tRNA mimics

Current Opinion in Structural Biology

Volumn 8, Issue 3, 1998, Pages 286-293

  Giegé, Richard ^a   Frugier, Magali ^a   Rudinger, Joëlle ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

BIOTECHNOLOGY; EVOLUTION; METABOLISM; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVIEW; RIBOSOME; RNA STRUCTURE;

EID: 0032104497     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80060-2     Document Type: Article

References (60)

1. Söll D. Transfer RNA: an RNA for all seasons. Gesteland RF, Atkins JF. The RNA World. 1993;157-184 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
2. Florentz C, Giegé R. tRNA-like structures in plant viral RNAs. Söll D, RajBhandary U. tRNA: Structure, Biosynthesis and Functions. 1995;141-163 American Society for Microbiology Press, Washington DC.
3. Ibba M, Curnow AW, Söll D. Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem Sci. 22:1997;39-42.
4. Giegé R. Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries. Proc Natl Acad Sci USA. 93:1996;12078-12081.
5. Lim VI. Analysis of interactions between the codon-anticodon duplexes within the ribosome: their role in translation. of special interest J Mol Biol. 266:1997;877-890 The author used graphic simulation to analyse the influence of interactions between the codon - anticodon duplexes formed by normal elongator tRNAs at the ribosomal aminoacyl-tRNA binding site, peptidyl-tRNA binding site and exit site during ribosomal translation.
6. Dirheimer G, Keith G, Dumas P, Westhof E. Primary, secondary, and tertiary structures of tRNAs. Söll D, RajBhandary U. tRNA: Structure, Biosynthesis and Functions. 1995;93-126 ASM Press, Washington DC.
7. Steinberg S, Leclerc F, Cedergren R. Structural rules and conformational compensations in the tRNA L-form. of outstanding interest J Mol Biol. 266:1997;269-282 The three-dimensional modeling of unusual mitochondrial tRNAs shows that the dihydrouridine and thymidine domains interact in the same way as in standard tRNAs, and highlights the different strategies used to compensate for the presence of noncanonical features.
8. Normanly J, Abelson J. tRNA identity. Annu Rev Biochem. 58:1989;1029-1049.
9. Giege R, Puglisi JD, Florentz C. tRNA structure and aminoacylation efficiency. Prog Nucleic Acid Res Mol Biol. 45:1993;129-206.
10. Saks ME, Sampson JR, Abelson JN. The transfer RNA identity problem: a search for rules. Science. 263:1994;191-197.
11. McClain WH. The tRNA identity problem: past, present, and future. Söll D, RajBhandary U. tRNA: Structure, Biosynthesis and Functions. 1995;347-355 ASM Press, Washington DC.
12. McClain WH, Guerrier-Takada C, Altman S. Model substrates for an RNA enzyme. Science. 238:1987;527-530.
13. Li Z, Sun Y, Thurlow DL. RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase. of special interest Biochem J. 327:1997;847-851 This paper shows that 21 different minihelices, each mimicking the acceptor branch of several tRNAs, are effective substrates for tRNA nucleotidyltransferases (CCases) from E. coli and yeast. Minihelices with purines at the three central positions of the T loop (positions 56-58) appear to be better substrates for CCases than those with pyrimidines.
14. Rudinger J, Blechschmidt B, Ribeiro S, Sprinzl M. Minimalist aminoacylated RNAs as efficient substrates for elongation factor Tu. Biochemistry. 33:1994;5682-5688.
15. Khvorova AM, Motorin YA, Wolfson AD, Gladilin KL. Anticodon-dependent aminoacylation of RNA minisubstrate by lysyl-tRNA synthetase. FEBS Lett. 314:1992;256-258.
16. Lys identity. Nucleic Acids Res. 20:1992;2335-2339.
17. Dumas P, Moras D, Florentz C, Giegé R, Verlaan P, Belkum AV, Pleij CWA. 3-D graphics modelling of the tRNA-like 3′-end of turnip yellow mosaic virus RNA: Structural and functional implications. J Biomol Struct Dyn. 4:1987;707-728.
18. Puglisi JD, Wyatt JR, Tinoco I. RNA pseudoknots. Accounts Chem Res. 24:1991;152-158.
