Nematode selenoproteome: The use of the selenocysteine insertion system to decode one codon in an animal genome?

Nucleic Acids Research

Volumn 33, Issue 7, 2005, Pages 2227-2238

  Taskov, Kalin ^b   Chapple, Charles ^a   Kryukov, Gregory V ^b   Castellano, Sergi ^a   Lobanov, Alexey V ^b   Korotkov, Konstantin V ^b   Guigó, Roderic ^a   Gladyshev, Vadim N ^b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; GUANOSINE; SELENOCYSTEINE; SELENOPROTEIN; THIOREDOXIN REDUCTASE; URACIL; CAENORHABDITIS ELEGANS PROTEIN; PROTEIN;

ARTICLE; CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; CODON; CONTROLLED STUDY; EVOLUTION; GENE INSERTION SEQUENCE; GENETIC ALGORITHM; GENETIC CODE; GENETIC CONSERVATION; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; AMINO ACID SEQUENCE; ANIMAL; GENETICS; GENOMICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEOMICS; REGULATORY RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALIA; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; EUKARYOTA; NEMATODA;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CODON; EVOLUTION, MOLECULAR; GENOMICS; MOLECULAR SEQUENCE DATA; NEMATODA; PROTEINS; PROTEOMICS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; SELENOCYSTEINE; SELENOPROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; THIOREDOXIN REDUCTASE (NADPH);

EID: 17644379382     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki507     Document Type: Article

References (40)

