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Ke J, Zhang DG, Lei XJ, Liu GH, Luo Z. Characterization and tissue expression of twelve selenoproteins in yellow catfish Pelteobagrus fulvidraco fed diets varying in oxidized fish oil and selenium levels. J Trace Elem Med Biol 2023; 79:127204. [PMID: 37244044 DOI: 10.1016/j.jtemb.2023.127204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/28/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Selenium (Se) functions through selenoproteins and is essential to growth and metabolism of vertebrates. The present study was conducted to identify twelve selenoproteins genes (selenoe, selenof, selenoh, selneoi, selenom, selenok, selneon, selenoo, selenot, selenos, selenou and msrb1) from yellow catfish. Their mRNA expression patterns, as well as their response to dietary oxidized fish oils and Se addition were explored. METHODS We use 3'and 5' RACE PCR to clone full-length cDNA sequence of twelve selenoprotein genes from yellow catfish. Their mRNA expression patterns were assessed via quantitative real-time PCR. Yellow catfish were fed diet adequate Se+ fresh fish oil, adequate Se+ oxidized fish oil, high Se+ fresh fish oil and high Se+ oxidized fish oil, respectively, for 10 weeks. Their kidney, heart, brain and testis were used to assess the mRNA expression of twelve selenoprotein. RESULTS Twelve selenoprotein genes had similar domains with mammals and the other fish. Their mRNAs were expressed widely in eleven tissues but varied with the tissues. Dietary oxidized fish oils and Se addition influenced their mRNA abundances of twelve selenoproteins in a tissue-dependent manner. CONCLUSION Our study demonstrated the characterization and expression of twelve selenoproteins, and elucidated their responses in yellow catfish fed diets varying in oxidized fish oils and Se addition, which increased our knowledge into the biological function and regulatory mechanism of Se and selenoproteins in fish.
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Affiliation(s)
- Jiang Ke
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Dian-Guang Zhang
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Xi-Jun Lei
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Guang-Hui Liu
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Zhi Luo
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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2
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Zhao Z, Mousa R, Metanis N. One-Pot Chemical Protein Synthesis Utilizing Fmoc-Masked Selenazolidine to Address the Redox Functionality of Human Selenoprotein F. Chemistry 2022; 28:e202200279. [PMID: 35112407 PMCID: PMC9304195 DOI: 10.1002/chem.202200279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/25/2022]
Abstract
Human SELENOF is an endoplasmic reticulum (ER) selenoprotein that contains the redox active motif CXU (C is cysteine and U is selenocysteine), resembling the redox motif of thiol-disulfide oxidoreductases (CXXC). Like other selenoproteins, the challenge in accessing SELENOF has somewhat limited its full biological characterization thus far. Here we present the one-pot chemical synthesis of the thioredoxin-like domain of SELENOF, highlighted by the use of Fmoc-protected selenazolidine, native chemical ligations and deselenization reactions. The redox potential of the CXU motif, together with insulin turbidimetric assay suggested that SELENOF may catalyze the reduction of disulfides in misfolded proteins. Furthermore, we demonstrate that SELENOF is not a protein disulfide isomerase (PDI)-like enzyme, as it did not enhance the folding of the two protein models; bovine pancreatic trypsin inhibitor and hirudin. These studies suggest that SELENOF may be responsible for reducing the non-native disulfide bonds of misfolded glycoproteins as part of the quality control system in the ER.
