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1996
Felden B, Florentz C, Giege 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 Article de journal
Dans: RNA, vol. 2, no. 3, p. 201-212, 1996, ISBN: 8608444, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support
@article{,
title = {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},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608444},
isbn = {8608444},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {3},
pages = {201-212},
abstract = {A three-dimensional model of the histidylable 3'-terminal tRNA-like domain of tobacco mosaic virus RNA is proposed on the basis of a comparative structural analysis, chemical and enzymatic probing, combined with graphical modeling of three RNA constructs of increasing size (38, 108, and 182 nt) derived from the 3'-terminal viral RNA sequence. The comparison between the probing patterns of the three RNAs allowed the determination of the relative orientation of these structural domains in the full-length viral tRNA-like structure. Modeling data indicate that only one of the two possible isomers of the three-way junction located at a central position of the tRNA-like domain is in agreement with structural data. Interestingly, this isomer gives rise to a molecule bearing a structural mimicry with the L-shape of canonical tRNAs. A pseudoknotted acceptor branch containing a T-like loop is located perpendicularly to an anticodon-like branch. Moreover, a single-stranded RNA stretch belonging to the pseudoknotted central core mimics a D-like loop and it is proposed that it interacts via two conserved guanosines with nucleotides of the T-like loop as found in canonical tRNAs. This model is valid for the 3' noncoding regions of tobamoviral RNAs as well as for the tRNA-like domain of the satellite tobacco mosaic virus RNA. All three molecules are substrates for yeast HisRS; however, whereas the complete viral genome is required for optimal histidylation capacities, both charging levels and affinity constants are decreased for the three RNA transcripts, suggesting that additional contacts located outside the tRNA-like domain are needed for an optimal aminoacylation process.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
A three-dimensional model of the histidylable 3'-terminal tRNA-like domain of tobacco mosaic virus RNA is proposed on the basis of a comparative structural analysis, chemical and enzymatic probing, combined with graphical modeling of three RNA constructs of increasing size (38, 108, and 182 nt) derived from the 3'-terminal viral RNA sequence. The comparison between the probing patterns of the three RNAs allowed the determination of the relative orientation of these structural domains in the full-length viral tRNA-like structure. Modeling data indicate that only one of the two possible isomers of the three-way junction located at a central position of the tRNA-like domain is in agreement with structural data. Interestingly, this isomer gives rise to a molecule bearing a structural mimicry with the L-shape of canonical tRNAs. A pseudoknotted acceptor branch containing a T-like loop is located perpendicularly to an anticodon-like branch. Moreover, a single-stranded RNA stretch belonging to the pseudoknotted central core mimics a D-like loop and it is proposed that it interacts via two conserved guanosines with nucleotides of the T-like loop as found in canonical tRNAs. This model is valid for the 3' noncoding regions of tobamoviral RNAs as well as for the tRNA-like domain of the satellite tobacco mosaic virus RNA. All three molecules are substrates for yeast HisRS; however, whereas the complete viral genome is required for optimal histidylation capacities, both charging levels and affinity constants are decreased for the three RNA transcripts, suggesting that additional contacts located outside the tRNA-like domain are needed for an optimal aminoacylation process.
