tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations

Biochimie

Volumn 87, Issue 9-10, 2005, Pages 835-845

  Ryckelynck, Michaël ^a   Giegé, Richard ^a   Frugier, Magali ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

Aminoacyl tRNA synthetase; Identity; tRNA

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; TRANSFER RNA;

AMINOACYLATION; CONFERENCE PAPER; ENZYME REGULATION; MOLECULAR EVOLUTION; PLASTICITY; RNA INTERFERENCE; RNA SPLICING; RNA STRUCTURE; RNA TRANSCRIPTION; SIGNAL TRANSDUCTION;

AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; BACILLUS SUBTILIS; BASE SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; MOLECULAR MIMICRY; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; PROTEIN KINASES; RNA, TRANSFER; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSFER RNA AMINOACYLATION;

EID: 24744432691     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2005.02.014     Document Type: Conference Paper

References (83)

1. J.P. Ebel, R. Gieǵ, J. Bonnet, D. Kern, N. Befort, C. Bollack, F. Fasiolo, J. Gangloff, and G. Dirheimer Factors determining the specificity of the tRNA aminoacylation reaction Biochimie 55 1973 547 557
2. T.L. Hendrickson, and P. Schimmel Transfer RNA-dependent amino acid discrimination by aminoacyl-tRNA synthetases J. Lapointe L. Brakier-Gingras Translation Mechanisms 2003 Landes Bioscience Georgetown, TX 34 64
3. R. Gieǵ, M. Sissler, and C. Florentz Universal rules and idiosyncratic features in tRNA identity Nucleic Acids Res. 26 1998 5017 5035
4. K. Musier-Forsyth, and P. Schimmel Aminoacylation of RNA oligonucleotides: minimalist structures and origin of specificity FASEB J. 7 1993 282 289
5. S.A. Wek, S. Zhu, and R.C. Wek The histidyl-tRNA synthetase-related sequence in the eIF-2α protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids Mol. Cell. Biol. 15 1995 4497 4506
6. S. Lanker, J.L. Bushman, A.G. Hinnebusch, H. Traschsel, and P.P. Mueller Autoregulation of the yeast lysyl-tRNA synthetase gene GCN5/KRS1 by translational and transcriptional control mechanisms Cell 70 1992 647 657
7. Y. Miyamoto, K. Machida, M. Mizunuma, Y. Emoto, N. Sato, K. Miyahara, D. Hirata, T. Usui, H. Takahashi, H. Osada, and T. Miyakawa Identification of Saccharomyces cerevisiae isoleucyl-tRNA synthetase as a target of the G1-specific inhibitor reveromycin A J. Biol. Chem. 277 2002 28810 28814
8. A.G. Hinnebusch General and pathway-specific regulatory mechanisms controlling the synthesis of amino acids biosynthetic enzymes in Saccharomyces cerevisiae J.R. Broach E.W. Jones J.R. Pringle The Molecular and Cellular Biology of the Yeast Saccharomyces cerevisiae: Gene Expression 1992 Cold Spring Harbor Laboratory Press New York 319 414
9. J. Dong, H. Qiu, M. Garcia-Barrio, J. Anderson, and A.G. Hinnebusch Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain Mol. Cell 6 2000 269 279
10. H. Qiu, J. Dong, C. Hu, C.S. Francklyn, and A.G. Hinnebusch The tRNA-binding moiety in GCN2 contains a dimerization domain that interacts with the kinase domain and is required for tRNA binding ans kinase activation EMBO J. 20 2001 1425 1438
11. H. Qiu, C. Hu, J. Dong, and A.G. Hinnebusch Mutations that bypass tRNA binding activate the intrinsically defective kinase domain in GCN2 Genes Dev. 16 2002 1271 1280
12. S. Irniger, and G.H. Braus Controlling transcription by destruction: the regulation of yeast GCN4p stability Curr. Genet. 1 2003 8 18
13. A.G. Hinnebusch Translational control of GCN4: an in vivo barometer of initiation-factor activity Trends Biochem. Sci. 19 1994 409 414
14. G. Fayat, J.-F. Mayaux, C. Sacerdot, M. Fromant, M. Springer, M. Grunberg-Manago, and S. Blanquet Escherichia coli phenylalanyl-tRNA synthetase operon region: evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20 J. Mol. Biol. 171 1983 239 261
15. T.-H. Wu, D.L. Wood, and M.M. Comer Transcription of a gene cluster coding for two aminoacyl-tRNA synthetases and an initiation factor in Escherichia coli J. Mol. Biol. 173 1984 177 209