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Affiliation(s)
- Zhenguang Zhao
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Reem Mousa
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Norman Metanis
- Institute of ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
- The Center for Nanoscience and NanotechnologyThe Hebrew University of JerusalemJerusalem9190401Israel
- Casali Center for Applied ChemistryThe Hebrew University of JerusalemJerusalem9190401Israel
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3
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Rathore SS, Murthy HS, Girisha SK, Nithin MS, Nasren S, Mamun MAA, Puneeth TG, Rakesh K, Kumar BTN, Pai M. Supplementation of nano-selenium in fish diet: Impact on selenium assimilation and immune-regulated selenoproteome expression in monosex Nile tilapia (Oreochromis niloticus). Comp Biochem Physiol C Toxicol Pharmacol 2021; 240:108907. [PMID: 33027705 DOI: 10.1016/j.cbpc.2020.108907] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022]
Abstract
Selenium (Se), a fundamental element of nutrigenomic science in fish nutrition, was used to investigate its impact on selenoproteome expression and Se regulation in tilapia. Different concentrations (T1 - 0, T2 - 0.5, T3 - 1.0 and T4 - 2.0 mg/kg of feed) of dietary nano-Se were incorporated in the diets of monosex Nile tilapia. A total of 180 tilapia fingerlings with initial weight (15.73 ± 0.05 g) were stocked in 150 L capacity FRP tanks categorized into four diet groups with triplicate each for a feeding trial of 90 days. At the end of first, second and third months of the feeding trial, gill, liver, kidney and muscle tissues were harvested to evaluate the effect on the kinetics of Se bioaccumulation and assimilation as well as immune-regulated selenoprotein transcripts (GPx2, SelJ, SelL, SelK, SelS, SelW and Sepp1a) and their synthesis factors (SPS1 and Scly). The findings depicted that significantly (p < 0.05) higher weight gain was found in the diet supplemented with 1.0 mg/kg of nano-Se. The theory of second-order polynomial regression supported the same. The liver showed significantly (p < 0.05) higher Se accumulation and concentration factor among the harvested tissues in a different timeline. All the selected immune-regulated selenoproteins and synthesis factors in different fish tissues showed significantly (p < 0.05) up-regulation in the diet supplemented with 1.0 mg/kg of nano-Se for the second month. Therefore, the present findings suggested that the supplementation of nano-Se could be more effective for improved growth, better selenium regulation and expression of immune-regulated selenoproteins in the fish model.
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Affiliation(s)
- S S Rathore
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India.
| | - H S Murthy
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - S K Girisha
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - M S Nithin
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - S Nasren
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - M A A Mamun
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - T G Puneeth
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - K Rakesh
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
| | - B T N Kumar
- Department of Aquatic Environment, College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, Punjab, India
| | - M Pai
- Department of Aquaculture, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore 575002, Karnataka, India
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Yim SH, Everley RA, Schildberg FA, Lee SG, Orsi A, Barbati ZR, Karatepe K, Fomenko DE, Tsuji PA, Luo HR, Gygi SP, Sitia R, Sharpe AH, Hatfield DL, Gladyshev VN. Role of Selenof as a Gatekeeper of Secreted Disulfide-Rich Glycoproteins. Cell Rep 2019; 23:1387-1398. [PMID: 29719252 PMCID: PMC9183203 DOI: 10.1016/j.celrep.2018.04.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/08/2018] [Accepted: 03/31/2018] [Indexed: 01/22/2023] Open
Abstract
Selenof (15-kDa selenoprotein; Sep15) is an endoplasmic reticulum (ER)-resident thioredoxin-like oxidoreductase that occurs in a complex with UDP-glucose:glycoprotein glucosyltransferase. We found that Selenof deficiency in mice leads to elevated levels of non-functional circulating plasma immunoglobulins and increased secretion of IgM during in vitro splenic B cell differentiation. However, Selenof knockout animals show neither enhanced bacterial killing capacity nor antigen-induced systemic IgM activity, suggesting that excess immunoglobulins are not functional. In addition, ER-to-Golgi transport of a target glycoprotein was delayed in Selenof knockout embryonic fibroblasts, and proteomic analyses revealed that Selenof deficiency is primarily associated with antigen presentation and ER-to-Golgi transport. Together, the data suggest that Selenof functions as a gatekeeper of immunoglobulins and, likely, other client proteins that exit the ER, thereby supporting redox quality control of these proteins.
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Affiliation(s)
- Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Frank A Schildberg
- Department of Microbiology and Immunobiology and Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Orsi
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milano, Italy
| | - Zachary R Barbati
- Department of Microbiology and Immunobiology and Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Kutay Karatepe
- Department of Pathology and Lab Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
| | - Dmitry E Fomenko
- Redox Biology Center and Computational Science Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Petra A Tsuji
- Department of Biological Sciences, Towson University, Towson, MD 21252, USA
| | - Hongbo R Luo
- Department of Pathology and Lab Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Roberto Sitia
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milano, Italy
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology and Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Dolph L Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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5
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Abstract
Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active center of selenoprotein is traditionally a terminal signal of protein translation. A gene assembly algorithm SelGenAmic has been constructed and presented in this chapter for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes from these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. The method based on the SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes.
