicating that G3BP1 is essential for normal SG–PB interactions and SG function.
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Affiliation(s)
- Anaïs Aulas
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Guillaume Caron
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Christos G Gkogkas
- Patrick Wild Centre and Centre for Integrative Physiology, University of Edinburgh, Edinburgh EH8 9XD, Scotland, UK Patrick Wild Centre and Centre for Integrative Physiology, University of Edinburgh, Edinburgh EH8 9XD, Scotland, UK
| | - Nguyen-Vi Mohamed
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Laurie Destroismaisons
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, Quebec H3A 1A3, Canada Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, Quebec H3A 1A3, Canada
| | - Nicole Leclerc
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - J Alex Parker
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Christine Vande Velde
- Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada Centre de recherché du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Biochemistry, and Department of Neuroscience, Université de Montréal, Montréal, QC, H2X 0A9, Canada
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12
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Zhou Y, Xiang Z, Li D, Han X. Regulation of microcystin-LR-induced toxicity in mouse spermatogonia by miR-96. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6383-6390. [PMID: 24803159 DOI: 10.1021/es500152m] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microcystin (MC)-LR is a cyclic heptapeptide that acts as a potent reproductive system toxin, especially by decreasing sperm quality through affecting spermatogonia. However, the molecular mechanisms of MC-induced spermatogonial cytotoxicity still remain unclear. The present study was designed to investigate changes in microRNA (miRNA) profiles and their potential functions in spermatogonia (GC-1 cell line) following treatment with MC-LR. With microarray analysis, 101 miRNAs were identified to be significantly altered in GC-1 cells treated with MC-LR. Among the 25 miRNAs associated with spermatogenesis, miR-96 was down-regulated most dramatically and thus selected for further functional analysis. Deleted-in azoospermia-associated protein 2 (DAZAP2) was predicted to have a binding sequence for miR-96 within its 3'-untranslated region. Fluorescent reporter assay confirmed that DAZAP2 was the target gene of miR-96. The expression of DAZAP2 decreased significantly when miR-96 was up-regulated. Consistently, down-regulation of miR-96 significantly increased the level of DAZAP2. Up-regulation of miR-96 promoted cell viability in GC-1 cells as a result of exposure to MC-LR. Our study suggested a crucial role for miR-96 in the regulation of cytotoxic effects of MC-LR in spermatogonia, which provides new perspectives in the diagnosis and treatment strategies for MC-induced male infertility.
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Affiliation(s)
- Yuan Zhou
- Immunology and Reproduction Biology Laboratory, Medical School, Nanjing University , Nanjing 210093, China
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13
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Kedersha N, Ivanov P, Anderson P. Stress granules and cell signaling: more than just a passing phase? Trends Biochem Sci 2013; 38:494-506. [PMID: 24029419 DOI: 10.1016/j.tibs.2013.07.004] [Citation(s) in RCA: 442] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) contain translationally-stalled mRNAs, associated preinitiation factors, and specific RNA-binding proteins. In addition, many signaling proteins are recruited to SGs and/or influence their assembly, which is transient, lasting only until the cells adapt to stress or die. Beyond their role as mRNA triage centers, we posit that SGs constitute RNA-centric signaling hubs analogous to classical multiprotein signaling domains such as transmembrane receptor complexes. As signaling centers, SG formation communicates a 'state of emergency', and their transient existence alters multiple signaling pathways by intercepting and sequestering signaling components. SG assembly and downstream signaling functions may require a cytosolic phase transition facilitated by intrinsically disordered, aggregation-prone protein regions shared by RNA-binding and signaling proteins.