1. Atkins,J.F. and Gesteland,R.F. (2000) The twenty-first amino acid. Nature, 407, 463.
2. Bock,A. (2000) Biosynthesis of selenoproteins - an overview. Biofactors, 11, 77-78.
3. Hatfield,D.L. and Gladyshev,V.N. (2002) How selenium has altered our understanding of the genetic code. Mol. Cell. Biol., 22, 3565-3576.
4. Driscoll,D.M. and Copeland,P.R. (2003) Mechanism and regulation of selenoprotein synthesis. Annu. Rev. Nutr., 23, 17-40.
5. Zinoni,F., Heider,J. and Bock,A. (1990) Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc. Natl Acad. Sci. USA, 87, 4660-4664.
6. Berry,M.J., Banu,L., Chen,Y.Y., Mandel,S.J., Kieffer,J.D., Harney,J.W. and Larsen,P.R. (1991) Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature, 353, 273-276.
7. Heider,J., Baron,C. and Bock,A. (1992) Coding from a distance: dissection of the mRNA determinants required for the incorporation of selenocysteine into protein. EMBO Rep., 11, 3759-3766.
8. Low,S.C. and Berry,M.J. (1996) Knowing when not to stop: Selenocysteine incorporation in eukaryotes. Trends Biochem. Sci., 21, 203-208.
9. Copeland,P.R., Fletcher,J.E., Carlson,B.A., Hatfield,D.L. and Driscoll,D.M. (2000) A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs. EMBO Rep., 19, 306-314.
10. Tujebajeva,R.M., Copeland,P.R., Xu,X.M., Carlson,B.A., Harney,J.W., Driscoll,D.M., Hatfield,D.L. and Berry,M.J. (2000) Decoding apparatus for eukaryotic selenocysteine insertion. EMBO Rep., 1, 158-163.
11. Fagegaltier,D., Hubert,N., Yamada,K., Mizutani,T., Carbon,P. and Krol,A. (2000a) Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. EMBO Rep., 19, 4796-4805.
12. Novoselov,S.V., Rao,M., Onoshko,N.V., Zhi,H., Kryukov,G.V., Xiang,Y., Weeks,D.P., Hatfield,D.L. and Gladyshev,V.N. (2002) Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii. EMBO Rep., 21, 3681-3693.
13. Fu,L.H., Wang,X.F., Eyal,Y., She,Y.M., Donald,L.J., Standing,K.G. and Ben-Hayyim,G. (2002) A selenoprotein in the plant kingdom. Mass spectrometry confirms that an opal codon (UGA) encodes selenocysteine in Chlamydomonas reinhardtii glutathione peroxidase. J. Biol. Chem., 277, 25983-25991.
14. Castellano,S., Novoselov,S.V., Kryukov,G.V., Lescure,A., Blanco,E., Krol,A., Gladyshev,V.N. and Guigo,R. (2004) Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep., 5, 71-77.
15. Kryukov,G.V., Castellano,S., Novoselov,S.V., Lobanov,A.V., Zehtab,O., Guigo,R. and Gladyshev,V.N. (2003) Characterization of mammalian selenoproteomes. Science, 300, 1439-1443.
16. Salvatore,D., Harney,J.W. and Larsen,P.R. (1999) Mutation of the Secys residue 266 in human type 2 selenodeiodinase alters 75Se incorporation without affecting its biochemical properties. Biochimie, 81, 535-538.
17. Hill,K.E., Lloyd,R.S. and Burk,R.F. (1993) Conserved nucleotide sequences in the open reading frame and 3′ untranslated region of selenoprotein P mRNA. Proc. Natl Acad. Sci. USA, 90, 537-541.
18. Castellano,S., Morozova,N., Morey,M., Berry,M.J., Serras,F., Corominas,M. and Guigo,R. (2001) In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep., 2, 697-702.
19. Martin-Romero,F.J., Kryukov,G.V., Lobanov,A.V., Carlson,B.A., Lee,B.J., Gladyshev,V.N. and Hatfield,D.L. (2001) Selenium metabolism in Drosophila: Selenoproteins, selenoprotein mRNA expression, fertility, and mortality. J. Biol. Chem., 276, 29798-29804.
20. Kryukov,G.V. and Gladyshev,V.N. (2000) Selenium metabolism in zebrafish: multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residues. Genes Cells, 5, 1049-1060.
21. Tujebajeva,R.M., Ransom,D.G., Harney,J.W. and Berry,M.J. (2000) Expression and characterization of nonmammalian selenoprotein P in the zebrafish, Danio rerio. Genes Cells, 5, 897-903.
22. Thisse,C., Degrave,A., Kryukov,G.V., Gladyshev,V.N., Obrecht-Pflumio,S., Krol,A., Thisse,B. and Lescure,A. (2003) Spatial and temporal expression patterns of selenoprotein genes during embryogenesis in zebrafish. Gene Expr. Patterns, 3, 525-532.
23. Gladyshev,V.N., Krause,M., Xu,X.M., Korotkov,K.V., Kryukov,G.V., Sun,Q.A., Lee,B.J., Wootton,J.C. and Hatfield,D.L. (1999) Selenocysteine-containing thioredoxinreductase in C.elegans. Biochem. Biophys. Res. Commun., 259, 244-249.
24. Buettner,C., Harney,J.W. and Berry,M.J. (1999) The Caenorhabditis elegans homologue of thioredoxin reductase contains a selenocysteine insertion sequence (SECIS) element that differs from mammalian SECIS elements but directs selenocysteine incorporation. J. Biol. Chem., 274, 21598-21602.
25. Kanzok,S.M., Fechner,A., Bauer,H., Ulschmid,J.K., Müller,H.M., Botella-Munoz,J., Schneuwly,S., Schirmer,R. and Becker,K. (2001) Substitution of the thioredoxin system for glutathione reductase in Drosophila melanogaster. Science, 291, 643-646.
26. Missirlis,F., Ulschmid,J.K., Hirosawa-Takamori,M., Grönke,S., Schäfer,U., Becker,K., Phillips,J.P. and Jäckle,H. (2002) Mitochondrial and cytoplasmic thioredoxin reductase variants encoded by a single Drosophila gene are both essential for viability. J. Biol. Chem., 277, 11521-11526.
27. C.elegans Sequencing Consortium. (1998) Genome sequence of the nematode C.elegans: A platform for investigating biologyScience, 282, 2012-2018.
28. Stein,L.D., Bao,Z., Blasiar,D., Blumenthal,T., Brent,M.R., Chen,N., Chinwalla,A., Clarke,L., Clee,C., Coghlan,A. et al. (2003) The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol., 1, E45.
29. Kryukov,G.V., Kryukov,V.M. and Gladyshev,V.N. (1999) New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J. Biol. Chem., 274, 33888-33897.
30. Lescure,A., Gautheret,D., Carbon,P. and Krol,A. (1999) Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif. J. Biol. Chem., 274, 38147-38154.
31. Parra,G., Blanco,E. and Guigo,R. (2000) GeneID in Drosophila. Genome Res., 10, 511-515.
32. Kryukov,G.V. and Gladyshev,V.N. (2004) The prokaryotic selenoproteome. EMBO Rep., 5, 538-543.
33. Arner,E.S., Sarioglu,H., Lottspeich,F., Holmgren,A. and Bock,A. (1999) High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the selA, selB and selC genes. J. Mol. Biol., 292, 1003-1016.
34. Arner,E.S. (2002) Recombinant expression of mammalian selenocysteine-containing thioredoxin reductase and other selenoproteins in Escherichia coli. Methods Enzymol., 347, 226-235.
35. Fagegaltier,D., Lescure,A., Walczak,R., Carbon,P. and Krol,A. (2000b) Structural analysis of new local features in SECIS RNA hairpins. Nucleic Acids Res., 28, 2679-2689.
36. Sun,Q.A., Kirnarsky,L., Sherman,S. and Gladyshev,V.N. (2001) Selenoprotein oxidoreductase with specificity for thioredoxin and glutathione systems. Proc. Natl Acad. Sci. USA, 98, 3673-3678.
37. Su,D. and Gladyshev,V.N. (2004) Alternative splicing involving the thioredoxin reductase module in mammals: A glutaredoxin-containing thioredoxin reductase 1. Biochemistry, 43, 12177-12188.
38. Salinas,G., Selkirk,M.E., Chalar,C., Maizels,R.M. and Fernandez,C. (2004) Linked thioredoxin-glutathione systems in platyhelminths. Trends Parasitol., 20, 340-346.
39. Gromer,S., Johansson,L., Bauer,H., Arscott,L.D., Rauch,S., Ballou,D.P., Williams,C.H.,Jr, Schirmer,R.H. and Arner,E.S. (2003) Active sites of thioredoxin reductases: Why selenoproteins? Proc. Natl Acad. Sci. USA, 100, 12618-12623.
40. Morell,V. (1996) TreeBASE: The roots of phylogeny. Science, 273, 569.