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6
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Mariotti M. SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins. Methods Mol Biol 2018; 1661:3-16. [PMID: 28917033 DOI: 10.1007/978-1-4939-7258-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step. This chapter constitutes a practical guide to use SECISearch3 and Seblastian, which can be run via webservers at http://seblastian.crg.eu / or http://gladyshevlab.org/SelenoproteinPredictionServer/ .
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Affiliation(s)
- Marco Mariotti
- Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. .,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, Spain.
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7
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Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. Selenoprotein Gene Nomenclature. J Biol Chem 2016; 291:24036-24040. [PMID: 27645994 DOI: 10.1074/jbc.m116.756155] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.
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Affiliation(s)
- Vadim N Gladyshev
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, .,the Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
| | - Elias S Arnér
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Marla J Berry
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | | | - Elspeth A Bruford
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Raymond F Burk
- the Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Bradley A Carlson
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Sergi Castellano
- the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurent Chavatte
- the Centre International de Recherche en Infectiologie, CIRI, INSERM U1111, and CNRS/ENS UMR5308, 69007 Lyon, France
| | - Marcus Conrad
- the Helmholtz Zentrum München, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Paul R Copeland
- the Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Alan M Diamond
- the Department of Pathology, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Donna M Driscoll
- the Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Ana Ferreiro
- the Pathophysiology of Striated Muscles Laboratory, Unit of Functional and Adaptive Biology (BFA), University Paris Diderot, Sorbonne Paris Cité, BFA, UMR CNRS 8251, 75250 Paris, France.,the AP-HP, Centre de Référence Maladies Neuromusculaires Paris-Est, Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Leopold Flohé
- the Universidad de la República, Facultad de Medicina, Departamento de Bioquímica, 11800 Montevideo, Uruguay.,the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Fiona R Green
- the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Roderic Guigó
- the Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.,the Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Diane E Handy
- the Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Dolph L Hatfield
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - John Hesketh
- the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the The Medical School, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Peter R Hoffmann
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | - Arne Holmgren
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Robert J Hondal
- the Department of Biochemistry, University of Vermont, Burlington, Vermont 05405
| | - Michael T Howard
- the Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Kaixun Huang
- the Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China
| | - Hwa-Young Kim
- the Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 42415, South Korea
| | - Ick Young Kim
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Josef Köhrle
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Alain Krol
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | | | - Byeong Jae Lee
- the School of Biological Sciences, Seoul National University, Seoul 151-742, South Korea
| | - Byung Cheon Lee
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Xin Gen Lei
- the Department of Animal Science, Cornell University, Ithaca, New York 14853
| | - Qiong Liu
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
| | - Alain Lescure
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France.,the Centre National de la Recherche Scientifique, 75794 Paris, France
| | - Alexei V Lobanov
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Joseph Loscalzo
- the Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Matilde Maiorino
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Marco Mariotti
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - K Sandeep Prabhu
- the Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Margaret P Rayman
- the Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Sharon Rozovsky
- the Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Gustavo Salinas
- the Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, CP11600 Montevideo, Uruguay
| | - Edward E Schmidt
- the Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Lutz Schomburg
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Ulrich Schweizer
- the Rheinische Friedrich-Wilhelms Universität Bonn, Institut für Biochemie und Molekularbiologie, 53115 Bonn, Germany
| | - Miljan Simonović
- the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Roger A Sunde
- the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Petra A Tsuji
- the Department of Biological Sciences, Towson University, Towson, Maryland 21252, and
| | - Susan Tweedie
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Fulvio Ursini
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Philip D Whanger
- the Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, Oregon 97331
| | - Yan Zhang
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
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8
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Penglase S, Hamre K, Ellingsen S. Selenium prevents downregulation of antioxidant selenoprotein genes by methylmercury. Free Radic Biol Med 2014; 75:95-104. [PMID: 25064324 DOI: 10.1016/j.freeradbiomed.2014.07.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 01/05/2023]
Abstract