16. M. Springer, M. Trudel, J. Plumbridge, G. Fayat, J.-F. Mayaux, C. Sacerdot, S. Blanquet, and M. Grunberg-Manago Escherichia coli phenylalanyl-tRNA synthetase operon is controlled by attenuation in vivo J. Mol. Biol. 171 1983 263 279
17. J.-F. Mayaux, G. Fayat, M. Panvert, M. Springer, M. Grunberg-Manago, and S. Blanquet Control of phenylalanyl-tRNA synthetase genetic expression J. Mol. Biol. 184 1985 31 44
18. Y. Mechulam, S. Blanquet, and G. Fayat Dual level control of the Escherichia coli pheST-himA operon expression J. Mol. Biol. 197 1987 453 470
19. D. Anathbandhu, I.P. Crawford, and C. Yanofsky Regulation of tryptophan operon expression by attenuation in cell-free extracts of Escherichia coli J. Biol. Chem. 257 1982 8795 8798
20. C. Yanofsky Transcription attenuation: once viewed as a novel regulatory strategy J. Bacteriol. 182 2000 1 8
21. T.M. Henkin, B.L. Glass, and F.J. Grundy Analysis of the Bacillus subtilis tyrS gene: conservation of a regulatory sequence in multiple tRNA synthetase genes J. Bacteriol. 174 1992 1299 1306
22. H. Putzer, N. Gendron, and M. Grunberg-Manago Co-ordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis: control by transcriptional antitermination involving a conserved regulatory sequence EMBO J. 11 1992 3117 3127
23. P.B. Vander Horn, and S.A. Zahler Cloning and nucleotide sequence of the leucyl-tRNA synthetase gene of Bacillus subtilis J. Bacteriol. 174 1992 3928 3935
24. Y. Gagnon, R. Breton, H. Putzer, M. Pelchat, M.M. Grunberg, and J. Lapointe Clustering and co-transcription of the Bacillus subtilis genes encoding the aminoacyl-tRNA synthetases specific for glutamate and for cysteine and the first enzyme for cysteine biosynthesis J. Biol. Chem. 269 1994 7473 7482
25. C. Condon, H. Putzer, and M. Grunberg-Manago Processing of the leader mRNA plays a major role in the induction of thrS expression following threonine starvation in Bacillus subtilis Proc. Natl. Acad. Sci. USA 93 1996 6992 6997
26. D. Luo, J. Leautey, M. Grunberg-Manago, and H. Putzer Structure and regulation of expression of the Bacillus subtilis valyl-tRNA synthetase gene J. Bacteriol. 179 1997 2472 2478
27. F.J. Grundy, S.E. Hodil, S.M. Rollin, and T.M. Henkin Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination J. Bacteriol. 179 1997 2587 2594
28. H. Frenkiel, J. Bardowsky, S.D. Ehrlich, and A. Chopin Transcription of the trp operon in Lactococcus lactis is controlled by antitermination in the leader region Microbiol. 144 1998 2103 2111
29. K. Steiner, and H. Malke relA-independent amino acid starvation response network of Streptococcus pyognes J. Bacteriol. 183 2001 7354 7364
30. H. Putzer, S. Laalami, A.A. Brakhage, C. Condon, and M. Grunberg-Manago Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis: induction, repression and growth rate regulation Mol. Microbiol. 16 1995 709 718
31. F.J. Grundy, T.R. Moir, M.T. Haldeman, and T.M. Henkin Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements Nucleic Acids Res. 30 2002 1646 1655
32. D. Luo, C. Condon, M. Grunberg-Manago, and H. Putzer In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis Nucleic Acids Res. 26 1998 5379 5387
33. F.J. Grundy, and T.M. Henkin tRNA as a positive regulator of transcription antitermination in B. subtilis Cell 74 1993 475 482
34. F.J. Grundy, S.M. Rollins, and T.M. Henkin Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base J. Bacteriol. 176 1994 4518 4526
35. M.S. Gerdeman, T.M. Henkin, and J.V. Hines In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: evidence for factor-independent tRNA acceptor stem binding specificity Nucleic Acids Res. 30 2002 1065 1072
36. M.S. Gerdeman, T.M. Henkin, and J.V. Hines Solution structure of the Bacillus subtilis T-box antiterminator RNA: Seven nucleotide bulge characterized by stacking and flexibility J. Mol. Biol. 326 2003 189 201
37. F.J. Grundy, W.C. Winkler, and T.M. Henkin tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome Proc. Natl. Acad. Sci. USA 99 2002 11121 11126
38. F.J. Grundy, J.A. Collins, S.M. Rollins, and T.M. Henkin tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene RNA 6 2000 1131 1141
