A chimaeric glutamyl:glutaminyl-tRNA synthetase: Implications for evolution

Biochemical Journal

Volumn 417, Issue 2, 2009, Pages 449-455

  Saha, Rajesh ^a,b   Dasgupta, Saumya ^a   Basu, Gautam ^a   Roy, Siddhartha ^c  

^a BOSE INSTITUTE   (India)

^b UNIVERSITY OF CALCUTTA   (India)

^c INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Chimaera; Complementation; Evolution; Specificity; Synthetase; tRNA

Indexed keywords

CHIMAERA; COMPLEMENTATION; EVOLUTION; SPECIFICITY; SYNTHETASE; TRNA;

AMINO ACIDS; BACTERIOLOGY; MERGERS AND ACQUISITIONS;

ESCHERICHIA COLI;

BACTERIAL ENZYME; BACTERIAL PROTEIN; CHIMERIC GLUTAMATE TRANSFER RNA LIGASE GLUTAMINE TRANSFER RNA LIGASE; CHIMERIC PROTEIN; ESCHERICHIA COLI DNAK; ESCHERICHIA COLI N TERMINAL GLUTAMYL TRNA SYNTHETASE; GLUTAMATE TRANSFER RNA LIGASE; GLUTAMINE TRANSFER RNA LIGASE; UNCLASSIFIED DRUG; AMINO ACID TRANSFER RNA LIGASE; GLUTAMINYL-TRNA SYNTHETASE; RECOMBINANT PROTEIN;

ANTICODON; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ISOLATION; ENZYME MODIFICATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; EUKARYOTE; GLUTAMYLATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY; THERMUS THERMOPHILUS;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA;

AMINO ACID SEQUENCE; AMINO ACYL-TRNA SYNTHETASES; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN; THERMUS THERMOPHILUS;

EID: 58249093555     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20080747     Document Type: Article

References (36)

