A present-day aminoacyl-tRNA synthetase with ancestral editing properties

RNA

Volumn 13, Issue 1, 2007, Pages 15-21

  Zhu, Bin ^a   Zhao, Ming Wei ^a   Eriani, Gilbert ^b   Wang, En Duo ^a,c  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b INST DE BIOL MOLEC ET CELLULAIRE   (France)

^c NONE   (China)

Author keywords

Aminoacyl tRNA synthetases; Evolution; Proofreading

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; ISOLEUCINE TRANSFER RNA LIGASE; LEUCINE TRANSFER RNA LIGASE; RNA PRECURSOR; TRANSFER RNA; VALINE TRANSFER RNA LIGASE;

AQUIFEX AEOLICUS; ARTICLE; CONTROLLED STUDY; NONHUMAN; PLESIOMORPHY; PRIORITY JOURNAL; RNA EDITING; RNA STRUCTURE; RNA TRANSLATION;

BACTERIA; BASE SEQUENCE; EVOLUTION, MOLECULAR; ISOLEUCINE-TRNA LIGASE; LEUCINE-TRNA LIGASE; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RNA EDITING; RNA, BACTERIAL; SUBSTRATE SPECIFICITY; TRANSFER RNA AMINOACYLATION; VALINE-TRNA LIGASE;

AQUIFEX AEOLICUS; BACTERIA (MICROORGANISMS);

EID: 33845901811     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.228707     Document Type: Article

References (34)

1. Ahel, I., Korencic, D., Ibba, M., and Söll, D. 2003. Trans-editing of mischarged tRNAs. Proc. Natl. Acad. Sci. 100: 15422-15427.
2. Pro by Haemophilus influenzae YbaK protein. J. Biol. Chem. 279: 42359-42362.
3. Apostol, I., Levine, J., Lippincott, J., Leach, J., Hess, E., Glascock, C., Weickert, M., and Blackmore, R. 1997. Incorporation of norvaline at leucine positions in recombinant human hemoglobin expressed in Escherichia coli. J. Biol. Chem. 272: 28980-28988.
4. Beebe, K., Ribas de Pouplana, L., and Schimmel, P. 2003. Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J. 22: 668-675.
5. Beuning, P.J. and Musier-Forsyth, K. 2000. Hydrolytic editing by a class II aminoacyl-tRNA synthetase. Proc. Natl. Acad. Sci. 97: 8916-8920.
6. Brown, J. and Doolittle, W. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. 92: 2441-2445.
7. Chen, J.F., Guo, N.N., Li, T., Wang, E.D., and Wang, Y.L. 2000. CP1 domain in Escherichia coli leucyl-tRNA synthetase is crucial for its editing function. Biochemistry 39: 6726-6731.
8. Cusack, S., Yaremchuk, A., and Tukalo, M. 2000. The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyladenylate analogue. EMBO J. 19: 2351-2361.
9. Dock-Bregeon, A., Sankaranarayanan, R., Romby, P., Caillet, J., Springer, M., Rees, B., Francklyn, C.S., Ehresmann, C., and Moras, D. 2000. Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 103: 877-884.
10. Döring, V., Mootz, H.D., Nangle, L.A., Hendrickson, T.L., de Crécy-Lagard, V., Schimmel, P., and Marlière, P. 2001. Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 292: 501-504.
11. Eldred, E.W. and Schimmel, P. 1972. Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J. Biol. Chem. 247: 2961-2964.
12. Englisch, S., Englisch, U., von der Haar, F., and Cramer, F. 1986. The proofreading of hydroxy analogues of leucine and isoleucine by leucyl-tRNA synthetases from E. coli and yeast. Nucleic Acids Res. 14: 7529-7539.
13. Eriani, G., Delarue, M., Poch, O., Gangloff, J., and Moras, D. 1990. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347: 203-206.
14. Fersht, A. and Kaethner, M. 1976. Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing. Biochemistry 15: 3342-3346.
15. Hendrickson, T.L., Nomanbhoy, T.K., and Schimmel, P. 2000. Errors from selective disruption of the editing center in a tRNA synthetase. Biochemistry 39: 8180-8186.
16. Ibba, M. and Söll, D. 2000. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69: 617-650.
17. Ishijima, J., Uchida, Y., Kuroishi, C., Tuzuki, C., Takahashi, N., Okazaki, N., Yutani, K., and Miyano, M. 2006. Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 Å resolution. Proteins 62: 1133-1137.
18. Korencic, D., Ahel, I., Schelert, J., Sacher, M., Ruan, B., Stathopoulos, C., Blum, P., Ibba, M., and Söll, D. 2004. A freestanding proofreading domain is required for protein synthesis quality control in Archaea. Proc. Natl. Acad. Sci. 101: 10260-10265.
19. Kotik-Kogan, O., Moor, N., Tworowski, D., and Safro, M. 2005. Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase. Structure 13: 1799-1807.
20. Li, Y., Wang, E., and Wang, Y. 1999. A modified procedure for fast purification of T7 RNA polymerase. Protein Expr. Purif. 16: 355-358.
21. Lin, L., Hale, S.P., and Schimmel, P. 1996. Aminoacylation error correction. Nature 384: 33-34.
22. Nordin, B. and Schimmel, P. 1999. RNA determinants for translational editing. Mischarging a minihelix substrate by a tRNA synthetase. J. Biol. Chem. 274: 6835-6838.
23. Nureki, O., Vassylyev, D., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T., Schimmel, P., and Yokoyama, S. 1998. Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science 280: 578-582.
24. Rodin, S., Rodin, A., and Ohno, S. 1996. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc. Natl. Acad. Sci. 93: 4537-4542.
25. Roy, H., Ling, J., Irnov, M., and Ibba, M. 2005. Post-transfer editing in vitro and in vivo by the b subunit of phenylalanyl-tRNA synthetase. EMBO J. 23: 4639-4648.
26. Cys deacylase. J. Biol. Chem. 280: 25887-25891.
27. Schimmel, P. 1987. Aminoacyl-tRNA synthetases: General scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu. Rev. Biochem. 56: 125-158.
28. Schimmel, P. and Ribas de Pouplana, L. 1995. Transfer RNA: From minihelix to genetic code. Cell 81: 983-986.
29. Schimmel, P. and Ribas de Pouplana, L. 2001. Formation of two classes of tRNA synthetases in relation to editing functions and genetic code. Cold Spring Harb. Symp. Quant. Biol. 66: 161-166.
30. Wong, F., Beuning, P., Silvers, C., and Musier-Forsyth, K. 2003. An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing. J. Biol. Chem. 278: 52857-52864.
31. Xu, M.G., Chen, J.F., Martin, F., Zhao, M.W., Eriani, G., and Wang, E.D. 2002. Leucyl-tRNA synthetase consisting of two subunits from hyperthermophilic bacteria Aquifex aeolicus. J. Biol. Chem. 277: 41590-41596.
32. Xu, M.G., Li, J., Du, X., and Wang, E.D. 2004a. Groups on the side chain of T252 in Escherichia coli leucyl-tRNA synthetase are important for discrimination of amino acids and cell viability. Biochem. Biophys. Res. Comm. 318: 11-16.
33. Xu, M.G., Zhao, M.W., and Wang, E.D. 2004b. Leucyl-tRNA synthetase from the hyperthermophilic bacterium Aquifex aeolicus recognizes minihelices. J. Biol. Chem. 279: 32151-32158.
34. Zhao, M.W., Zhu, B., Hao, R., Xu, M.G., Eriani, G., and Wang, E.D. 2005. Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution. EMBO J. 24: 1430-1439.