Publications
2002
Walter F, Putz J, Giege R, Westhof E
Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation Article de journal
Dans: EMBO J, vol. 21, no. 4, p. 760-768, 2002, ISBN: 11847123, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Base Sequence Carbohydrate Sequence Fluorescence Polarization Molecular Sequence Data *Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism Saccharomyces cerevisiae/*genetics Support, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tobramycin/*metabolism, Transfer, Unité ARN, WESTHOF
@article{,
title = {Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation},
author = {F Walter and J Putz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11847123},
isbn = {11847123},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {4},
pages = {760-768},
abstract = {Aminoglycosides inhibit translation in bacteria by binding to the A site in the ribosome. Here, it is shown that, in yeast, aminoglycosides can also interfere with other processes of translation in vitro. Steady-state aminoacylation kinetics of unmodified yeast tRNA(Asp) transcript indicate that the complex between tRNA(Asp) and tobramycin is a competitive inhibitor of the aspartylation reaction with an inhibition constant (K(I)) of 36 nM. Addition of an excess of heterologous tRNAs did not reverse the charging of tRNA(Asp), indicating a specific inhibition of the aspartylation reaction. Although magnesium ions compete with the inhibitory effect, the formation of the aspartate adenylate in the ATP-PP(i) exchange reaction by aspartyl-tRNA synthetase in the absence of the tRNA is not inhibited. Ultraviolet absorbance melting experiments indicate that tobramycin interacts with and destabilizes the native L-shaped tertiary structure of tRNA(Asp). Fluorescence anisotropy using fluorescein-labelled tobramycin reveals a stoichiometry of one molecule bound to tRNA(Asp) with a K(D) of 267 nM. The results indicate that aminoglycosides are biologically effective when their binding induces a shift in a conformational equilibrium of the RNA.},
note = {0261-4189
Journal Article},
keywords = {Acylation Base Sequence Carbohydrate Sequence Fluorescence Polarization Molecular Sequence Data *Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism Saccharomyces cerevisiae/*genetics Support, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tobramycin/*metabolism, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Cristofari G, Bampi C, Wilhelm M, Wilhelm F X, Darlix J L
A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition Article de journal
Dans: EMBO J, vol. 21, no. 16, p. 4368-4379, 2002, ISBN: 12169639, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Complementary/biosynthesis *Gene Expression Regulation, DNA, Fungal In Vitro Nucleic Acid Conformation Phylogeny RNA, Fungal/chemistry/*metabolism RNA, Genetic, Messenger/chemistry/*metabolism Retroelements/*genetics Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't *Transcription, Unité ARN
@article{,
title = {A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition},
author = {G Cristofari and C Bampi and M Wilhelm and F X Wilhelm and J L Darlix},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12169639},
isbn = {12169639},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {16},
pages = {4368-4379},
abstract = {LTR-retrotransposons are abundant components of all eukaryotic genomes and appear to be key players in their evolution. They share with retroviruses a reverse transcription step during their replication cycle. To better understand the replication of retrotransposons as well as their similarities to and differences from retroviruses, we set up an in vitro model system to examine minus-strand cDNA synthesis of the yeast Ty1 LTR-retrotransposon. Results show that the 5' and 3' ends of Ty1 genomic RNA interact through 14 nucleotide 5'-3' complementary sequences (CYC sequences). This 5'-3' base pairing results in an efficient initiation of reverse transcription in vitro. Transposition of a marked Ty1 element and Ty1 cDNA synthesis in yeast rely on the ability of the CYC sequences to base pair. This 5'-3' interaction is also supported by phylogenic analysis of all full-length Ty1 and Ty2 elements present in the Saccharomyces cerevisiae genome. These novel findings lead us to propose that circularization of the Ty1 genomic RNA controls initiation of reverse transcription and may limit reverse transcription of defective retroelements.},
note = {0261-4189
Journal Article},
keywords = {Complementary/biosynthesis *Gene Expression Regulation, DNA, Fungal In Vitro Nucleic Acid Conformation Phylogeny RNA, Fungal/chemistry/*metabolism RNA, Genetic, Messenger/chemistry/*metabolism Retroelements/*genetics Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't *Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2000
Fechter P, Rudinger-Thirion J, Théobald-Dietrich A, Giege R
Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features Article de journal
Dans: Biochemistry, vol. 39, no. 7, p. 1725-1733, 2000, ISBN: 10677221, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon/chemistry/metabolism Base Sequence Escherichia coli/enzymology/genetics Heat Methanococcus/enzymology/genetics Molecular Mimicry Molecular Sequence Data Nucleic Acid Denaturation RNA Processing, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tyrosine/chemistry/*metabolism Tyrosine-tRNA Ligase/chemistry/*metabolism, Post-Transcriptional RNA, Transfer, Tyr/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Structure-Activity Relationship Support, Unité ARN
