Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo

Nucleic Acids Research

Volumn 32, Issue 13, 2004, Pages 4081-4089

  Martin, Franck ^a   Barends, Sharief ^a,b   Eriani, Gilbert ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; ARGININE; ASPARTYL TRANSFER RNA LIGASE; BETA GALACTOSIDASE; GLUTAMIC ACID; TRANSFER RNA; UNCLASSIFIED DRUG; AMINOACYL TRANSFER RNA; ASPARTATE TRANSFER RNA LIGASE; ASPARTIC ACID; TRNA, ASPARTIC ACID; TRNA, ASPARTIC ACID-;

AMINO TERMINAL SEQUENCE; AMINOACYLATION; ANTICODON; ARTICLE; BINDING SITE; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE; ESCHERICHIA COLI; GENE INSERTION; GENE REPRESSION; GENETIC SELECTION; IN VIVO STUDY; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DOMAIN; REPORTER GENE; AMINO ACID SUBSTITUTION; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MUTATION; PHENOTYPE; PROTEIN ENGINEERING; PROTEIN TERTIARY STRUCTURE;

ESCHERICHIA; INSERTION SEQUENCES; PROKARYOTA;

AMINO ACID SUBSTITUTION; ANTICODON; ASPARTATE-TRNA LIGASE; ASPARTIC ACID; BINDING SITES; MODELS, MOLECULAR; MUTATION; PHENOTYPE; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; RNA, TRANSFER, AMINO ACYL;

EID: 3242890837     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh751     Document Type: Article

References (56)