39. M. van de Guchte, S.D. Ehrlich, and A. Chopin Identity elements in tRNA-mediated transcription antitermination: implication of tRNA D- and T-arms in mRNA recognition Microbiology 147 2001 1223 1233
40. H. Putzer, C. Condon, D. Brechemier-Baey, R. Brito, and M. Grunberg-Manago Transfer RNA-mediated antitermination in vitro Nucleic Acids Res. 30 2002 3026 3033
41. C. Condon, H. Putzer, D. Luo, and M. Grunberg-Manago Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent in Escherichia coli J. Mol. Biol. 268 1997 235 242
42. His; possible general regulatory implications Proc. Natl. Acad. Sci. USA 80 1983 5240 5242
43. F. Dardel, M. Panvert, and G. Fayat Transcription and regulation of expression of the Escherichia coli methionyl-tRNA synthetase gene Mol. Gen. Genet. 223 1990 121 133
44. His in aminoacylation Nucleic Acids Res. 17 1989 7855 7863
45. L.D. Schulman, and J. Abelson Recent excitement in understanding transfer RNA identity Science 240 1988 1591 1592
46. P. Romby, and M. Springer Bacterial translational control at atomic resolution Trends Genet. 19 2003 155 161
47. P. Lestienne, J.A. Plumbridge, M. Grunberg-Manago, and S. Blanquet Autogenous repression of Escherichia coli threonyl-tRNA synthetase expression in vitro J. Biol. Chem. 259 1984 5232 5237
48. M. Springer, J.A. Plumbridge, J.S. Butler, M. Graffe, J. Dondon, J.F. Mayaux, G. Fayat, P. Lestienne, S. Blanquet, and M. Grunberg-Manago Autogenous control of Escherichia coli threonyl-tRNA synthetase expression in vivo J. Mol. Biol. 185 1985 93 104
49. J.S. Butler, M. Springer, J. Dondon, and M. Grunberg-Manago Posttranscriptional autoregulation of Escherichia coli threonyl tRNA synthetase expression in vivo J. Bacteriol. 165 1986 198 203
50. W. Freist, and D.H. Gauss Threonyl-tRNA synthetase Biol. Hoppe Seyler 376 1995 213 224
51. R. Sankaranarayanan, A.-C. Dock-Bregeon, B. Rees, M. Bovee, J. Caillet, P. Romby, C.S. Francklyn, and D. Moras Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase Nat. Struct. Biol. 7 2000 461 465
52. M. Springer, M. Graffe, J.S. Butler, and M. Grunberg-Manago Genetic definition of the translational operator of the threonine tRNA ligase gene in Escherichia coli Proc. Natl. Acad. Sci. USA 83 1986 4384 4388
53. H. Moine, B. Ehresmann, P. Romby, J.-P. Ebel, M. Grunberg-Manago, M. Springer, and C. Ehresmann The translational regulation of threonyl-tRNA synthetase. Fonctional relationship between the enzyme, the cognate tRNA and the ribosome Biochim. Biophys. Acta 1050 1990 343 350
54. C. Sacerdot, J. Caillet, M. Graffe, F. Eyermann, B. Ehresmann, C. Ehresmann, M. Springer, and P. Romby The E. coli threonyl-tRNA synthetase gene contains a split ribosomal binding site interrupted by a hairpin structure that is essential for autoregulation Mol. Microbiol. 29 1998 1077 1090
55. J. Caillet, T. Nogueira, B. Masquida, F. Winter, M. Graffe, A.C. Dock-Bŕgeon, A. Torres-Larios, R. Sankaranarayanan, E. Westhof, B. Ehresmann, C. Ehresmann, P. Romby, and M. Springer The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression Mol. Microbiol. 47 2003 961 974
56. P. Romby, C. Brunel, J. Caillet, M. Springer, M. Grunberg-Manago, E. Westhof, C. Ehresmann, and B. Ehresmann Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules Nucleic Acids Res. 20 1992 5633 5640
57. T. Hasegawa, M. Miyano, H. Himeno, Y. Sano, K. Kimura, and M. Shimizu Identity determinants of E. coli threonine tRNA Biochem. Biophys. Res. Commun. 184 1992 478 484
58. C. Brunel, J. Caillet, P. Lesage, M. Graffe, J. Dondon, H. Moine, P. Romby, C. Ehresmann, B. Ehresmann, M. Grunberg-Manago, and M. Springer Domains of the Escherichia coli threonyl-tRNA synthetase translational operator and their relation to threonine tRNA isoacceptors J. Mol. Biol. 227 1992 621 634
59. M. Graffe, J. Dondon, J. Caillet, P. Romby, C. Ehresmann, B. Ehresmann, and M. Springer The specificity of translational control switched using tRNA identity rules Science 255 1992 994 996
