Evolutionarily different RNA motifs and RNA-protein complexes to achieve selenoprotein synthesis

Biochimie

Volumn 84, Issue 8, 2002, Pages 765-774

  Krol, Alain ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

RNA structure; SBP2; SECIS RNA; SECIS binding proteins; SelB; Selenium; Selenocysteine

Indexed keywords

BINDING PROTEIN; MESSENGER RNA; PROTEIN; RNA; SELENOCYSTEINE; SELENOPROTEIN; ELONGATION FACTOR; RNA BINDING PROTEIN;

3' UNTRANSLATED REGION; ARCHAEBACTERIUM; CHEMICAL STRUCTURE; COMPLEX FORMATION; EUBACTERIUM; EUKARYOTE; EVOLUTION; GENE INSERTION SEQUENCE; NONHUMAN; PROTEIN MOTIF; PROTEIN SYNTHESIS; REVIEW; SEQUENCE ANALYSIS; STOP CODON; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION; TRANSLATION REGULATION; CHEMISTRY; CODON; CONFORMATION; EUKARYOTIC CELL; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

BASE SEQUENCE; CODON; CONSERVED SEQUENCE; EUBACTERIUM; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE ELONGATION FACTORS; PROTEIN BIOSYNTHESIS; PROTEINS; RNA; RNA-BINDING PROTEINS; SELENOCYSTEINE; SELENOPROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0036703297     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(02)01405-0     Document Type: Article

References (67)