19. Czworkowski J, Wang J, Steitz TA, Moore PB. The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13:1994;3661-3668.
20. Aevarsson A, Brazhnikov E, Garber M, Zheltonosova J, Chirgadze Y, Al-Karadaghi S, Svensson LA, Liljas A. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J. 13:1994;3669-3677.
21. Nyborg J, Nissen P, Kjeldgaard M, Tnirup S, Polekhina G, Clark BFC. Structure of the ternary complex of EF-Tu: macromolecular mimicry in translation. Trends Biochem Sci. 21:1996;81-82.
22. Martinis SA, Schimmel P. Small RNA oligonucleotide substrates for specific aminoacylation. Söll D, RajBhandary U. tRNA: Structure, Biosynthesis and Functions. 1995;349-370 ASM Press, Washington DC.
23. Grosjean H, Edqvist J, Straby KB, Giegé R. Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J Mol Biol. 255:1996;67-85.
24. Yarmolinsky MB, de la Haba GL. Inhibition by puromycin of amino acid incorporation into proteins. Proc Natl Acad Sci USA. 45:1959;1721-1729.
25. Caprara MG, Lehnert V, Lambowitz AM, Westhof E. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell. 87:1996;1135-1145.
26. Herbert CJ, Labouesse M, Dujardin G, Slonimski PP. The NAM2 proteins from S. cerevisiae and S. douglasii are mitochondrial leucyl-tRNA synthetases, and are involved in mRNA splicing. EMBO J. 7:1988;473-483.
27. Rietveld K, Van Poelgeest R, Pleij CWA, Van Boom JH, Bosch L. The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res. 10:1982;1929-1946.
28. Felden B, Florentz C, Giegé R, Westhof E. A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5′ upstream pseudoknots in the 3′ terminus of tobacco mosaic virus RNA. RNA. 2:1996;201-212.
29. Felden B, Florentz C, Giegé R, Westhof E. Solution structure of the tRNA-like 3′-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs. J Mol Biol. 235:1994;508-531.
30. Felden B, Florentz C, Westhof E, Giegé R. Transfer RNA identity rules and conformation of the tyrosine tRNA-like domain of BMW RNA imply additional charging by histidine and valine. Biochem Biophys Res Commun. 243:1998;426-434.
31. His) and its mimic in tRNA-like domains, as the main histidine identity signal.
32. Dreher TW, Tsai C-H, Skuzeski JM. Aminoacylation identity switch of turnip yellow mosaic viral RNA from valine to methionine results in an infectious virus. Proc Natl Acad Sci USA. 93:1996;12212-12216.
33. Chen B, Lambowitz AM. De novo and DNA primer-mediated initiation of cDNA synthesis by the Mauriceville retroplasmid reverse transcriptase involve recognition of a 3′-CCA sequence. of special interest J Mol Biol. 271:1997;311-332 During replication of the mitochondrial Mauriceville retroplasmid of Neurospora, the reverse transcriptase initiates cDNA synthesis at the 3′ end of a tRNA-like structure. The authors show that the 3′ CCA end of the plasmid transcript is the major structural feature recognized by the reverse transcriptase.
34. Maizel N, Weiner A. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA. 91:1994;6729-6734.
35. Komine Y, Kitabatake M, Yokogawa T, Nishikawa K. A tRNA-like structure is present in 10SA RNA, a small stable RNA from Escherichia coli. Proc Natl Acad Sci USA. 91:1994;9223-9277.
36. Williams KP, Bartel DP. The tmRNA website. of special interest Nucleic Acids Res. 26:1998;163-165 The outline of a comprehensive and evolving database on the structure and function of tmRNA (or 10Sa RNA) is presented. This database lists the presence of this RNA in 37 species belonging to a diverse bacterial phyla.
37. Keiler KC, Waller RH, Sauer RT. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science. 271:1996;990-993.
38. Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). of outstanding interest RNA. 3:1997;89-103 The authors have determined a two-dimensional model of E. coli 10Sa RNA using chemical and enzymatic probes. The structure explains the dual biological functions of this molecule, behaving as both a tRNA and mRNA.