60. M. Springer, M. Graffe, J. Dondon, and M. Grunberg-Manago tRNA-like structures and gene regulation at the translational level. A case of molecular mimicry in E. coli EMBO J. 8 1989 2417 2424
61. P. Romby, J. Caillet, C. Ebel, C. Sacerdot, M. Graffe, F. Eyermann, C. Brunel, H. Moine, C. Ehresmann, B. Ehressman, and M. Springer The expression of E. coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions EMBO J. 15 1996 5976 5987
62. Thr complex enlightens its repressor activity and reveals an essential zinc ion in the active site Cell 97 1999 371 381
63. A. Torres-Larios, A.-C. Dock-Bregeon, P. Romby, B. Rees, R. Sankaranarayanan, J. Caillet, M. Springer, C. Ehresmann, B. Ehresmann, and D. Moras Structural basis of translational control by Escherichia coli threonyl-tRNA synthetase Nat. Struct. Biol. 9 2002 343 347
64. B. Schray, and R. Knippers Binding of human glutaminyl-transfer RNA synthetase to a specific site of its messenger RNA Nucleic Acids Res. 19 1991 5307 5312
65. M. Frugier, and R. Gieǵ Yeast aspartyl-tRNA synthetase binds specifically its own mRNA J. Mol. Biol. 331 2003 375 383
66. R. Gieǵ, and M. Frugier Transfer RNA structure and identity J. Lapointe L. Brakier-Gringas Translation Mechanisms 2003 Landes Sciences Georgetown, TX 1 24
67. R. Gieǵ, M. Frugier, and J. Rudinger tRNA mimics Curr. Opin. Struct. Biol. 8 1998 286 293
68. A.B. Tolstrup, A. Bejder, J. Fleckner, and J. Justesen Transcriptional regulation of the Interferon-γ-inducible tryptophanyl-tRNA synthetase includes alternative splicing J. Biol. Chem. 270 1995 397 403
69. K. Kawakami, K. Ito, and Y. Nakamura Differential regulation of two genes encoding lysyl-tRNA synthetases in Escherichia coli: lysU-constitutive mutations compensate for a lysS null mutatuion Mol. Microbiol. 13 1992 1739 1745
70. S.D. Putney, and P. Schimmel An aminoacyl-tRNA synthetase bind to a specific DNA sequence and regulates its gene transcription Nature 291 1981 632 635
71. P. Mucha Aminoacyl-tRNA synthetases and aminoacylation of tRNA in the nucleus Acta Biochim. Pol. 49 2002 1 10
72. Y.G. Ko, H. Park, and S. Kim Novel regulatory interactions and activities of mammalian tRNA synthetases Proteomics 2 2002 1304 1310
73. K.W. Lynch Consequences of regulated pre-mRNA splicing in the immune system Nat. Rev. 4 2004 931 940
74. C.A. Myers, G.J. Wallweber, R. Rennard, Y. Kemel, M.G. Caprara, G. Mohr, and A.M. Lambowitz A tyrosyl-tRNA synthetase suppresses structural defects in the two major helical domains of the groupe I intron catalytic core J. Mol. Biol. 262 1996 87 104
75. C.A. Myers, B. Kuhla, S. Cusack, and A.M. Lambowitz tRNA-like recognition of group I introns by a tyrosyl-tRNA synthetase Proc. Natl. Acad. Sci. USA 99 2002 2630 2635
76. S.B. Rho, T.L.J. Lincecum, and S.A. Martinis An inserted region of leucyl-tRNA synthetase plays a critical role in group I intron splicing EMBO J. 21 2002 6874 6881
77. P. Sampath, B. Mazumder, V. Seshadri, C.A. Gerber, L. Chavatte, M. Kinter, S.M. Ting, J.D. Digman, S. Kim, D.M. Driscoll, and P.L. Fox Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation Cell 119 2004 195 208
78. P. Sampath, B. Mazumder, V. Seshadri, and P.L. Fox Transcript-selective translational silencing by gamma interferon is directed by a novel structural element in the ceruloplasmin mRNA 3′ untranslated region Mol. Cell. Biol. 23 2003 1509 1519
79. B. Cahuzac, E. Berthonneau, N. Birlirakis, E. Guittet, and M. Mirande A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases EMBO J. 19 2000 445 452
80. J.W. Baick, J.H. Yoon, S. Namgoong, D. Söll, S. Kim, S.H. Eom, and K.W. Hong Growth inhibition of Escherichia coli during heterologous expression of Bacillus subtilis glutamyl-tRNA synthetase that catalyzes the formation of mischarged glutamyl-tRNA1 Gln J. Microbiol. 42 2004 111 116
81. Asp charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase J. Biol. Chem. 278 2003 9683 9690
82. L.H. Schulman, and H. Pelka Anticodon switching changes the identity of methionine and valine transfer RNAs Science 242 1988 765 768
83. Asp by cognate aspartyl-tRNA synthetase Science 252 1991 1696 1699