Sissler M, Giege R, Florentz C
Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts Article de journal
Dans: EMBO J, vol. 15, no. 18, p. 5069-5076, 1996, ISBN: 8890180, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Arginine/*metabolism Base Sequence Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Arg/*chemistry/metabolism RNA, Asp/chemistry/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Fungal/*chemistry/metabolism RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts},
author = {M Sissler and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8890180},
isbn = {8890180},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {18},
pages = {5069-5076},
abstract = {Yeast arginyl-tRNA synthetase recognizes the non-modified wild-type transcripts derived from both yeast tRNA(Arg) and tRNA(Asp) with equal efficiency. It discriminates its cognate natural substrate, tRNA(Arg), from non-cognate tRNA(Asp) by a negative discrimination mechanism whereby a single methyl group acts as an anti-determinant. Considering these facts, recognition elements responsible for specific arginylation in yeast have been searched by studying the in vitro arginylation properties of a series of transcripts derived from yeast tRNA(Asp), considered as an arginine isoacceptor tRNA. In parallel, experiments on similar tRNA(Arg) transcripts were performed. Unexpectedly, in the tRNA(Arg) context, arginylation is basically linked to the presence of residue C35, whereas in the tRNA(Asp) context, it is deeply related to that of C36 and G37 but is insensitive to the nucleotide at position 35. Each of these nucleotides present in one host, is absent in the other host tRNA. Thus, arginine identity is dependent on two different specific recognition sets according to the tRNA framework investigated.},
note = {0261-4189
Journal Article},
keywords = {*Anticodon Arginine/*metabolism Base Sequence Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Arg/*chemistry/metabolism RNA, Asp/chemistry/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Fungal/*chemistry/metabolism RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yeast arginyl-tRNA synthetase recognizes the non-modified wild-type transcripts derived from both yeast tRNA(Arg) and tRNA(Asp) with equal efficiency. It discriminates its cognate natural substrate, tRNA(Arg), from non-cognate tRNA(Asp) by a negative discrimination mechanism whereby a single methyl group acts as an anti-determinant. Considering these facts, recognition elements responsible for specific arginylation in yeast have been searched by studying the in vitro arginylation properties of a series of transcripts derived from yeast tRNA(Asp), considered as an arginine isoacceptor tRNA. In parallel, experiments on similar tRNA(Arg) transcripts were performed. Unexpectedly, in the tRNA(Arg) context, arginylation is basically linked to the presence of residue C35, whereas in the tRNA(Asp) context, it is deeply related to that of C36 and G37 but is insensitive to the nucleotide at position 35. Each of these nucleotides present in one host, is absent in the other host tRNA. Thus, arginine identity is dependent on two different specific recognition sets according to the tRNA framework investigated.
Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.
Giege R, Florentz C, Kern D, Gangloff J, Eriani G, Moras D
Aspartate identity of transfer RNAs Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 605-623, 1996, ISBN: 8955904, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN
@article{,
title = {Aspartate identity of transfer RNAs},
author = {R Giege and C Florentz and D Kern and J Gangloff and G Eriani and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955904},
isbn = {8955904},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {605-623},
abstract = {Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.
Felden B, Florentz C, Westhof E, Giege R
Usefulness of functional and structural solution data for the modeling of tRNA-like structures Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 3-9, 1996, ISBN: 8786997, (0031-6865 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Models, Chemical Molecular Sequence Data RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry Solutions Support, Unité ARN
@article{,
title = {Usefulness of functional and structural solution data for the modeling of tRNA-like structures},
author = {B Felden and C Florentz and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8786997},
isbn = {8786997},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {3-9},
abstract = {Structures of large RNAs are not easily solved by X-ray crystallography or by NMR spectroscopy. This paper reviews the alternate methodology based on enzymatic and chemical mapping data collected on RNAs combined with graphical modeling for the construction of three-dimensional models. The different steps that lead to the establishment of the models are critically discussed. It is shown how the correctness of an RNA model can be strengthened by establishing correlations between the structure and the functionality of the molecule and its variants. Finally, the predictive potential of a model is discussed The approach is illustrated by results obtained on plant viral tRNA-like structures, and particularly on that of brome mosaic virus (BMV) RNA.},
note = {0031-6865
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Models, Chemical Molecular Sequence Data RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry Solutions Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Structures of large RNAs are not easily solved by X-ray crystallography or by NMR spectroscopy. This paper reviews the alternate methodology based on enzymatic and chemical mapping data collected on RNAs combined with graphical modeling for the construction of three-dimensional models. The different steps that lead to the establishment of the models are critically discussed. It is shown how the correctness of an RNA model can be strengthened by establishing correlations between the structure and the functionality of the molecule and its variants. Finally, the predictive potential of a model is discussed The approach is illustrated by results obtained on plant viral tRNA-like structures, and particularly on that of brome mosaic virus (BMV) RNA.