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Affiliation(s)
- Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115, USA
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14
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Zou T, Rao JN, Liu L, Xiao L, Cui YH, Jiang Z, Ouyang M, Donahue JM, Wang JY. Polyamines inhibit the assembly of stress granules in normal intestinal epithelial cells regulating apoptosis. Am J Physiol Cell Physiol 2012; 303:C102-11. [PMID: 22555848 DOI: 10.1152/ajpcell.00009.2012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polyamines regulate multiple signaling pathways and are implicated in many aspects of cellular functions, but the exact molecular processes governed by polyamines remain largely unknown. In response to environmental stress, repression of translation is associated with the assembly of stress granules (SGs) that contain a fraction of arrested mRNAs and are thought to function as mRNA storage. Here we show that polyamines modulate the assembly of SGs in normal intestinal epithelial cells (IECs) and that induced SGs following polyamine depletion are implicated in the protection of IECs against apoptosis. Increasing the levels of cellular polyamines by ectopic overexpression of the ornithine decarboxylase gene decreased cytoplasmic levels of SG-signature constituent proteins eukaryotic initiation factor 3b and T-cell intracellular antigen-1 (TIA-1)-related protein and repressed the assembly of SGs induced by exposure to arsenite-induced oxidative stress. In contrast, depletion of cellular polyamines by inhibiting ornithine decarboxylase with α-difluoromethylornithine increased cytoplasmic eukaryotic initiation factor 3b and TIA-1 related protein abundance and enhanced arsenite-induced SG assembly. Polyamine-deficient cells also exhibited an increase in resistance to tumor necrosis factor-α/cycloheximide-induced apoptosis, which was prevented by inhibiting SG formation with silencing SG resident proteins Sort1 and TIA-1. These results indicate that the elevation of cellular polyamines represses the assembly of SGs in normal IECs and that increased SGs in polyamine-deficient cells are crucial for increased resistance to apoptosis.
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Affiliation(s)
- Tongtong Zou
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, USA
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15
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Ehrlichia chaffeensis TRP32 interacts with host cell targets that influence intracellular survival. Infect Immun 2012; 80:2297-306. [PMID: 22547548 DOI: 10.1128/iai.00154-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ehrlichia chaffeensis is an obligately intracellular bacterium that exhibits tropism for mononuclear phagocytes and survives by evading host cell defense mechanisms. Recently, molecular interactions of E. chaffeensis tandem repeat proteins 47 and 120 (TRP47 and -120) and the eukaryotic host cell have been described. In this investigation, yeast two-hybrid analysis demonstrated that an E. chaffeensis type 1 secretion system substrate, TRP32, interacts with a diverse group of human proteins associated with major biological processes of the host cell, including protein synthesis, trafficking, degradation, immune signaling, cell signaling, iron metabolism, and apoptosis. Eight target proteins, including translation elongation factor 1 alpha 1 (EF1A1), deleted in azoospermia (DAZ)-associated protein 2 (DAZAP2), ferritin light polypeptide (FTL), CD63, CD14, proteasome subunit beta type 1 (PSMB1), ring finger and CCCH-type domain 1 (RC3H1), and tumor protein p53-inducible protein 11 (TP53I11) interacted with TRP32 as determined by coimmunoprecipitation assays, colocalization with TRP32 in HeLa and THP-1 cells, and/or RNA interference. Interactions between TRP32 and host targets localized to the E. chaffeensis morulae or in the host cell cytoplasm adjacent to morulae. Common or closely related interacting partners of E. chaffeensis TRP32, TRP47, and TRP120 demonstrate a molecular convergence on common cellular processes and molecular cross talk between Ehrlichia TRPs and host targets. These findings further support the role of TRPs as effectors that promote intracellular survival.
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16
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Kim B, Cooke HJ, Rhee K. DAZL is essential for stress granule formation implicated in germ cell survival upon heat stress. Development 2012; 139:568-78. [PMID: 22223682 DOI: 10.1242/dev.075846] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mammalian male germ cells should be maintained below body temperature for proper development. Here, we investigated how male germ cells respond to heat stress. A short exposure of mouse testes to core body temperature induced phosphorylation of eIF2α and the formation of stress granules (SGs) in male germ cells. We observed that DAZL, a germ cell-specific translational regulator, was translocated to SGs upon heat stress. Furthermore, SG assembly activity was significantly diminished in the early male germ cells of Dazl-knockout mice. The DAZL-containing SGs played a protective role against heat stress-induced apoptosis by the sequestration of specific signaling molecules, such as RACK1, and the subsequent blockage of the apoptotic MAPK pathway. Based on these results, we propose that DAZL is an essential component of the SGs, which prevent male germ cells from undergoing apoptosis upon heat stress.
