A Method for Identification of Selenoprotein Genes in Archaeal Genomes

Genomics, Proteomics and Bioinformatics

Volumn 7, Issue 1-2, 2009, Pages 62-70

  Li, Mingfeng ^a   Huang, Yanzhao ^a   Xiao, Yi ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

archaea; gene prediction; SECIS; SelB; selenocysteine; selenoprotein

Indexed keywords

SELENOCYSTEINE; SELENOPROTEIN;

ANALYTIC METHOD; ARCHAEAL GENE; ARCHAEAL GENOME; ARTICLE; COMPUTER ANALYSIS; GENE IDENTIFICATION; METHANOSARCINA; METHANOSARCINA ACETIVORANS; NUCLEOTIDE SEQUENCE; PREDICTION;

AMINO ACID SEQUENCE; ARCHAEA; GENOME, ARCHAEAL; GENOMICS; METHANOSARCINA; MOLECULAR SEQUENCE DATA; SELENOPROTEINS; SEQUENCE ALIGNMENT;

ARCHAEA; METHANOSARCINA ACETIVORANS;

EID: 67649635453     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(08)60034-0     Document Type: Article

References (41)

1. Chambers I., et al. The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the "termination" codon, TGA. EMBO J. 5 (1986) 1221-1227
2. Low S.C., and Berry M.J. Knowing when not to stop: selenocysteine incorporation in eukaryotes. Trends Biochem. Sci. 21 (1996) 203-208
3. Atkins J.F., and Gesteland R.F. The twentyfirst amino acid. Nature 407 (2000) 463-465
4. Ibba M., and Söl D. Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev. 18 (2004) 731-738
5. Berry M.J. Knowing when not to stop. Nat. Struct. Mol. Biol. 12 (2005) 389-390
6. Srinivasan G., et al. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296 (2002) 1459-1462
7. Hao B., et al. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296 (2002) 1462-1466
8. Borodovsky M., and McIninc J. GeneMark: parallel gene recognition for both DNA strands. Comput. Chem. 17 (1993) 123-133
9. Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
10. Lukashin A.V., and Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26 (1998) 1107-1115
11. Delcher A.L., et al. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27 (1999) 4636-4641
12. Castellano S., et al. In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep. 2 (2001) 697-702
13. Hüttenhofe A., et al. Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SELB. RNA 2 (1996) 354-366
14. Fourmy D., et al. Structure of prokaryotic SE-CIS mRNA hairpin and its interaction with elongation factor SelB. J. Mol. Biol. 324 (2002) 137-150
15. Driscoll D.M., and Copeland P.R. Mechanism and regulation of selenoprotein synthesis. Annu. Rev. Nutr. 23 (2003) 17-40
16. Liu Z., et al. The nature of the minimal 'selenocysteine insertion sequence' (SECIS) in Escherichia coli. Nucleic Acids Res. 26 (1998) 896-902
17. Zhang Y., and Gladyshev V.N. An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics 21 (2005) 2580-2589
18. Berry M.J., et al. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untraslated region. Nature 353 (1991) 273-276
19. Walczak R., et al. A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs. RNA 2 (1996) 367-379
20. Wilting R., et al. Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion. J. Mol. Biol. 266 (1997) 637-641
21. Fagegaltier D., et al. Structural analysis of new local features in SECIS RNA hairpins. Nucleic Acids Res. 28 (2000) 2679-2689
22. Kryukov G.V., et al. Characterization of mammalian selenoproteomes. Science 300 (2003) 1439-1443
23. Kryukov G.V., and Gladyshev V.N. The prokaryotic selenoproteome. EMBO Rep. 5 (2004) 538-543
24. Zhang Y., et al. The microbial selenoproteome of the Sargasso Sea. Genome Biol. 6 (2005) R37
25. Böc A. Biosynthesis of selenoproteins-an overview. Biofactors 11 (2000) 77-78
26. Rother M., et al. Selenoprotein synthesis in archaea. Biofactors 14 (2001) 75-83
27. Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31 (2003) 3429-3431
28. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
29. Hofacker I.L. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125 (1994) 167-188
30. Lambert A., et al. A survey of metazoan selenocysteine insertion sequences. Biochime 84 (2002) 953-959
31. Gladyshev V.N., and Kryukov G.V. Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. Biofactors 14 (2001) 87-92
32. Chivers P.T., et al. The CXXC motif: imperatives for the formation of native disulfide bonds in the cell. EMBO J. 15 (1996) 2659-2667
33. Fomenko D.E., and Gladyshev V.N. Identity and functions of CxxC-derived motifs. Biochemistry 42 (2003) 11214-11225
34. Moutevelis E., and Warwicker J. Prediction of pKa and redox properties in the thioredoxin superfamily. Protein Sci. 13 (2004) 2744-2752
35. Baron C., and Böc A. The length of the aminoacyl-acceptor stem of the selenocysteine-specific tRNA(Sec) of Escherichia coli is the determinant for binding to elongation factors SELB or Tu. J. Mol. Biol. 266 (1991) 20375-20379
36. Kawashima T., et al. The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5Å resolution. Nature 379 (1996) 511-518
37. Kromayer M., et al. Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J. Mol. Biol. 262 (1996) 413-420
38. Rother M., et al. Identification and characterisation of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschii. J. Mol. Biol. 299 (2000) 351-358
39. Fagegaltier D., et al. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. EMBO J. 19 (2000) 4796-4805
40. Copeland P.R., et al. A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs. EMBO J. 19 (2000) 306-314
41. Fletcher J.E., et al. The selenocysteine incorporation machinery: interactions between the SECIS RNA and the SECIS-binding protein SBP2. RNA 7 (2001) 1442-1453