1994
Rudinger J, Florentz C, Giege R
Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 23, p. 5031-5037, 1994, ISBN: 7800496, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics Base Sequence Genes, Asp/genetics RNA, FLORENTZ, His/*chemistry/*genetics RNA, Non-U.S. Gov't Tymovirus/genetics Yeasts/enzymology, Synthetic/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Transfer, Unité ARN, Viral/metabolism Support
@article{,
title = {Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context},
author = {J Rudinger and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7800496},
isbn = {7800496},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {23},
pages = {5031-5037},
abstract = {Residue G-1 and discriminator base C73 are the major histidine identity elements in prokaryotes. Here we evaluate the importance of these two nucleotides in yeast histidine aminoacylation identity. Deletion of G-1 in yeast tRNA(His) transcript leads to a drastic loss of histidylation specificity (about 500-fold). Mutation of discriminator base A73, common to all yeast tRNA(His) species, into G73 has a more moderate but still significant effect with a 22-fold decrease in histidylation specificity. Changes at position 36 in the anticodon loop has negligible effect on histidylation. The role of residues -1 and 73 for specific aminoacylation by yeast HisRS was further investigated by studying the histidylation capacities of seven minihelices derived from the Turnip Yellow Mosaic Virus tRNA-like structure. Changes in the nature of nucleotides -1 and 73 modulate this activity but do not suppress it. The optimal mini-substrate for HisRS presents a G.A mismatch at the position equivalent to residues G-1.A73 in yeast tRNA(His), confirms the importance of this structural feature in yeast histidine identity. The fact that the minisubstrates contain a pseudoknot in which position -1 is mimicked by an internal nucleotide from the pseudoknot highlights further the necessity of a stacking interaction of this position over the amino acid accepting branch of the tRNA during the aminoacylation process. Individual transplantation of G-1 or A73 into yeast tRNA(Asp) transcript improves the histidylation efficiency of the engineered tRNA(Asp). However, a tRNA(Asp) transcript presenting simultaneously both residues G-1 and A73 becomes a less good substrate for HisRS, suggesting the importance of the structural context and/or the presence of antideterminants for an optimal expression of these two identity elements.},
note = {0305-1048
Journal Article},
keywords = {Anticodon/genetics Base Sequence Genes, Asp/genetics RNA, FLORENTZ, His/*chemistry/*genetics RNA, Non-U.S. Gov't Tymovirus/genetics Yeasts/enzymology, Synthetic/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Transfer, Unité ARN, Viral/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Residue G-1 and discriminator base C73 are the major histidine identity elements in prokaryotes. Here we evaluate the importance of these two nucleotides in yeast histidine aminoacylation identity. Deletion of G-1 in yeast tRNA(His) transcript leads to a drastic loss of histidylation specificity (about 500-fold). Mutation of discriminator base A73, common to all yeast tRNA(His) species, into G73 has a more moderate but still significant effect with a 22-fold decrease in histidylation specificity. Changes at position 36 in the anticodon loop has negligible effect on histidylation. The role of residues -1 and 73 for specific aminoacylation by yeast HisRS was further investigated by studying the histidylation capacities of seven minihelices derived from the Turnip Yellow Mosaic Virus tRNA-like structure. Changes in the nature of nucleotides -1 and 73 modulate this activity but do not suppress it. The optimal mini-substrate for HisRS presents a G.A mismatch at the position equivalent to residues G-1.A73 in yeast tRNA(His), confirms the importance of this structural feature in yeast histidine identity. The fact that the minisubstrates contain a pseudoknot in which position -1 is mimicked by an internal nucleotide from the pseudoknot highlights further the necessity of a stacking interaction of this position over the amino acid accepting branch of the tRNA during the aminoacylation process. Individual transplantation of G-1 or A73 into yeast tRNA(Asp) transcript improves the histidylation efficiency of the engineered tRNA(Asp). However, a tRNA(Asp) transcript presenting simultaneously both residues G-1 and A73 becomes a less good substrate for HisRS, suggesting the importance of the structural context and/or the presence of antideterminants for an optimal expression of these two identity elements.
Putz J, Florentz C, Benseler F, Giege R
A single methyl group prevents the mischarging of a tRNA Article de journal
Dans: Nat Struct Biol, vol. 1, no. 9, p. 580-582, 1994, ISBN: 7634096, (1072-8368 Letter).
