Abstract
Selenoproteins are widely distributed in prokaryotes and eukaryotes. The catalytic site of selenoproteins is selenocysteine (Sec) encoded by a traditional stop codon UGA. The dual functions of UGA as either a stop signal or encoding a Sec residue result in difficulty in the prediction of selenoproteins via bioinformatics. General programs for gene analysis fail to correctly assign the TGA function, leading to the mis-annotation of selenoproteins in the released genomic sequences. Recently, several methods have been developed for in silico identification of selenoproteins from genomic sequences, including the search for SECIS elements, re-analysis of selenoprotein coding regions, and local sequence alignment for Sec/Cys pairs. Application of those methods has made a great achievement in discovering new selenoproteins and identifying selenoproteomes in a variety of organisms. In addition, it also accelerates other selenoprotein-related researches, such as the analysis of selenoprotein evolution, identification of catalytic cysteine residues, study on dual-functional genetic codes and setup of selenoprotein databases. The fast growing results from the bioinformatics of selenoproteins not only help us to obtain insights into global trends of selenium utilization and distribution in life systems and the environment, but also provide theoretical bases for the discovery and design of new drugs against cancer and other diseases.
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References
Fu LH, Wang XF, Eyal Y, She YM, Donald LJ, Standing KG, Ben-Hayyim G (2002) J Biol Chem 277: 259983
Kryukov GV, Castellano S, Novoselov SV, Lobanov A, Zehtab O, Guigo R, Gladyshev VN (2003) Science 300: 1439
Kryukov GV, Gladyshev VN (2004) EMBO Rep 5: 538
Lobanov AV, Gromer S, Salinas G, Gladyshev VN (2006) Nucleic Acids Res 34: 4012
Zhang Y, Romero H, Salinas G, Gladyshev VN (2006) Genome Biol 7: R94
Gursinsky T, Gröbe D, Schierhorn A, Jäger J, Andreesen JR, Söhling B (2008) Appl Environ Microb 74(5): 1385
Hatfield DL, Berry MJ, Gladyshev VN (eds) (2006) Selenium. Its Molecular Biology and Role in Human Health. 2nd ed., Springer Science Business Media, LLC
Böck A (2000) Biofactors 11: 77
Burge CB, Karlin S (1997) J Mol Biol 268: 78
Salamov A, Solovyev V (2000) Genome Res 10: 516
Parra G, Blanco E, Guigo R (2000) Genome Res 10: 511
Castellano S, Morozova N, Morey M, Berry MJ, Serras F, Corominas M, Guigo R (2001) EMBO Rep 2: 697
Novoselov SV, Rao M, Onoshko NV, Zhi H, Kryukov GV, Xiang Y (2002) EMBO J 21: 3681
Taskov K, Chapple C, Kryukov GV, Castellano S, Lobanov AV, Korotkov KV, Guigo R, Gladyshev VN (2005) Nucleic Acids Res 33: 2227
Novoselov SV, Hua D, Lobanov AV, Gladyshev VN (2006) Biochem J 394: 575
Zhang Y, Gladyshev VN (2008) PLoS Genetics 4: e1000095
Kim HY, Zhang Y, Lee BC, Kim JR, Gladyshe VN (2009) Proteins 74: 1008
Papp LV, Wang J, Kennedy D, Boucher D, Zhang Y, Gladyshev VN, Singh RN, Khanna KK (2008) Nucleic Acids Res 36: 7192
Hatfield DL, Gladyshev VN (2002) Mol Cell Biol 22: 3565
Rother M, Resch A, Wilting R, Bock A (2001) Biofactors 14: 75
Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD, Harney JW, Larsen PR (1991) Nature 353:273
Berry MJ, Banu L, Harney JW, Larsen PR (1993) EMBO J 12: 3315
Howard MT, Aggarwal G, Anderson CB, Khatri S, Flanigan KM, Atkins JF (2005) EMBO J 24: 1596
Howard MT, Moyle MW, Aggarwal G, Carlson BA, Anderson CB (2007) RNA 13: 912
Lee BJ, Worland PJ, Davis JN, Stadtman TC, Hatfield DL (1989) J Biol Chem 264: 9724
Papp LV, Lu J, Holmgren A, Khanna KK (2007) Antioxid Redox Signal 9: 775
Copeland PR, Driscoll DM (1999) J Biol Chem 274: 25447
Copeland PR, Fletcher JE, Carlson BA, Hatfield DL, Driscoll DM (2000) EMBO J 19: 306
Fagegaltier D, Hubert N, Yamada K, Mizutani T, Carbon P, Krol A (2000) EMBO J 19: 4796
Tujebajeva RM, Copeland PR, Xu XM, Carlson BA, Harney JW, Driscoll DM, Hatfield DL, Berry MJ (2000) EMBO Rep 1: 158
Chavatte L, Brown BA, Driscoll DM (2005) Nat Struct Mol Biol 12: 408
Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL (2007) PLoS Biol 5: e4
Kryukov GV, Kryukov VM, Gladyshev VN (1999) J Biol Chem 274: 33888
Korotkov KV, Novoselov SV, Hatfield DL, Gladyshev VN (2002) Mol Cell Biol 22: 1402
Zhang Y, Gladyshev VN (2005) Bioinformatics 21: 2580
Staden R (1984) Nucleic Acids Res 12: 505
Lambert A, Lescure A, Gautheret D (2002) Biochimie 84: 953
Chapple CE, Guigó R, Krol A (2009) Bioinformatics 25: 674
Busch A, Will S, Backofen R (2005) Bioinformatics 21: 3312
Castellano S, Novoselov SV, Roderic G, et al. (2004) EMBO rep 5: 71
Jiang L, Liu Q, Ni J (2010) BMC genomics 11: 289
Chaudhuri BN, Yeates TO (2005) Genome Biol 6: R79
Fujita M, Mihara H, Goto S, et al. (2007) BMC Bioinformatics 8: 225
Zhang Y, Fomenko DE, Gladyshev VN (2005) Genome Biol 6: R37
Lobanov AV, Fomenko DE, Zhang Y (2007) Genome Biol 8: R198
Lobanov AV, Hatfield DL, Gladyshev VN (2008) Genome Biol 9: R62
Chapple CE, Guigó R (2008) PLoS ONE 3: e2968
Karol KG, McCourt RM, Cimino MT, Delwiche CF (2001) Science 294: 2351
Castellano S, Novoselov SV, Kryukov GV, Lescure A, Blanco E, Krol A, Gladyshev VN, Guigó R (2004) EMBO Rep 5: 71
Fomenko DE, Xing W, Adair BM, Thomas DJ, Gladyshev VN (2007) Science 315: 387
Lobanov AV, Kryukov GV, Hatfield DL, Gladyshev VN (2006) Trends Genet 22: 357
Fujita M, Mihara H, Goto S, Esaki N, Kanehisa M (2007) BMC Bioinformatics 8: 225
Atkins JF, Baranov PV (2007) Nature 448: 1004
Castellano S, Gladyshev VN, Guigó R, Berry MJ (2008) Nucleic Acids Res 36: D332
Miao J, Lu F (2006) Computer and Digital Engineering 34: 1 (in Chinese)
Lu F, L ZD, Xiao Y (2006) Mini-micro Systems 7: 492 (in Chinese)
Zhang G, Gong H, Lu Q, Zeng S, Luo Q (2004) Space Medicine and Medical Engineering 17: 64 (in Chinese)
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© 2011 Zhejiang University Press, Hangzhou and Springer-Verlag Berlin Heidelberg
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Liu, Q., Jiang, L. (2011). Bioinformatics of Selenoproteins. In: Selenoproteins and Mimics. Advanced Topics in Science and Technology in China. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22236-8_9
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DOI: https://doi.org/10.1007/978-3-642-22236-8_9
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