Selenium (Se) is an essential nutrient required by Se-dependent proteins, termed selenoproteins. The selenoprotein family is small but diverse and includes key proteins in antioxidant, redox signaling, thyroid hormone metabolism, and protein folding pathways. Methylmercury (MeHg) is a toxic environmental contaminant that affects seafood safety. Selenium can reduce MeHg toxicity, but it is unclear how selenoproteins are affected in this interaction. In this study we explored how Se and MeHg interact to affect the mRNA expression of selenoprotein genes in whole zebrafish (Danio rerio) embryos. Embryos were obtained from adult zebrafish fed MeHg with or without elevated Se in a 2×2 factorial design. The embryo mRNA levels of 30 selenoprotein genes were then measured. These genes cover most of the selenoprotein families, including members of the glutathione peroxidase (GPX), thioredoxin reductase, iodothyronine deiodinase, and methionine sulfoxide reductase families, along with selenophosphate synthetase 2 and selenoproteins H, J-P, T, W, sep15, fep15, and fam213aa. GPX enzyme activity and larval locomotor activity were also measured. We found that around one-quarter of the selenoprotein genes were downregulated by elevated MeHg. These downregulated genes were dominated by selenoproteins from antioxidant pathways that are also susceptible to Se-deficiency-induced downregulation. MeHg also decreased GPX activity and induced larval hypoactivity. Elevated Se partially prevented MeHg-induced disruption of selenoprotein gene mRNA levels, GPX activity, and larval locomotor activity. Overall, the MeHg-induced downregulation and subsequent rescue by elevated Se levels of selenogenes regulated by Se status suggest that Se deficiency is a contributing factor to MeHg toxicity.
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Affiliation(s)
- S Penglase
- National Institute of Nutrition and Seafood Research, NO-5817 Bergen, Norway; Department of Biology, University of Bergen, 5020 Bergen, Norway.
| | - K Hamre
- National Institute of Nutrition and Seafood Research, NO-5817 Bergen, Norway
| | - S Ellingsen
- National Institute of Nutrition and Seafood Research, NO-5817 Bergen, Norway
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9
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Labunskyy VM, Hatfield DL, Gladyshev VN. Selenoproteins: molecular pathways and physiological roles. Physiol Rev 2014; 94:739-77. [PMID: 24987004 DOI: 10.1152/physrev.00039.2013] [Citation(s) in RCA: 825] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Selenium is an essential micronutrient with important functions in human health and relevance to several pathophysiological conditions. The biological effects of selenium are largely mediated by selenium-containing proteins (selenoproteins) that are present in all three domains of life. Although selenoproteins represent diverse molecular pathways and biological functions, all these proteins contain at least one selenocysteine (Sec), a selenium-containing amino acid, and most serve oxidoreductase functions. Sec is cotranslationally inserted into nascent polypeptide chains in response to the UGA codon, whose normal function is to terminate translation. To decode UGA as Sec, organisms evolved the Sec insertion machinery that allows incorporation of this amino acid at specific UGA codons in a process requiring a cis-acting Sec insertion sequence (SECIS) element. Although the basic mechanisms of Sec synthesis and insertion into proteins in both prokaryotes and eukaryotes have been studied in great detail, the identity and functions of many selenoproteins remain largely unknown. In the last decade, there has been significant progress in characterizing selenoproteins and selenoproteomes and understanding their physiological functions. We discuss current knowledge about how these unique proteins perform their functions at the molecular level and highlight new insights into the roles that selenoproteins play in human health.
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Affiliation(s)
- Vyacheslav M Labunskyy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Dolph L Hatfield
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Seale LA, Gilman CL, Moorman BP, Berry MJ, Grau EG, Seale AP. Effects of acclimation salinity on the expression of selenoproteins in the tilapia, Oreochromis mossambicus. J Trace Elem Med Biol 2014; 28:284-92. [PMID: 24854764 PMCID: PMC4082732 DOI: 10.1016/j.jtemb.2014.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 01/06/2023]
Abstract
Selenoproteins are ubiquitously expressed, act on a variety of physiological redox-related processes, and are mostly regulated by selenium levels in animals. To date, the expression of most selenoproteins has not been verified in euryhaline fish models. The Mozambique tilapia, Oreochromis mossambicus, a euryhaline cichlid fish, has a high tolerance for changes in salinity and survives in fresh water (FW) and seawater (SW) environments which differ greatly in selenium availability. In the present study, we searched EST databases for cichlid selenoprotein mRNAs and screened for their differential expression in FW and SW-acclimated tilapia. The expression of mRNAs encoding iodothyronine deiodinases 1, 2 and 3 (Dio1, Dio2, Dio3), Fep15, glutathione peroxidase 2, selenoproteins J, K, L, M, P, S, and W, was measured in the brain, eye, gill, kidney, liver, pituitary, muscle, and intraperitoneal white adipose tissue. Gene expression of selenophosphate synthetase 1, Secp43, and selenocysteine lyase, factors involved in selenoprotein synthesis or in selenium metabolism, were also measured. The highest variation in selenoprotein and synthesis factor mRNA expression between FW- and SW-acclimated fish was found in gill and kidney. While the branchial expression of Dio3 was increased upon transferring tilapia from SW to FW, the inverse effect was observed when fish were transferred from FW to SW. Protein content of Dio3 was higher in fish acclimated to FW than in those acclimated to SW. Together, these results outline tissue distribution of selenoproteins in FW and SW-acclimated tilapia, and indicate that at least Dio3 expression is regulated by environmental salinity.