Liens | BibTeX | Étiquettes: Arginine/*genetics Arginine-tRNA Ligase/metabolism Base Sequence Methylation Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*genetics/metabolism, FLORENTZ, Transfer, Unité ARN
@article{,
title = {A single methyl group prevents the mischarging of a tRNA},
author = {J Putz and C Florentz and F Benseler and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7634096},
isbn = {7634096},
year = {1994},
date = {1994-01-01},
journal = {Nat Struct Biol},
volume = {1},
number = {9},
pages = {580-582},
note = {1072-8368
Letter},
keywords = {Arginine/*genetics Arginine-tRNA Ligase/metabolism Base Sequence Methylation Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*genetics/metabolism, FLORENTZ, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nureki O, Niimi T, Muramatsu T, Kanno H, Kohno T, Florentz C, Giege R, Yokoyama S
Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli Article de journal
Dans: J Mol Biol, vol. 236, no. 3, p. 710-724, 1994, ISBN: 8114089, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/chemistry Base Composition Base Sequence Binding Sites Computer Graphics Escherichia coli/genetics/*metabolism Genes, Bacterial Genes, FLORENTZ, Ile/*chemistry/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Non-U.S. Gov't, Structural, Synthetic Isoleucine-tRNA Ligase/*metabolism Models, Transfer, Unité ARN
@article{,
title = {Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli},
author = {O Nureki and T Niimi and T Muramatsu and H Kanno and T Kohno and C Florentz and R Giege and S Yokoyama},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8114089},
isbn = {8114089},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {236},
number = {3},
pages = {710-724},
abstract = {Molecular recognition of Escherichia coli tRNA(Ile) by the cognate isoleucyl-tRNA synthetase (IleRS) was studied by analyses of chemical footprinting with N-nitroso-N-ethylurea and aminoacylation kinetics of variant tRNA(Ile) transcripts prepared with bacteriophage T7 RNA polymerase. IleRS binds to the acceptor, dihydrouridine (D), and anticodon stems as well as to the anticodon loop. The "complete set" of determinants for the tRNA(Ile) identity consists of most of the nucleotides in the anticodon loop (G34, A35, U36, t6A37 and A38), the discriminator nucleotide (A73), and the base-pairs in the middle of the anticodon, D and acceptor stems (C29.G41, U12.A23 and C4.G69, respectively). As for the tertiary base-pairs, two are indispensable for the isoleucylation activity, whereas the others are dispensable. Correspondingly, some of the phosphate groups of these dispensable tertiary base-pair residues were shown to be exposed to N-nitroso-N-ethylurea when tRNA(Ile) was bound with IleRS. Furthermore, deletion of the T psi C-arm only slightly impaired the tRNA(Ile) activity. Thus, it is proposed that the recognition by IleRS of all the widely distributed identity determinants is coupled with a global conformational change that involves the loosening of a particular set of tertiary base-pairs of tRNA(Ile).},
note = {0022-2836
Journal Article},
keywords = {Anticodon/chemistry Base Composition Base Sequence Binding Sites Computer Graphics Escherichia coli/genetics/*metabolism Genes, Bacterial Genes, FLORENTZ, Ile/*chemistry/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Non-U.S. Gov't, Structural, Synthetic Isoleucine-tRNA Ligase/*metabolism Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Molecular recognition of Escherichia coli tRNA(Ile) by the cognate isoleucyl-tRNA synthetase (IleRS) was studied by analyses of chemical footprinting with N-nitroso-N-ethylurea and aminoacylation kinetics of variant tRNA(Ile) transcripts prepared with bacteriophage T7 RNA polymerase. IleRS binds to the acceptor, dihydrouridine (D), and anticodon stems as well as to the anticodon loop. The "complete set" of determinants for the tRNA(Ile) identity consists of most of the nucleotides in the anticodon loop (G34, A35, U36, t6A37 and A38), the discriminator nucleotide (A73), and the base-pairs in the middle of the anticodon, D and acceptor stems (C29.G41, U12.A23 and C4.G69, respectively). As for the tertiary base-pairs, two are indispensable for the isoleucylation activity, whereas the others are dispensable. Correspondingly, some of the phosphate groups of these dispensable tertiary base-pair residues were shown to be exposed to N-nitroso-N-ethylurea when tRNA(Ile) was bound with IleRS. Furthermore, deletion of the T psi C-arm only slightly impaired the tRNA(Ile) activity. Thus, it is proposed that the recognition by IleRS of all the widely distributed identity determinants is coupled with a global conformational change that involves the loosening of a particular set of tertiary base-pairs of tRNA(Ile).