1. L. Flohé, J.R. Andreesen, R. Brigelius-Flohé, M. Maiorino, F. Ursini, Selenium, the element of the Moon, in life on Earth, Life 49 (2000) 411-420.
2. G.V. Kryukov, V.N. Gladyshev, Selenium metabolism in zebrafish: multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residues, Genes to Cells 5 (2000) 1049-1060.
3. J. Köhrle, R. Brigelius-Flohé, A. Böck, R. Gärtner, O. Meyer, L. Flohé, Selenium in biology: facts and medical perspectives, Biol. Chem. 381 (2000) 849-864.
4. M. Hirosawa-Takamori, H. Jäckle, G. Vorbrüggen, The class 2 selenophosphate synthetase gene of Drosophila contains a functional mammalian-type SECIS, EMBO Rep. 1 (2000) 441-446.
5. F.J. Martin-Romero, G. Kryukov, A.V. Lobanov, B.A. Carlson, B.J. Lee, V.N. Gladyshev, D.L. Hatfield, Selenium metabolism in Drosophila, J. Biol. Chem. 276 (2001) 29798-29804.
6. S. Castellano, N. Morozova, M. Morey, M.J. Berry, F. Serras, M. Corominas, R. Guigo, In silico identification of novel selenoproteins in the Drosophila melanogaster genome, EMBO Rep. 2 (2001) 697-702.
7. F. Ursini, S. Heim, M. Kiess, M. Maiorino, A. Roveri, J. Wissing, L. Flohé, Dual function of the selenoprotein PHGPx during sperm maturation, Science 285 (1999) 1393-1396.
8. H. Pfeifer, M. Conrad, D. Roethlein, A. Kyriakopoulos, M. Brielmeier, G.W. Bornkamm, D. Behne, Identification of a specific sperm nuclei selenoenzyme necessary for protamine thiol cross-linking during sperm maturation, FASEB J. 15 (2001) 1236-1238.
9. B. Moghadaszadeh, N. Petit, C. Jaillard, M. Brockington, S. Quijano-Roy, L. Merlini, N. Romero, B. Estournet, I. Desguerre, D. Chaigne, F. Muntoni, H. Topaloglu, P. Guicheney, Mutations in SEPN1 cause congenital muscular dystrophy with spinal rigidity and restrictive respiratory syndrome, Nature Gen. 29 (2001) 17-18.
10. F. Zinoni, A. Birkmann, T.C. Stadtman, A. Böck, Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate-dehydrogenase from E. coli, Proc. Natl. Acad. Sci. USA 83 (1986) 4560-4564.
11. B.L. Berg, C. Baron, V. Stewart, Nitrate-inducible formate dehydrogenase in E. coli K12. II. Evidence that a mRNA stem-loop structure is essential for decoding opal (UGA) as selenocysteine, J. Biol. Chem. 33 (1991) 22386-22391.
12. G. Sawers, J. Heider, E. Zehelein, A. Böck, Expression and operon structure of the sel genes of E. coli and identification of a third selenium-containing formate dehydrogenase isoenzyme, J. Bact. 173 (1991) 4983-4993.
13. J. Heider, K. Forchhammer, G. Sawers, A. Böck, Interspecies compatibility of selenoprotein biosynthesis in Enterobacteriaceae, Arch. Microbiol. 155 (1991) 221-228.
14. N.K. Menon, H.D. Peck, J. LeGall, A.E. Przybyala, Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFeSe] hydrogenase of Desulfovibrio baculatus, J. Bact. 169 (1987) 5401-5407.
15. G.E. Garcia, T.C. Stadtman, Selenoprotein A component of the glycine reductase complex from Clostridium purinolyticum: nucleotide sequence of the genes shows that selenocysteine is encoded by UGA, J. Bact. 173 (1991) 2093-2098.
16. T. Gursinsky, J. Jäger, J.R. Andreesen, B. Söhling, A selDABC cluster for selenocysteine incorporation in Eubacterium acidaminophilum, Arch. Microbiol. 174 (2000) 200-212.
17. M. Thanbichler, A. Böck, Functional analysis of prokaryotic SelB proteins, BioFactors 14 (2001) 53-59.
18. A. Lescure, D. Fagegaltier, P. Carbon, A. Krol, Protein factors mediating selenoprotein synthesis, Curr. Prot. Pept. Sci. 3 (2002) 143-151.
19. C. Baron, J. Heider, A. Böck, Mutagenesis of selC, the gene for the selenocysteine-inserting tRNA-species in E. coli: effects on in vivo function, Nucleic Acids Res. 18 (1990) 6761-6766.
20. F. Zinoni, J. Heider, A. Böck, Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine, Proc. Natl. Acad. Sci. USA 87 (1990) 4660-4664.
21. J. Heider, C. Baron, A. Böck, Coding from a distance: dissection of the mRNA determinants required for the incorporation of selenocysteine into protein, EMBO J. 11 (1992) 3759-3766.
22. A. Hüttenhofer, E. Westhof, A. Böck, Solution structure of mRNA hairpins promoting selenocysteine incorporation in E. coli and their base-specific interaction with special elongation factor SelB, RNA 2 (1996) 345-366.