1. Doolittle, R. F. (1995) The multiplicity of domains in proteins. Annu. Rev. Biochem. 64, 287-314
2. Babushok, D. V., Ostertag, E. M. and Kazazian, Jr, H. H. (2007) Current topics in genome evolution: molecular mechanisms of new gene formation. Cell. Mol. Life Sci. 64, 542-554
3. Gilbert, W., de Souza, S. J. and Long, M. (1997) Origin of genes. Proc. Natl. Acad. Sci. U.S.A. 94, 7698-7703
4. Patthy, L. (1987) Intron-dependent evolution: preferred types of exons and introns. FEBS Lett. 214, 1-7
5. Alexander, R. W. and Schimmel, P. (2001) Domain-domain communication in aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res. Mol. Biol. 69, 317-349
6. Buechter, D. D. and Schimmel, P. (1993) Aminoacylation of RNA minihelices: implications for tRNA synthetase structural design and evolution. Crit. Rev. Biochem. Mol. Biol. 28, 309-322
7. Moras, D. (1992) Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem. Sci. 17, 159-164
8. Pham, Y., Li, L., Kim, A., Erdogan, O., Weinreb, V., Butterfoss, G. L., Kuhlman, B. and Carter, Jr, C. W. (2007) A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol. Cell 25, 851-862
9. Siatecka, M., Rozek, M., Barciszewski, J. and Mirande, M. (1998) Modular evolution of the Glx-tRNA synthetase family - rooting of the evolutionary tree between the bacteria and archaea/eukarya branches. Eur. J. Biochem. 256, 80-87
10. Nureki, O., Vassylyev, D. G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S. and Morikawa, K. (1995) Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267, 1958-1965
11. Rould, M. A., Perona, J. J. and Steitz, T. A. (1991) Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352, 213-218
12. Urban, A., Neukirchen, S. and Jaeger, K. E. (1997) A rapid and efficient method for site-directed mutagenesis using one-step overlap extension PCR. Nucleic Acids Res. 25, 2227-2228
13. Lin, S. X., Brisson, A., Liu, J., Roy, P. H. and Lapointe, J. (1992) Higher specific activity of the Escherichia coli glutamyl-tRNA synthetase purified to homogeneity by a six-hour procedure. Protein Expr. Purif. 3, 71-74
14. Banerjee, R., Dubois, D. Y., Gauthier, J., Lin, S. X., Roy, S. and Lapointe, J. (2004) The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm. Eur. J. Biochem. 271, 724-733
15. Banerjee, R., Mandal, A. K., Saha, R., Guha, S., Samaddar, S., Bhattacharyya, A. and Roy, S. (2003) Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases. Nucleic Acids Res. 31, 6035-6042
16. Bhattacharyya, T., Bhattacharyya, A. and Roy, S. (1991) A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism. Eur. J. Biochem. 200, 739-745
17. Lapointe, J. and Delcuve, G. (1975) Thermosensitive mutants of Escherichia coli K-12 altered in the catalytic subunit and in a regulatory factor of the glutamyl-transfer ribonucleic acid synthetase. J. Bacteriol. 122, 352-358
18. Russell, R. R. and Pittard, A. J. (1971) Mutants of Escherichia coli unable to make protein at 42 C. J. Bacteriol. 108, 790-798
19. Racher, K. I., Kalmar, G. B. and Borgford, T. J. (1991) Expression and characterization of a recombinant yeast isoleucyl-tRNA synthetase. J. Biol. Chem. 266, 17158-17164
20. Ibba, M., Hong, K. W., Sherman, J. M., Sever, S. and Soll, D. (1996) Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc. Natl. Acad. Sci. U.S.A. 93, 6953-6958
21. Roy, S. (2004) Fluorescence quenching methods to study protein-nucleic acid interactions. Methods Enzymol. 379, 175-187
22. Jencks, W. P. (1975) Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410
23. Brown, J. R. and Doolittle, W. F. (1999) Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49, 485-495
24. 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. U.S.A. 91, 8670-8674
25. Nureki, O., Vassylyev, D. G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S. and Morikawa, K. (1995) Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267, 1958-1965
26. Weygand-Durasevic, I., Nalaskowska, M. and Soll, D. (1994) Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli. J. Bacteriol. 176, 232-239
27. Sekine, S., Nureki, O., Tateno, M. and Yokoyama, S. (1999) The identity determinants required for the discrimination between tRNAGlu and tRNAAsp by glutamyl-tRNA synthetase from Escherichia coli. Eur. J. Biochem. 261, 354-360
28. Rogers, M. J., Adachi, T., Inokuchi, H. and Soll, D. (1994) Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proc. Natl. Acad. Sci. U.S.A. 91, 291-295
29. Sherman, J. M., Thomann, H. U. and Soll, D. (1996) Functional connectivity between tRNA-binding domains in glutaminyl-tRNA synthetase. J. Mol. Biol. 256, 818-828
30. Weygand-Durasevic, I., Rogers, M. J. and Soll, D. (1994) Connecting anticodon recognition with the active site of Escherichia coli glutaminyl-tRNA synthetase. J. Mol. Biol. 240, 111-118
31. Uter, N. T. and Perona, J. J. (2004) Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics. Proc. Natl. Acad. Sci. U.S.A. 101, 14396-14401
32. Guha, S., Sahu, K., Roy, D., Mondal, S. K., Roy, S. and Bhattacharyya, K. (2005) Slow solvation dynamics at the active site of an enzyme: implications for catalysis. Biochemistry 44, 8940-8947
33. Ghosh, A. and Vishveshwara, S. (2007) A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc. Natl. Acad. Sci. U.S.A. 104, 15711-15716
34. Diaz, E., Lopez, R. and Garcia, J. L. (1990) Chimeric phage-bacterial enzymes: a clue to the modular evolution of genes. Proc. Natl. Acad. Sci. U.S.A. 87, 8125-8129
35. SternJohn, J., Hati, S., Siliciano, P. G. and Musier-Forsyth, K. (2007) Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain. Proc. Natl. Acad. Sci. U.S.A. 104, 2127-2132
36. Nixon, A. E., Warren, M. S. and Benkovic, S. J. (1997) Assembly of an active enzyme by the linkage of two protein modules. Proc. Natl. Acad. Sci. U.S.A. 94, 1069-1073