1. Ibba,M. and Söll,D. (2000) Aminoacyl-tRNA synthesis. Annu. Rev. Biochem., 69, 617-650.
2. McClain,W.H. (1993) Transfer RNA identity. FASEB J., 7, 72-78.
3. Giegé,R., Sissler,M. and Florentz,C. (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res., 26, 5017-5035. 4 Swanson,R., Hoben,P., Sumner-Smith,M., Uemura,H., Watson,L. and Söll,D. (1988) Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science, 242, 1548-1551.
4. Swanson,R., Hoben,P., Sumner-Smith,M., Uemura,H., Watson,L. and Söll,D. (1988) Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science, 242, 1548-1551.
5. Sherman,J.M., Rogers,K., Rogers,M.J. and Söll,D. (1992) Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants. J. Mol. Biol., 228, 1055-1062.
6. Tumbula,D.L., Becker,H.D., Chang,W.Z. and Söll, D. (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature, 407, 106-110.
7. Min,B., Pelaschier,J.T., Graham,D.E., Tumbula-Hansen,D. and Söll, D. (2002) Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl Acad. Sci. USA, 99, 2678-2683.
8. Glu in B. subtilis and efficiently misacylates E. coli tRNAGln in vitro. J. Bacteriol., 165, 88-93.
9. Becker,H. and Kern,D. (1998) T. thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl Acad. Sci. USA, 95, 12832-12837.
10. Sekine,S., Nureki,O., Shimada,A., Vassylyev,D.G. and Yokoyama,S. (2001) Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nature Struct. Biol., 8, 203-206.
11. Feng,L., Tumbula-Hansen,D., Toogood,H. and Söll,D. (2003) Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc. Natl Acad. Sci. USA, 100, 5676-5681.
12. Salazar,J., Ivan Ahel,I., Orellana,O., Tumbula-Hansen,D., Krieger,R., Daniels,L. and Söll,D. (2003) Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates. Proc. Natl Acad. Sci. USA, 100, 13863-13868.
13. Skouloubris,S., Ribas de Pouplana,L., de Reuse,H. and Hendrickson,T. (2003) A noncognate aminoacyl-tRNA synthetase that may resolve a missing link in protein evolution. Proc. Natl Acad. Sci. USA, 100, 11297-11302.
14. Auld,D.S. and Schimmel,P. (1995) Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide. Science, 267, 1994-1996.
15. Auld,D.S. and Schimmel,P. (1996) Single sequence of a helix-loop peptide confers functional anticodon recognition on two tRNA synthetases. EMBO J., 15, 1142-1148.
16. Meinnel,T., Mechulam,Y., LeCorre,D., Panvert,M., Blanquet,S. and Fayat,G. (1991) Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site. Proc. Natl Acad. Sci. USA, 88, 291-295.
17. Schmitt,E., Meinnel,T., Panvert,M., Mechulam,Y. and Blanquet,S. (1993) Two acidic residues of Escherichia coli methionyl-tRNA synthetase act as negative discriminants towards the binding of non-cognate tRNA anticodons. J. Mol. Biol., 233, 615-628.
18. Brevet,A., Chen,J., Commans,S., Lazennec,C., Blanquet,S. and Plateau,P. (2003) Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation. J. Biol. Chem., 278, 30927-30935.
19. Kisselev,L. (1985) The role of the anticodon in recognition of tRNA by aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res. Mol. Biol., 32, 237-266.
20. Messing,J., Crea,R. and Seeburg,P.H. (1981) A system for shotgun DNA sequencing. Nucleic Acids Res., 9, 309-321.
21. Greener,A. and Callahan,M. (1994) XL1-red: a highly efficient random mutagenesis strain. Strateg. Mol. Biol. - Newslett., 7, 32-34.
22. Miller,J.H. and Albertini,A.M. (1983) Effects of surrounding sequence on the suppression of nonsense codons. J. Mol. Biol., 164, 59-71.
23. Shurvinton,C.E., Lloyd,R.G., Benson,F.E. and Attfield,P.V. (1984) Genetic analysis and molecular cloning of the E. coli ruv gene. Mol. Gen. Genet., 194, 322-329.
24. Martin,F., Sharples,G.J., Lloyd,R.G., Eiler,S., Moras,D., Gangloff,J. and Eriani,G. (1997) Characterization of a thermosensitive E. coli aspartyl-tRNA synthetase mutant. J. Bacteriol., 179, 3691-3696.
25. Martinez,E., Bartolomé,B. and de la Cruz,F. (1988) pACYC184-derived cloning vectors containing the multiple cloning site and lacZα reporter gene of pUC8/9 and pUC18/19 plasmids. Gene, 68, 159-162.
26. Aman,E., Ochs,B. and Abel,K.J. (1988) Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in E. coli. Gene, 69, 301-305.
27. Asp amber suppressor mutants having alanine, arginine, glutamine, and lysine identity. RNA, 2, 919-927.
28. Asp acylation. J. Mol. Biol., 234, 965-974.
29. Eriani,G., Dirheimer,G. and Gangloff,J. (1990) Aspartyl-tRNA synthetase from E. coli: cloning and characterization of the gene, homologies of its translated amino acid sequence with asparaginyl- and lysyl-tRNA synthetases. Nucleic Acids Res., 18, 7109-7117.
30. Schulman,L.H. and Pelka,H. (1988) Anticodon switching changes the identity of methionine and valine transfer RNAs. Science, 242, 765-768.
31. Asp in Escherichia coli - a snapshot of the second step. EMBO J., 18, 6532-6541.
32. Asp binding in the ground and transition-state complex and discriminate against non-cognate tRNAs. J. Mol. Biol., 291, 761-773.
33. Asp recognition by its cognate class II aminoacyl-tRNA synthetase. Nature, 362, 181-184.
34. Ador,L., Camasses,A., Erbs,P., Cavarelli,J., Moras,D., Gangloff,J. and Eriani,G. (1999) Active site mapping of yeast aspartyl-tRNA synthetase by in vivo selection of enzyme mutations lethal for cell growth. J. Mol. Biol., 288, 231-242.
35. Chang,A.C.Y. and Cohen,S.N. (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol., 134, 1141-1156.
36. Asp is involved in amino acid acceptor activity. Biochem. Biophys. Res. Commun., 163, 1534-1538.
37. Asp recognition mechanism differing from that of the yeast system. Biochem. Biophys. Res. Commun., 189, 856-862.
38. Asp by cognate aspartyl-tRNA synthetase. Science, 252, 1696-1699.
39. Frugier,M., Florentz,C., Schimmel,P. and Giegé,R. (1993) Triple aminoacylation specificity of a chimerized transfer RNA. Biochemistry, 32, 14053-14061.
40. Murzin,A.G. (1993) OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J., 12, 861-867.
41. Conte,L.L., Brenner,S.E., Hubbard,T.J.P., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
42. Asp complex reveals a tRNA-dependent control mechanism. EMBO J., 20, 5290-5301.
43. Asp by aspartyl-tRNA synthetase. J. Mol. Biol., 299, 1051-1060.
44. Lys transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J., 15, 6321-6334.
45. Pastrnak,M., Magliery,T.J. and Schultz,P.G. (2000) A new orthogonal suppressor tRNA/aminoacyl-tRNA synthetase pair for evolving an organism with expanded genetic code. Helv. Chim. Acta, 83, 2277-2286.
46. Ador,L., Jaeger,S., Geslain,R., Martin,F., Cavarelli,J. and Eriani,G. (2004) Mutation and evolution of the magnesium-binding site of a class II aminoacyl-tRNA synthetase. Biochemistry, 43, 7028-7037.
47. Loftfield,R.B. and Vanderjagt,M.A. (1972) The frequency of errors in protein biosynthesis. Biochem. J., 128, 1353-1356.
48. Bosshard,H. (1992) Theories of enzyme specificity and their application to proteases and aminoacyl-transfer RNA synthetases. Experientia, 32, 949-963.
49. Ebel,J.-P., Giegé,R., Bonnet,J., Kern,D., Befort,N., Bollack,C., Fasiolo,F., Gangloff,J. and Dirheimer,G. (1973) Factors determining the specificity of the tRNA aminoacylation reaction. Non-absolute specificity of tRNA-aminoacyl-tRNA synthetase recognition and particular importance of the maximal velocity. Biochimie, 55, 547-557.
50. Stanzel,M., Schön,A. and Sprinzl,M. (1994) Discrimination against misacylated tRNA by chloroplast elongation factor Tu. Eur. J. Biochem., 219, 435-439.
51. LaRiviere,F.J., Wolfson,A.D. and Uhlenbeck,O.C. (2001) Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science, 294, 165-168.
52. Lamour,V., Quevillon,S., Diriong,S., N'Guyen,V.C., Lipinski,M. and Mirande,M. (1994) Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer. Proc. Natl Acad. Sci. USA, 91, 8670-8674.
53. Chihade,J.W. and Schimmel,P. (1999) Assembly of a catalytic unit for RNA microhelix aminoacylation using nonspecific RNA binding domains. Proc. Natl Acad. Sci. USA, 96, 12316-12321.
54. Frugier,M., Giegé,R. and Schimmel,P. (2003) RNA recognition by designed peptide fusion creates 'artificial' tRNA synthetase. Proc. Natl Acad. Sci. USA, 100, 7471-7475.
55. Aroul-Selvam,R., Hubbard,T. and Sasidharan,R. (2004) Domain insertions in protein structures. J. Mol. Biol., 338, 633-641.
56. Wolf,Y.I., Aravind,L., Grishin,N.V. and Koonin,E.V. (1999) Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res., 9, 689-710.