Frugier M, Soll D, Giege R, Florentz C
Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases Article de journal
Dans: Biochemistry, vol. 33, no. 33, p. 9912-9921, 1994, ISBN: 8060999, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases},
author = {M Frugier and D Soll and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8060999},
isbn = {8060999},
year = {1994},
date = {1994-01-01},
journal = {Biochemistry},
volume = {33},
number = {33},
pages = {9912-9921},
abstract = {High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.},
note = {0006-2960
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.
Frugier M, Florentz C, Hosseini M W, Lehn J M, Giege R
Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 14, p. 2784-2790, 1994, ISBN: 8052534, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support
@article{,
title = {Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase},
author = {M Frugier and C Florentz and M W Hosseini and J M Lehn and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8052534},
isbn = {8052534},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {14},
pages = {2784-2790},
abstract = {The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.},
note = {0305-1048
Journal Article},
keywords = {Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.
Frugier M, Florentz C, Giege R
Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide Article de journal
Dans: EMBO J, vol. 13, no. 9, p. 2218-2226, 1994, ISBN: 8187774, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8187774},
isbn = {8187774},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {9},
pages = {2218-2226},
abstract = {We show here that small RNA helices which recapitulate part or all of the acceptor stem of yeast aspartate tRNA are efficiently aminoacylated by cognate class II aspartyl-tRNA synthetase. Aminoacylation is strongly dependent on the presence of the single-stranded G73 'discriminator' identity nucleotide and is essentially insensitive to the sequence of the helical region. Substrates which contain as few as 3 bp fused to G73CCAOH are aspartylated. Their charging is insensitive to the sequence of the loop closing the short helical domains. Aminoacylation of the aspartate mini-helix is not stimulated by a hairpin helix mimicking the anticodon domain and containing the three major anticodon identity nucleotides. A thermodynamic analysis demonstrates that enzyme interactions with G73 in the resected RNA substrates and in the whole tRNA are the same. Thus, if the resected RNA molecules resemble in some way the earliest substrates for aminoacylation with aspartate, then the contemporary tRNA(Asp) has quantitatively retained the influence of the major signal for aminoacylation in these substrates.},
note = {0261-4189
Journal Article},
keywords = {Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We show here that small RNA helices which recapitulate part or all of the acceptor stem of yeast aspartate tRNA are efficiently aminoacylated by cognate class II aspartyl-tRNA synthetase. Aminoacylation is strongly dependent on the presence of the single-stranded G73 'discriminator' identity nucleotide and is essentially insensitive to the sequence of the helical region. Substrates which contain as few as 3 bp fused to G73CCAOH are aspartylated. Their charging is insensitive to the sequence of the loop closing the short helical domains. Aminoacylation of the aspartate mini-helix is not stimulated by a hairpin helix mimicking the anticodon domain and containing the three major anticodon identity nucleotides. A thermodynamic analysis demonstrates that enzyme interactions with G73 in the resected RNA substrates and in the whole tRNA are the same. Thus, if the resected RNA molecules resemble in some way the earliest substrates for aminoacylation with aspartate, then the contemporary tRNA(Asp) has quantitatively retained the influence of the major signal for aminoacylation in these substrates.
Felden B, Florentz C, McPherson A, Giege R
A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 15, p. 2882-2886, 1994, ISBN: 8065897, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support
@article{,
title = {A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA},
author = {B Felden and C Florentz and A McPherson and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8065897},
isbn = {8065897},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {15},
pages = {2882-2886},
abstract = {A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.},
note = {0305-1048
Journal Article},
keywords = {Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support},
pubstate = {published},
tppubtype = {article}
}
A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.
Felden B, Florentz C, Giege R, Westhof E
Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs Article de journal
Dans: J Mol Biol, vol. 235, no. 2, p. 508-531, 1994, ISBN: 8289279, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8289279},
isbn = {8289279},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {235},
number = {2},
pages = {508-531},
abstract = {The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.