39. Himeno H, Sato M, Takadi T, Fukushima M, Ushida C, Muto A. In vitro trans translation mediated by alanine-charged 10Sa RNA. of special interest J Mol Biol. 268:1997;803-808 This paper describes a model system for in vitro studies on 10Sa RNA (tmRNA) mediated tagging of proteins synthesized from damaged mRNA, leading to the degradation of these targets, as occurs in vivo [36].
40. Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M. 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.
41. Graffe M, Dondon J, Caillet J, Romby P, Ehresmann C, Ehresmann B, Springer M. The specificity of translational control switched using tRNA identity rules. Science. 255:1992;994-996.
42. Phe variants from a randomized library using two proteins. EMBO J. 12:1993;2959-2967.
43. Tinkle Peterson E, Pan T, Coleman J, Uhlenbeck OC. In vitro selection of small RNAs that bind to Escherichia coli phenylalanyl-tRNA synthetase. J Mol Biol. 242:1994;186-192.
44. 2 group of charged amino acids. Nucleic Acids Res. 25:1997;1862-1863.
45. Wilson C, Szostak JW. In vitro evolution of a self-alkylating ribozyme. Nature. 374:1995;777-782.
46. Hale SP, Schimmel P. Protein synthesis editing by a DNA aptamer. Proc Natl Acad Sci USA. 93:1996;2755-2758.
47. Hale SP, Auld DS, Schmidt E, Schimmel P. Discrete determinants in transfer RNA for editing and aminoacylation. of outstanding interest Science. 276:1997;1250-1252 This paper investigates the structural basis for RNA-dependent amino acid discrimination by E. coli lleRS. This editing system is highly specific for the D loop sequence of the tRNA.
48. Phe anticodon domain. Nat Struct Biol. 3:1996;38-44.
49. f, to Escherichia coli methionyl-tRNA synthetase. J Mol Biol. 220:1991;205-208.
50. Frugier M, Florentz C, Giege R. Anticodon-independent aminoacylation of an RNA minihelix with valine. Proc Natl Acad Sci USA. 89:1992;3990-3994.
51. Hipps D, Schimmel P. Cell growth inhibition by sequence-specific RNA minihelices. EMBO J. 14:1995;4050-4055.
52. Leehey MA, Squassoni CA, Friederich MW, Mills JB, Hagerman PJ. A noncanonical tertiary conformation of a human mitochondrial transfer RNA. Biochemistry. 34:1995;16235-16239.
53. Gln has lost all glutaminylation activity and is not recognized by any synthetase, except an engineered GlnRS. Further engineering of this synthetase in order to activate an un-natural amino acid is in progress.
54. Schimmel P, Söll D. When protein engineering confronts the RNA world. of special interest Proc Natl Acad Sci USA. 94:1997;10007-10009 This commentary on the paper by Liu et al. [53] describes clearly and pedagogically the different steps allowing creation of an 'orthogonal' tRNA and synthetase pair. The authors discuss not only the large potential of such engineering in expansion of the genetic code but also the possible problems that such mutants pose for translation.
55. 13 independent fusions, corresponding to random sequences of about 27 amino acids.
56. Nemoto N, Miyamoto-Sato E, Husimi Y, Yanagawa H. In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. of outstanding interest FEBS Lett. 414:1997;405-408 A similar approach to that given in [55] for examining protein evolution in a test tube for a selection of proteins with a given function.
57. Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 15:1993;675-687.
58. Schimmel P, Giege R, Moras D, Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci USA. 90:1993;8763-8768.
59. Herderson BS, Schimmel P. RNA-RNA interactions between oligonucleotide substrates for aminoacylation. of outstanding interest Bioorg Med Chem. 5:1997;1071-1079 This paper describes the design and characterization of complexes formed through a lateral loop - loop base pairing of RNA hairpin substrates for aminoacylation. It establishes an experimental basis for microhelix association in primordial noncoded peptide synthesis.
60. Massire C, Gaspin C, Westhof E. DRAWNA: a program for drawing schematic views of nucleic acids. J Mol Graphics. 12:1994;201-206.