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Affiliation(s)
- Lucia A Seale
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
| | - Christy L Gilman
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Benjamin P Moorman
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
| | - Marla J Berry
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - E Gordon Grau
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
| | - Andre P Seale
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
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Roman M, Jitaru P, Barbante C. Selenium biochemistry and its role for human health. Metallomics 2014; 6:25-54. [DOI: 10.1039/c3mt00185g] [Citation(s) in RCA: 421] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Romagné F, Santesmasses D, White L, Sarangi GK, Mariotti M, Hübler R, Weihmann A, Parra G, Gladyshev VN, Guigó R, Castellano S. SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. Nucleic Acids Res 2013; 42:D437-43. [PMID: 24194593 PMCID: PMC3965025 DOI: 10.1093/nar/gkt1045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. In addition, we annotate the homologous genes containing cysteine (Cys) instead of Sec. Finally, we have surveyed genetic variation in the annotated genes in humans. We use exon capture and resequencing approaches to identify single-nucleotide polymorphisms in more than 50 human populations around the world. We thus present a detailed view of the genetic divergence of Sec- and Cys-containing genes in animals and their diversity in humans. The addition of these datasets into the second release of the database provides a valuable resource for addressing medical and evolutionary questions in selenium biology.
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Affiliation(s)
- Frédéric Romagné
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Jiang L, Ni J, Liu Q. Evolution of selenoproteins in the metazoan. BMC Genomics 2012; 13:446. [PMID: 22943432 PMCID: PMC3473315 DOI: 10.1186/1471-2164-13-446] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/20/2012] [Indexed: 11/10/2022] Open
Abstract
Background The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes. Result A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges. Conclusion Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.
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Affiliation(s)
- Liang Jiang
- College of Life Sciences, Shenzhen University, Shenzhen, 518060, Guangdong Province, PR, China
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Composition and evolution of the vertebrate and mammalian selenoproteomes. PLoS One 2012; 7:e33066. [PMID: 22479358 PMCID: PMC3316567 DOI: 10.1371/journal.pone.0033066] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 02/03/2012] [Indexed: 01/10/2023] Open
Abstract
Background Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24. Methodology/Principal Findings We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian (25 proteins) selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events), gene loss (10 events) and replacement of Sec with cysteine (12 events). We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2). Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes. Conclusions/Significance This analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.
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Chen H, Jiang L, Ni J, Liu Q, Zhang J. Bioinformatic prediction of selenoprotein genes in the dolphin genome. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-011-4970-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hauser-Davis RA, de Campos RC, Ziolli RL. Fish metalloproteins as biomarkers of environmental contamination. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2012; 218:101-123. [PMID: 22488605 DOI: 10.1007/978-1-4614-3137-4_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fish are well-recognized bioindicators of environmental contamination. Several recent proteomic studies have demonstrated the validity and value of using fish in the search and discovery of new biomarkers. Certain analytical tools, such as comparative protein expression analyses, both in field and lab exposure studies, have been used to improve the understanding of the potential for chemical pollutants to cause harmful effects. The metallomic approach is in its early stages of development, but has already shown great potential for use in ecological and environmental monitoring contexts. Besides discovering new metalloproteins that may be used as biomarkers for environmental contamination, metallomics can be used to more comprehensively elucidate existing biomarkers, which may enhance their effectiveness. Unfortunately, metallomic profiling for fish has not been explored, because only a few fish metalloproteins have thus far been discovered and studied. Of those that have, some have shown ecological importance, and are now successfully used as biomarkers of environmental contamination. These biomarkers have been shown to respond to several types of environmental contamination, such as cyanotoxins, metals, and sewage effluents, although many do not yet possess any known function. Examples of successes include MMPs, superoxide dismutases, selenoproteins, and iron-bound proteins. Unfortunately, none of these have, as yet, been extensively studied. As data are developed for them, valuable new information on their roles in fish physiology and in inducing environmental effects should become available.