1993
Putz J, Puglisi J D, Florentz C, Giege R
Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA Article de journal
Dans: EMBO J, vol. 12, no. 7, p. 2949-2957, 1993, ISBN: 8335008, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA},
author = {J Putz and J D Puglisi and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8335008},
isbn = {8335008},
year = {1993},
date = {1993-01-01},
journal = {EMBO J},
volume = {12},
number = {7},
pages = {2949-2957},
abstract = {We have investigated the functional relationship between nucleotides in yeast tRNAAsp that are important for aspartylation by yeast aspartyl-tRNA synthetase. Transcripts of tRNAAsp with two or more mutations at identity positions G73, G34, U35, C36 and base pair G10-U25 have been prepared and the steady-state kinetics of their aspartylation were measured. Multiple mutations affect the catalytic activities of the synthetase mainly at the level of the catalytic constant, kcat. Kinetic data were expressed as free energy variation at transition state of these multiple mutants and comparison of experimental values with those calculated from results on single mutants defined three types of relationships between the identity nucleotides of this tRNA. Nucleotides located far apart in the three-dimensional structure of the tRNA act cooperatively whereas nucleotides of the anticodon triplet act either additively or anti-cooperatively. These results are related to the specific interactions of functional groups on identity nucleotides with amino acids in the protein as revealed by the crystal structure of the tRNAAsp/aspartyl-tRNA synthetase complex. These relationships between identity nucleotides may play an important role in the biological function of tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We have investigated the functional relationship between nucleotides in yeast tRNAAsp that are important for aspartylation by yeast aspartyl-tRNA synthetase. Transcripts of tRNAAsp with two or more mutations at identity positions G73, G34, U35, C36 and base pair G10-U25 have been prepared and the steady-state kinetics of their aspartylation were measured. Multiple mutations affect the catalytic activities of the synthetase mainly at the level of the catalytic constant, kcat. Kinetic data were expressed as free energy variation at transition state of these multiple mutants and comparison of experimental values with those calculated from results on single mutants defined three types of relationships between the identity nucleotides of this tRNA. Nucleotides located far apart in the three-dimensional structure of the tRNA act cooperatively whereas nucleotides of the anticodon triplet act either additively or anti-cooperatively. These results are related to the specific interactions of functional groups on identity nucleotides with amino acids in the protein as revealed by the crystal structure of the tRNAAsp/aspartyl-tRNA synthetase complex. These relationships between identity nucleotides may play an important role in the biological function of tRNAs.
Puglisi J D, Putz J, Florentz C, Giege R
Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 1, p. 41-49, 1993, ISBN: 8441619, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN
@article{,
title = {Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase},
author = {J D Puglisi and J Putz and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8441619},
isbn = {8441619},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {1},
pages = {41-49},
abstract = {Mutations have been designed that disrupt the tertiary structure of yeast tRNA(Asp). The effects of these mutations on both tRNA structure and specific aspartylation by yeast aspartyl-tRNA synthetase were assayed. Mutations that disrupt tertiary interactions involving the D-stem or D-loop result in destabilization of the base-pairing in the D-stem, as monitored by nuclease digestion and chemical modification studies. These mutations also decrease the specificity constant (kcat/Km) for aspartylation by aspartyl-tRNA synthetase up to 10(3)-10(4) fold. The size of the T-loop also influences tRNA(Asp) structure and function; change of its T-loop to a tetraloop (-UUCG-) sequence results in a denatured D-stem and an almost 10(4) fold decrease of kcat/Km for aspartylation. The negative effects of these mutations on aspartylation activity are significantly alleviated by additional mutations that stabilize the D-stem. These results indicate that a critical role of tertiary structure in tRNA(Asp) for aspartylation is the maintenance of a base-paired D-stem.},
note = {0305-1048
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mutations have been designed that disrupt the tertiary structure of yeast tRNA(Asp). The effects of these mutations on both tRNA structure and specific aspartylation by yeast aspartyl-tRNA synthetase were assayed. Mutations that disrupt tertiary interactions involving the D-stem or D-loop result in destabilization of the base-pairing in the D-stem, as monitored by nuclease digestion and chemical modification studies. These mutations also decrease the specificity constant (kcat/Km) for aspartylation by aspartyl-tRNA synthetase up to 10(3)-10(4) fold. The size of the T-loop also influences tRNA(Asp) structure and function; change of its T-loop to a tetraloop (-UUCG-) sequence results in a denatured D-stem and an almost 10(4) fold decrease of kcat/Km for aspartylation. The negative effects of these mutations on aspartylation activity are significantly alleviated by additional mutations that stabilize the D-stem. These results indicate that a critical role of tertiary structure in tRNA(Asp) for aspartylation is the maintenance of a base-paired D-stem.
