Abstract
Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Low S C, Berry M J. Knowing when not to stop: Selenocysteine incorporation in eukaryotes. Trends Biochem Sci, 1996, 21: 203–208
Stadman T C. Selenocysteine. Annu Rev Biochem, 1996, 65: 83–100
Liu Q, Jiang L, Tian J, et al. The molecular biology of selenoproteins and their effects on diseases. Prog Chem, 2009, 21: 819–830
Kryukov G V, Kryukov V M, Gladyshev V N. New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J Biol Chem, 1999, 274: 33888–33897
Castellano S, Morozova N, Morey M, et al. Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution. Embo Rep, 2004, 5: 71–77
Novoselov S V, Hua D, Lobanov A V, et al. Identification and characterization of Fep15, a new selenocys-teine-containing member of the Sep15 protein family. Biochem J, 2006, 394: 575–579
Korotkov K V, Novoselov S V, Hatfield D L, et al. Mammalian selenoprotein in which selenocysteine (Sec) in-corporation is supported by a new form of sec insertion sequence element. Mol Cell Biol, 2002, 22: 1402–1411
Kryukov G V, Chapple C, Gladyshev V N. Selenium metabolism in zebrafish: Multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residues. Genes Cells, 2000, 5: 1049–1060
Zhang Y, Gladyshev V N. An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics, 2005, 21: 2580–2589
Kryukov G V, Castellano S, Novoselov S V, et al. Characterization of mammalian selenoproteomes. Science, 2003, 300: 1439–1443
Zhang Y, Gladyshev V N. Trends in selenium utilization in marine microbial world revealed through the analysis of the Global Ocean Sampling (GOS) Project. PLoS Genet, 2008, 4: e1000095
Jiang L, Liu Q, Ni J. In silico identification of the sea squirt selenoproteome. BMC Genomics, 2010, 11: 289
Lobanov A V, Fomenko D E, Zhang Y, et al. Evolutionary dynamics of eukaryotic selenoproteomes: Large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol, 2007, 8: R198
Jiang L, Liu Q, Chen P, et al. New selenoproteins identified in silico from the genome of Anopheles gambiae. Sci China Ser C Life Sci, 2007, 50: 251–257
Taskov K, Chapple C, Kryukov G V, et al. Nematode selenoproteome: The use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res, 2005, 33: 2227–2238
Tujebajeva R M, Harney J W, Berry M J. Selenoprotein P expression, purification, and immunochemical characterization. J Biol Chem, 2000, 275: 6288–6294
Shchedrina V A, Novoselov S V, Malinouski M Y, et al. Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif. Proc Natl Acad Sci USA, 2007, 104: 13919–13924
Erfurt J, Averianov A. Enigmatic ungulate-like mammals from the eocene of central Asia. Naturwissen-Schafien, 2005, 92: 182–187
Price S A, Bininda-Emonds O R, Gittleman J L. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biol Rev, 2005, 80: 445–473
Author information
Authors and Affiliations
Corresponding author
Additional information
These authors contributed equally to the work.
This article is published with open access at Springerlink.com
Rights and permissions
This article is published under an open access license. Please check the 'Copyright Information' section either on this page or in the PDF for details of this license and what re-use is permitted. If your intended use exceeds what is permitted by the license or if you are unable to locate the licence and re-use information, please contact the Rights and Permissions team.
About this article
Cite this article
Chen, H., Jiang, L., Ni, J. et al. Bioinformatic prediction of selenoprotein genes in the dolphin genome. Chin. Sci. Bull. 57, 1533–1541 (2012). https://doi.org/10.1007/s11434-011-4970-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11434-011-4970-5