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Affiliation(s)
- Rachel Ann Hauser-Davis
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marquês de São Vicente, 225, Gávea, CEP: 22453-900, Rio de Janeiro, RJ, Brazil.
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Yoshida S, Haratake M, Fuchigami T, Nakayama M. Selenium in Seafood Materials. ACTA ACUST UNITED AC 2011. [DOI: 10.1248/jhs.57.215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sakura Yoshida
- Graduate School of Biomedical Sciences, Nagasaki University
| | | | | | - Morio Nakayama
- Graduate School of Biomedical Sciences, Nagasaki University
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Mariotti M, Guigó R. Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics 2010; 26:2656-63. [PMID: 20861026 PMCID: PMC2958745 DOI: 10.1093/bioinformatics/btq516] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases. Results: We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queries to scan genomic sequences. Results of the scan are processed through a number of steps, to produce highly accurate predictions of selenoprotein genes with little or no human intervention. Selenoprofiles is a valuable tool for bioinformatic characterization of eukaryotic selenoproteomes, and can complement genome annotation pipelines. Availability and Implementation: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. The program is available at http://big.crg.cat/services/selenoprofiles. The predictions presented in this article are available through DAS at http://genome.crg.cat:9000/das/Selenoprofiles_ensembl. Contact:marco.mariotti@crg.es Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- M Mariotti
- Bioinformatics and genomics group, Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
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Jiang L, Liu Q, Ni J. In silico identification of the sea squirt selenoproteome. BMC Genomics 2010; 11:289. [PMID: 20459719 PMCID: PMC2874816 DOI: 10.1186/1471-2164-11-289] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 05/10/2010] [Indexed: 11/24/2022] Open
Abstract
Background Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins. Results A gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA) was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before. Conclusion The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.
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Affiliation(s)
- Liang Jiang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, PR China
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Lobanov AV, Hatfield DL, Gladyshev VN. Eukaryotic selenoproteins and selenoproteomes. Biochim Biophys Acta Gen Subj 2009; 1790:1424-8. [PMID: 19477234 DOI: 10.1016/j.bbagen.2009.05.014] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/08/2009] [Accepted: 05/19/2009] [Indexed: 11/19/2022]
Abstract
Selenium is an essential trace element for which both beneficial and toxic effects in human health have been described. It is now clear that the importance of having adequate amounts of this micronutrient in the diet is primarily due to the fact that selenium is required for biosynthesis of selenocysteine, the twenty first naturally occurring amino acid in protein. In this review, we provide an overview of eukaryotic selenoproteins and selenoproteomes, which are sets of selenoproteins in these organisms. In eukaryotes, selenoproteins show a mosaic occurrence, with some organisms, such as vertebrates and algae, having dozens of these proteins, while other organisms, such as higher plants and fungi, having lost all selenoproteins during evolution. We also discuss selenoprotein functions and evolutionary trends in the use of these proteins in eukaryotes. Functional analysis of selenoproteins is critical for better understanding of the role of selenium in human health and disease.