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Affiliation(s)
- Byunghyuk Kim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
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17
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Popova A, Kzhyshkowska J, Nurgazieva D, Goerdt S, Gratchev A. Smurf2 regulates IL17RB by proteasomal degradation of its novel binding partner DAZAP2. Immunobiology 2012; 217:321-8. [DOI: 10.1016/j.imbio.2011.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 10/16/2022]
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18
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Park SM, Paek KY, Hong KY, Jang CJ, Cho S, Park JH, Kim JH, Jan E, Jang SK. Translation-competent 48S complex formation on HCV IRES requires the RNA-binding protein NSAP1. Nucleic Acids Res 2011; 39:7791-802. [PMID: 21715376 PMCID: PMC3177222 DOI: 10.1093/nar/gkr509] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Translation of many cellular and viral mRNAs is directed by internal ribosomal entry sites (IRESs). Several proteins that enhance IRES activity through interactions with IRES elements have been discovered. However, the molecular basis for the IRES-activating function of the IRES-binding proteins remains unknown. Here, we report that NS1-associated protein 1 (NSAP1), which augments several cellular and viral IRES activities, enhances hepatitis C viral (HCV) IRES function by facilitating the formation of translation-competent 48S ribosome-mRNA complex. NSAP1, which is associated with the solvent side of the 40S ribosomal subunit, enhances 80S complex formation through correct positioning of HCV mRNA on the 40S ribosomal subunit. NSAP1 seems to accomplish this positioning function by directly binding to both a specific site in the mRNA downstream of the initiation codon and a 40S ribosomal protein (or proteins).
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Affiliation(s)
- Sung Mi Park
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
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19
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Matsunami M, Yoshioka T, Minoura T, Okano Y, Muto Y. Evolutionary features and intracellular behavior of the PRTB protein. Biochem Genet 2011; 49:458-73. [PMID: 21274613 DOI: 10.1007/s10528-011-9422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 09/21/2010] [Indexed: 11/28/2022]
Abstract
Human PRTB encodes a proline-rich protein of 168 amino acids (PRTB). We analyzed the evolutionary patterns of PRTB from various vertebrate species. Maximum likelihood analyses indicated that while mammalian PRTB has been very well conserved and underwent a significantly slower rate of evolution, only the branch leading to fish PRTB has undergone adaptive evolution. We generated several mutant PRTBs fused to the GFP variant, Venus, and found that the degradation of PRTB was enhanced by the transfection of an E2, UbcH5. Since mutation of the K153 site in PRTB was refractory to its degradation, proteolysis was suggested to be mediated by ubiquitination of K153. The subcellular localization of PRTB was also investigated, which showed that mutation of the K4 site completely prevented the nuclear localization of this protein. Together, these results suggest that Lys residues might play important roles in regulating the intracellular dynamics of the PRTB protein.