@article{,
title = {Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features},
author = {P Fechter and J Rudinger-Thirion and A Théobald-Dietrich and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10677221},
isbn = {10677221},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {7},
pages = {1725-1733},
abstract = {The specific aminoacylation of tRNA by yeast tyrosyl-tRNA synthetase does not rely on the presence of modified residues in tRNA(Tyr), although such residues stabilize its structure. Thus, the major tyrosine identity determinants were searched by the in vitro approach using unmodified transcripts produced by T7 RNA polymerase. On the basis of the tyrosylation efficiency of tRNA variants, the strongest determinants are base pair C1-G72 and discriminator residue A73 (the 5'-phosphoryl group on C1, however, is unimportant for tyrosylation). The three anticodon bases G34, U35, and A36 contribute also to the tyrosine identity, but to a lesser extent, with G34 having the most pronounced effect. Mutation of the GUA tyrosine anticodon into a CAU methionine anticodon, however, leads to a loss of tyrosylation efficiency similar to that obtained after mutation of the C1-G72 or A73 determinants. Transplantation of the six determinants into four different tRNA frameworks and activity assays on heterologous Escherichia coli and Methanococcus jannaschii tRNA(Tyr) confirmed the completeness of the tyrosine set and the eukaryotic character of the C1-G72 base pair. On the other hand, it was found that tyrosine identity in yeast does not rely on fine architectural features of the tRNA, in particular the size and sequence of the D-loop. Noticeable, yeast TyrRS efficiently charges a variant of E. coli tRNA(Tyr) with a large extra-region provided its G1-C72 base pair is changed to a C1-G72 base pair. Finally, tyrosylation activity is compatible with a +1 shift of the anticodon in the 3'-direction but is strongly inhibited if this shift occurs in the opposite 5'-direction.},
note = {0006-2960
Journal Article},
keywords = {Acylation Anticodon/chemistry/metabolism Base Sequence Escherichia coli/enzymology/genetics Heat Methanococcus/enzymology/genetics Molecular Mimicry Molecular Sequence Data Nucleic Acid Denaturation RNA Processing, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tyrosine/chemistry/*metabolism Tyrosine-tRNA Ligase/chemistry/*metabolism, Post-Transcriptional RNA, Transfer, Tyr/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Structure-Activity Relationship Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1997
Sissler M, Eriani G, Martin F, Giege R, Florentz C
Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 24, p. 4899-4906, 1997, ISBN: 9396794, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/chemistry Arginine-tRNA Ligase/classification/*metabolism Aspartate-tRNA Ligase/classification/*metabolism Base Sequence DNA Footprinting Escherichia coli Fungal Proteins/classification/*metabolism Models, Arg/chemistry/*metabolism RNA, Asp/chemistry/*metabolism Recombinant Fusion Proteins/metabolism Saccharomyces cerevisiae/metabolism Stereoisomerism Substrate Specificity Support, ERIANI, FLORENTZ, Fungal/chemistry/*metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase},
author = {M Sissler and G Eriani and F Martin and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9396794},
isbn = {9396794},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {24},
pages = {4899-4906},
abstract = {Gene cloning, overproduction and an efficient purification protocol of yeast arginyl-tRNA synthetase (ArgRS) as well as the interaction patterns of this protein with cognate tRNAArgand non-cognate tRNAAspare described. This work was motivated by the fact that the in vitro transcript of tRNAAspis of dual aminoacylation specificity and is not only aspartylated but also efficiently arginylated. The crystal structure of the complex between class II aspartyl-tRNA synthetase (AspRS) and tRNAAsp, as well as early biochemical data, have shown that tRNAAspis recognized by its variable region side. Here we show by footprinting with enzymatic and chemical probes that transcribed tRNAAspis contacted by class I ArgRS along the opposite D arm side, as is homologous tRNAArg, but with idiosyncratic interaction patterns. Besides protection, footprints also show enhanced accessibility of the tRNAs to the structural probes, indicative of conformational changes in the complexed tRNAs. These different patterns are interpreted in relation to the alternative arginine identity sets found in the anticodon loops of tRNAArgand tRNAAsp. The mirror image alternative interaction patterns of unmodified tRNAAspwith either class I ArgRS or class II AspRS, accounting for the dual identity of this tRNA, are discussed in relation to the class defining features of the synthetases. This study indicates that complex formation between unmodified tRNAAspand either ArgRS and AspRS is solely governed by the proteins.},
note = {0305-1048
Journal Article},
keywords = {Anticodon/chemistry Arginine-tRNA Ligase/classification/*metabolism Aspartate-tRNA Ligase/classification/*metabolism Base Sequence DNA Footprinting Escherichia coli Fungal Proteins/classification/*metabolism Models, Arg/chemistry/*metabolism RNA, Asp/chemistry/*metabolism Recombinant Fusion Proteins/metabolism Saccharomyces cerevisiae/metabolism Stereoisomerism Substrate Specificity Support, ERIANI, FLORENTZ, Fungal/chemistry/*metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}