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Affiliation(s)
- Alexey V Lobanov
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
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Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol 2008; 8:R198. [PMID: 17880704 PMCID: PMC2375036 DOI: 10.1186/gb-2007-8-9-r198] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 09/18/2007] [Accepted: 09/19/2007] [Indexed: 12/23/2022] Open
Abstract
In silico and metabolic labeling studies of the selenoproteomes of several eukaryotes revealed distinct selenoprotein patterns as well as an ancient origin of selenoproteins and massive, independent losses in land plants, fungi, nematodes, insects and some protists, suggesting that the environment plays an important role in selenoproteome evolution. Background Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all. Results We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified by metabolic labeling of O. tauri and D. discoideum with 75Se. More than half of the selenoprotein families were shared by unicellular eukaryotes and mammals, consistent with their ancient origin. Further analyses identified massive, independent selenoprotein losses in land plants, fungi, nematodes, insects and some protists. Comparative analyses of selenoprotein-rich and -deficient organisms revealed that aquatic organisms generally have large selenoproteomes, whereas several groups of terrestrial organisms reduced their selenoproteomes through loss of selenoprotein genes and replacement of Sec with cysteine. Conclusion Our data suggest many selenoproteins originated at the base of the eukaryotic domain and show that the environment plays an important role in selenoproteome evolution. In particular, aquatic organisms apparently retained and sometimes expanded their selenoproteomes, whereas the selenoproteomes of some terrestrial organisms were reduced or completely lost. These findings suggest a hypothesis that, with the exception of vertebrates, aquatic life supports selenium utilization, whereas terrestrial habitats lead to reduced use of this trace element due to an unknown environmental factor.
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Affiliation(s)
- Alexey V Lobanov
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Dmitri E Fomenko
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Yan Zhang
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Aniruddha Sengupta
- Section on the Molecular Biology of Selenium, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dolph L Hatfield
- Section on the Molecular Biology of Selenium, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vadim N Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
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Biochemical analysis of selenoprotein expression in brain cell lines and in distinct brain regions. Cell Tissue Res 2008; 332:403-14. [DOI: 10.1007/s00441-008-0575-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
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Wessjohann LA, Schneider A, Abbas M, Brandt W. Selenium in chemistry and biochemistry in comparison to sulfur. Biol Chem 2008; 388:997-1006. [PMID: 17937613 DOI: 10.1515/bc.2007.138] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
What makes selenoenzymes--seen from a chemist's view--so special that they cannot be substituted by just more analogous or adapted sulfur proteins? This review compiles and compares physicochemical properties of selenium and sulfur, synthetic routes to selenocysteine (Sec) and its peptides, and comparative studies of relevant thiols and selenols and their (mixed) dichalcogens, required to understand the special role of selenium in selenoproteins on the atomic molecular level. The biochemically most relevant differences are the higher polarizability of Se- and the lower pKa of SeH. The latter has a strikingly different pH-dependence than thiols, with selenols being active at much lower pH. Finally, selected typical enzymatic mechanisms which involve selenocysteine are critically discussed, also in view of the authors' own results.
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Affiliation(s)
- Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany.
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Shchedrina VA, Novoselov SV, Malinouski MY, Gladyshev VN. Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif. Proc Natl Acad Sci U S A 2007; 104:13919-24. [PMID: 17715293 PMCID: PMC1955791 DOI: 10.1073/pnas.0703448104] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Indexed: 11/18/2022] Open
Abstract
Selenocysteine (Sec, U) insertion into proteins is directed by translational recoding of specific UGA codons located upstream of a stem-loop structure known as Sec insertion sequence (SECIS) element. Selenoproteins with known functions are oxidoreductases containing a single redox-active Sec in their active sites. In this work, we identified a family of selenoproteins, designated SelL, containing two Sec separated by two other residues to form a UxxU motif. SelL proteins show an unusual occurrence, being present in diverse aquatic organisms, including fish, invertebrates, and marine bacteria. Both eukaryotic and bacterial SelL genes use single SECIS elements for insertion of two Sec. In eukaryotes, the SECIS is located in the 3' UTR, whereas the bacterial SelL SECIS is within a coding region and positioned at a distance that supports the insertion of either of the two Sec or both of these residues. SelL proteins possess a thioredoxin-like fold wherein the UxxU motif corresponds to the catalytic CxxC motif in thioredoxins, suggesting a redox function of SelL proteins. Distantly related SelL-like proteins were also identified in a variety of organisms that had either one or both Sec replaced with Cys. Danio rerio SelL, transiently expressed in mammalian cells, incorporated two Sec and localized to the cytosol. In these cells, it occurred in an oxidized form and was not reducible by DTT. In a bacterial expression system, we directly demonstrated the formation of a diselenide bond between the two Sec, establishing it as the first diselenide bond found in a natural protein.
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Affiliation(s)
| | | | | | - Vadim N. Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664
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