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Affiliation(s)
- Miki Matsunami
- Department of Molecular Pathobiochemistry, Gifu University Graduate School of Medicine, Yanagido, Gifu, Japan
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20
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The arginylation-dependent association of calreticulin with stress granules is regulated by calcium. Biochem J 2010; 429:63-72. [PMID: 20423325 DOI: 10.1042/bj20091953] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Post-translational modifications of proteins are important for the regulation of cell functions; one of these modifications is post-translational arginylation. In the present study, we show that cytoplasmic CRT (calreticulin) is arginylated by ATE1 (arginyl-tRNA protein transferase). We also show that a pool of CRT undergoes retrotranslocation from the ER (endoplasmic reticulum) to the cytosol, because in CRT-knockout cells transfected with full-length CRT (that has the signal peptide), cytoplasmic CRT appears as a consequence of its expression and processing in the ER. After the cleavage of the signal peptide, an N-terminal arginylatable residue is revealed prior to retrotranslocation to the cytoplasm where arginylation takes place. SGs (stress granules) from ATE1-knockout cells do not contain CRT, indicating that CRT arginylation is required for its association to SGs. Furthermore, R-CRT (arginylated CRT) in the cytoplasm associates with SGs in cells treated with several stressors that lead to a reduction of intracellular Ca2+ levels. However, in the presence of stressors that do not affect Ca2+ levels, R-CRT is not recruited to these loci despite the fact that SGs are formed, demonstrating Ca2+-dependent R-CRT association to SGs. We conclude that post-translational arginylation of retrotranslocated CRT, together with the decrease in intracellular Ca2+, promotes the association of CRT to SGs.
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21
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Kim DM, Chung KS, Choi SJ, Jung YJ, Park SK, Han GH, Ha JS, Song KB, Choi NS, Kim HM, Won M, Seo YS. RhoB induces apoptosis via direct interaction with TNFAIP1 in HeLa cells. Int J Cancer 2009; 125:2520-7. [PMID: 19637314 DOI: 10.1002/ijc.24617] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RhoB, a tumor suppressor, has emerged as an interesting cancer target, and extensive studies aimed at understanding its role in apoptosis have been performed. In our study, we investigated the involvement of RhoB-interacting molecules in apoptosis. To identify RhoB-interacting proteins, we performed yeast-two hybrid screening assays using RhoB as a bait and isolated TNFAIP1, a TNFalpha-induced protein containing the BTB/POZ domain. The interaction between RhoB and TNFAIP1 was demonstrated in vivo through coimmunoprecipitation studies and in vitro binding assays. RFP-TNFAIP1 was found to be partially colocalized with EGFP-RhoB. The partial colocalization of RhoB and TNFAIP1 in endosomes suggests that RhoB-TNFAIP1 interactions may have a functional role in apoptosis. TNFAIP1 elicited proapoptotic activity, while simultaneous expression of RhoB and TNFAIP1 resulted in a dramatic increase in apoptosis in HeLa cells. Furthermore, knockdown of RhoB using siRNA clearly rescued cells from apoptosis induced by TNFAIP1. This finding suggests that interactions between RhoB and TNFAIP1 are crucial for induction of apoptosis in HeLa cells. The observation of increased SAPK/JNK phosphorylation in apoptotic cells and the finding that a JNK inhibitor suppressed apoptosis indicates that SAPK/JNK signaling may be involved in apoptosis induced by RhoB-TNFAIP1 interactions. In conclusion, we found that RhoB interacts with TNFAIP1 to regulate apoptosis via a SAPK/JNK-mediated signal transduction mechanism.
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Affiliation(s)
- Dong-Myung Kim
- Department of Biological Science, KAIST, Daejeon 305-701, Korea
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22
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Roche DD, Liu KJ, Harland RM, Monsoro-Burq AH. Dazap2 is required for FGF-mediated posterior neural patterning, independent of Wnt and Cdx function. Dev Biol 2009; 333:26-36. [PMID: 19555680 DOI: 10.1016/j.ydbio.2009.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/19/2009] [Accepted: 06/15/2009] [Indexed: 01/15/2023]
Abstract
The organization of the embryonic neural plate requires coordination of multiple signal transduction pathways, including fibroblast growth factors (FGFs), bone morphogenetic proteins (BMPs), and WNTs. Many studies have suggested that a critical component of this process is the patterning of posterior neural tissues by an FGF-caudal signaling cascade. Here, we have identified a novel player, Dazap2, and show that it is required in vivo for posterior neural fate. Loss of Dazap2 in embryos resulted in diminished expression of hoxb9 with a concurrent increase in the anterior marker otx2. Furthermore, we found that Dazap2 is required for FGF dependent posterior patterning; surprisingly, this is independent of Cdx activity. Furthermore, in contrast to FGF activity, Dazap2 induction of hoxb9 is not blocked by loss of canonical Wnt signaling. Functionally, we found that increasing Dazap2 levels alters neural patterning and induces posterior neural markers. This activity overcomes the anteriorizing effects of noggin, and is downstream of FGF receptor activation. Our results strongly suggest that Dazap2 is a novel and essential branch of FGF-induced neural patterning.