23. A. Hüttenhofer, A. Böck, RNA structures involved in selenoprotein synthesis, in: R. Simons, M. Grunberg-Manago (Eds.), RNA Structure and Function, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1998, pp. 603-639.
24. G.F.T. Chen, L. Fang, M. Inouye, Effect of the relative position of the UGA codon to the unique secondary structure in the fdhF mRNA on its decoding by selenocysteyl tRNA in E. coli, J. Biol. Chem. 268 (1993) 23128-23131.
25. S. Kreimer, J.A. Andreesen, Glycine reductase of Clostridium litorale, Eur. J. Biochem. 234 (1995) 192-199.
26. R. Wilting, S. Schorling, B.C. Persson, A. Böck, Selenoprotein synthesis in Archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion, J. Mol. Biol. 266 (1997) 637-641.
27. M. Rother, A. Resch, W.L. Gardner, W.B. Whitman, A. Böck, Heterologous expression of archaeal selenoprotein genes by the SECIS element located in the 3′ non-translated region, Mol. Microbiol. 40 (2001) 900-908.
28. M.J. Berry, L. Banu, Y.Y. Chen, S.J. Mandel, J.D. Kieffer, J.W. Harney, P.R. Larsen, Recognition of UGA as a selenocysteine codon in type 1 deiodinase requires sequences in the 3′ terminal untranslated region, Nature 353 (1991) 273-276.
29. C. Buettner, J.W. Harney, P.R. Larsen, The 3′ untranslated region of human type 2 iodothyronine deiodinase mRNA contains a functional selenocysteine insertion sequence element, J. Biol. Chem. 273 (1998) 33374-33378.
30. M.J. Berry, L. Banu, J.W. Harney, P.R. Larsen, Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons, EMBO J. 12 (1993) 3315-3322.
31. Q. Shen, F.F. Chu, P.E. Newburger, Sequences in the 3′ untranslated region of the human cellular glutathione peroxidase gene are necessary and sufficient for selenocysteine incorporation at the UGA codon, J. Biol. Chem. 268 (1993) 11463-11469.
32. H. Kollmus, L. Flohé, J.E.G. McCarthy, Analysis of eukaryotic mRNA structures directing cotranslational incorporation of selenocysteine, Nucleic Acids Res. 24 (1996) 1195-1201.
33. G.W. Martin III, J.W. Harney, M.J. Berry, Selenocysteine incorporation in eukaryotes: insights into mechanism and efficiency from sequence, structure, and spacing proximity studies of the type 1 deiodinase SECIS element, RNA 2 (1996) 171-182.
34. Q. Shen, J.L. Leonard, P.E. Newburger, Structure and function of the selenium translation element in the 3′ untranslated region of human cellular glutathione peroxidase mRNA, RNA 1 (1995) 519-525.
35. R. Walczak, E. Westhof, P. Carbon, A. Krol, A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs, RNA 2 (1996) 367-379.
36. G.W. Martin III, J.W. Harney, M.J. Berry, Functionality of mutations at conserved nucleotides in eukaryotic SECIS elements is determined by the identity of a single nonconserved nucleotide, RNA 4 (1998) 65-73.
37. R. Walczak, P. Carbon, A. Krol, An essential non-Watson-Crick base pair motif in 3′ UTR to mediate selenoprotein translation, RNA 4 (1998) 74-84.
38. E. Grundner-Culemann, G.W. Martin, J.W. Harney, M.J. Berry, Two distinct SECIS structures capable of directing selenocysteine incorporation in eukaryotes, RNA 5 (1999) 625-635.
39. C. Buettner, J.W. Harney, M.J. Berry, The C. elegans homologue of thioredoxin reductase contains a SECIS element that differs from mammalian SECIS elements but directs selenocysteine incorporation, J. Biol. Chem. 274 (1999) 21598-21602.
40. D. Fagegaltier, A. Lescure, R. Walczak, P. Carbon, A. Krol, Structural analysis of new local features in SECIS RNA hairpins, Nucleic Acids Res. 28 (2000) 2679-2689.
41. K.V. Korotkov, S.V. Novoselov, D.L. Hatfield, V.N. Gladyshev, Mammalian selenoprotein in which selenocysteine incorporation is supported by a new form of Sec insertion sequence element, Mol. Cell. Biol. 22 (2002) 1402-1411.
42. T. Hermann, E. Westhof, Non-Watson-Crick base pairs in RNA-protein recognition, Chem. Biol. 6 (1999) R335-R343.
43. K.E. Hill, R.S. Lloyd, J.G. Yang, R. Read, R.F. Burk, The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame, J. Biol. Chem. 266 (1991) 10050-10053.
44. R.M. Tujebajeva, D.G. Ransom, J.W. Harney, M.J. Berry, Expression and characterization of nonmammalian selenoprotein P in the zebrafish, Danio rerio, Genes to Cells 5 (2000) 897-903.