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Affiliation(s)
- Daniel D Roche
- Institut Curie, CNRS, UMR146, Centre Universitaire, Batiment 110, 91405 Orsay Cedex, France
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23
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Thomas MG, Martinez Tosar LJ, Desbats MA, Leishman CC, Boccaccio GL. Mammalian Staufen 1 is recruited to stress granules and impairs their assembly. J Cell Sci 2009; 122:563-73. [PMID: 19193871 DOI: 10.1242/jcs.038208] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Stress granules are cytoplasmic mRNA-silencing foci that form transiently during the stress response. Stress granules harbor abortive translation initiation complexes and are in dynamic equilibrium with translating polysomes. Mammalian Staufen 1 (Stau1) is a ubiquitous double-stranded RNA-binding protein associated with polysomes. Here, we show that Stau1 is recruited to stress granules upon induction of endoplasmic reticulum or oxidative stress as well in stress granules induced by translation initiation blockers. We found that stress granules lacking Stau1 formed in cells depleted of this molecule, indicating that Stau1 is not an essential component of stress granules. Moreover, Stau1 knockdown facilitated stress granule formation upon stress induction. Conversely, transient transfection of Stau1 impaired stress granule formation upon stress or pharmacological initiation arrest. The inhibitory capacity of Stau1 mapped to the amino-terminal half of the molecule, a region known to bind to polysomes. We found that the fraction of polysomes remaining upon stress induction was enriched in Stau1, and that Stau1 overexpression stabilized polysomes against stress. We propose that Stau1 is involved in recovery from stress by stabilizing polysomes, thus helping stress granule dissolution.
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24
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Lukas J, Mazna P, Valenta T, Doubravska L, Pospichalova V, Vojtechova M, Fafilek B, Ivanek R, Plachy J, Novak J, Korinek V. Dazap2 modulates transcription driven by the Wnt effector TCF-4. Nucleic Acids Res 2009; 37:3007-20. [PMID: 19304756 PMCID: PMC2685103 DOI: 10.1093/nar/gkp179] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A major outcome of the canonical Wnt/beta-catenin-signalling pathway is the transcriptional activation of a specific set of target genes. A typical feature of the transcriptional response induced by Wnt signalling is the involvement of Tcf/Lef factors that function in the nucleus as the principal mediators of signalling. Vertebrate Tcf/Lef proteins perform two well-characterized functions: in association with beta-catenin they activate gene expression, and in the absence of Wnt ligands they bind TLE/Groucho proteins to act as transcriptional repressors. Although the general characteristics of Tcf/Lef factors are well understood, the mechanisms that control their specific roles in various cellular backgrounds are much less defined. In this report we reveal that the evolutionary conserved Dazap2 protein functions as a TCF-4 interacting partner. We demonstrate that a short region proximal to the TCF-4 HMG box mediates the interaction and that all Tcf/Lef family members associate with Dazap2. Interestingly, knockdown of Dazap2 not only reduced the activity of Wnt signalling as measured by Tcf/beta-catenin reporters but additionally altered the expression of Wnt-signalling target genes. Finally, chromatin immunoprecipitation studies indicate that Dazap2 modulates the affinity of TCF-4 for its DNA-recognition motif.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Vladimir Korinek
- *To whom correspondence should be addressed. Tel:+4202 4106 3146; Fax:+4202 4447 2282;
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