45. A. Lescure, D. Gautheret, P. Carbon, A. Krol, Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif, J. Biol. Chem 274 (1999) 38147-38154.
46. G.V. Kryukov, V.M. Kryukov, V.N. Gladyshev, New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements, J. Biol. Chem. 274 (1999) 33888-33897.
47. A. Lescure, D. Gautheret, A. Krol, Novel selenoproteins identified from genomic sequence data, Methods Enzymol. 347 (2002) 57-70.
48. G.V. Kryukov, V.N. Gladyshev, Mammalian selenoprotein gene signature: identification and functional analysis of selenoprotein genes using bioinformatics methods, Methods Enzymol. 347 (2002) 84-100.
49. K. Forchhamer, W. Leinfelder, A. Böck, Identification of a novel translation factor necessary for the incorporation of selenocysteine into proteins, Nature 342 (1989) 453-456.
50. J.F. Atkins, A. Böck, S. Matsufuji, R.F. Gesteland, Dynamics of the genetic code, in: R.F. Gesteland, T.R. Cech, J.F. Atkins (Eds.), The RNA World, second ed, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1999, pp. 637-673.
51. D. Fagegaltier, P. Carbon, A. Krol, Distinctive features in the SelB family of elongation factors for selenoprotein synthesis. A glimpse of an evolutionary complexified translation apparatus, BioFactors 14 (2001) 5-10.
52. M. Kromayer, R. Wilting, P. Tormay, A. Böck, Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB, J. Mol. Biol. 262 (1996) 413-420.
53. C. Li, M. Reches, H. Engelberg-Kulka, The bulged nucleotide in the E. coli minimal selenocysteine insertion sequence SECIS participates in the interaction with SelB: a genetic approach, J. Bact. 182 (2000) 6302-6307.
54. M. Kromayer, B. Neuhierl, A. Friebel, A. Böck, Genetic probing of the interaction between the translation factor SelB and its mRNA binding element in E. coli, Mol. Gen. Genet. 262 (1999) 800-806.
55. S. Klug, A. Hüttenhofer, M. Kromayer, M. Famulok, In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB, Proc. Natl. Acad. Sci. USA 94 (1997) 6676-6681.
56. A. Hüttenhofer, A. Böck, Selenocysteine inserting RNA elements modulate GTP hydrolysis of elongation factor SelB, Biochem. 37 (1998) 885-890.
57. A. Hüttenhofer, J. Heider, A. Böck, Interaction of the E. coli fdhF mRNA hairpin promoting selenocysteine incorporation with the ribosome, Nucleic Acids Res. 24 (1996) 3903-3910.
58. D. Fagegaltier, N. Hubert, K. Yamada, T. Mizutani, P. Carbon, A. Krol, Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation, EMBO J. 19 (2000) 4796-4805.
59. R.M. Tujebajeva, P.R. Copeland, X.M. Xu, B.A. Carlson, J.W. Harney, D.M. Driscoll, D.L. Hatfield, M.J. Berry, Decoding apparatus for eukaryotic selenocysteine insertion, EMBO Rep. 1 (2000) 158-163.
60. M. Rother, R. Wilting, S. Commans, A. Böck, Identification and characterization of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschii, J. Mol. Biol. 299 (2000) 351-358.
61. P.R. Copeland, J.E. Fletcher, B.A. Carlson, D.L. Hatfield, D.M. Driscoll, A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs, EMBO J. 19 (2000) 306-314.
62. P.R. Copeland, V.A. Stepanik, D.M. Driscoll, Insight into mammalian selenocysteine insertion: domain structure and ribosome binding properties of Sec insertion sequence binding protein 2, Mol. Cell. Biol. 21 (2001) 1491-1498.
63. A. Lescure, C. Allmang, K. Yamada, P. Carbon, A. Krol, cDNA cloning, expression pattern and RNA binding analysis of human SECIS binding protein 2, Gene (2000) in press.
64. E.V. Koonin, P. Bork, C. Sander, A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? Nucleic Acids Res. 22 (1994) 2166-2167.
65. H. Mao, S.A. White, J.R. Williamson, A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex, Nature Struct. Biol. 6 (1999) 1139-1147.
66. J.E. Fletcher, P.R. Copeland, D.M. Driscoll, A. Krol, The selenocysteine incorporation machinery: interactions between the SECIS RNA and the SECIS-binding protein SBP2, RNA 7 (2001) 1442-1453.
67. V.N. Gladyshev, M. Krause, X.M. Xu, K.V. Korotkov, G.V. Kryukov, Q.A. Sun, B.J. Lee, J.C. Wootton, D.L. Hatfield, Selenocysteine-containing thioredoxin reductase in C. elegans, Biochem. Biophys. Res. Commun. 259 (1999) 244-249.