Giege R, Puglisi J D, Florentz C
tRNA structure and aminoacylation efficiency Article de journal
Dans: Prog Nucleic Acid Res Mol Biol, vol. 45, p. 129-206, 1993, ISBN: 8341800, (0079-6603 Journal Article Review Review, Academic).
Liens | BibTeX | Étiquettes: Acylation Amino Acids/metabolism Amino Acyl-tRNA Ligases/metabolism Animals Base Sequence Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry/metabolism Support, Unité ARN
@article{,
title = {tRNA structure and aminoacylation efficiency},
author = {R Giege and J D Puglisi and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8341800},
isbn = {8341800},
year = {1993},
date = {1993-01-01},
journal = {Prog Nucleic Acid Res Mol Biol},
volume = {45},
pages = {129-206},
note = {0079-6603
Journal Article
Review
Review, Academic},
keywords = {Acylation Amino Acids/metabolism Amino Acyl-tRNA Ligases/metabolism Animals Base Sequence Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R, Florentz C, Dreher T W
The TYMV tRNA-like structure Article de journal
Dans: Biochimie, vol. 75, no. 7, p. 569-582, 1993, ISBN: 8268257, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Transfer/*chemistry/metabolism RNA, Unité ARN, Viral/*chemistry/metabolism Tymovirus/*genetics
@article{,
title = {The TYMV tRNA-like structure},
author = {R Giege and C Florentz and T W Dreher},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268257},
isbn = {8268257},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {7},
pages = {569-582},
abstract = {The genomic RNA from turnip yellow mosaic virus presents a 3'-end functionally and structurally related to tRNAs. This report summarizes our knowledge about the peculiar structure of the tRNA-like domain and its interaction with tRNA specific proteins, like RNAse P, tRNA nucleotidyl-transferase, aminoacyl-tRNA synthetases, and elongation factors. It discusses also the biological role of this structure in the viral life cycle. A brief survey of our knowledge of other tRNA mimicries in biological systems, as well as their relevance for understanding canonical tRNA, will also be presented.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Transfer/*chemistry/metabolism RNA, Unité ARN, Viral/*chemistry/metabolism Tymovirus/*genetics},
pubstate = {published},
tppubtype = {article}
}
The genomic RNA from turnip yellow mosaic virus presents a 3'-end functionally and structurally related to tRNAs. This report summarizes our knowledge about the peculiar structure of the tRNA-like domain and its interaction with tRNA specific proteins, like RNAse P, tRNA nucleotidyl-transferase, aminoacyl-tRNA synthetases, and elongation factors. It discusses also the biological role of this structure in the viral life cycle. A brief survey of our knowledge of other tRNA mimicries in biological systems, as well as their relevance for understanding canonical tRNA, will also be presented.
Frugier M, Florentz C, Schimmel P, Giege R
Triple aminoacylation specificity of a chimerized transfer RNA Article de journal
Dans: Biochemistry, vol. 32, no. 50, p. 14053-14061, 1993, ISBN: 8268184, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Triple aminoacylation specificity of a chimerized transfer RNA},
author = {M Frugier and C Florentz and P Schimmel and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268184},
isbn = {8268184},
year = {1993},
date = {1993-01-01},
journal = {Biochemistry},
volume = {32},
number = {50},
pages = {14053-14061},
abstract = {We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.},
note = {0006-2960
Journal Article},
keywords = {Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.
Felden B, Florentz C, Westhof E, Giege R
Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA Article de journal
Dans: Biochimie, vol. 75, no. 12, p. 1143-1157, 1993, ISBN: 8199250, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Genome, FLORENTZ, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Promoter Regions (Genetics) RNA, Non-U.S. Gov't Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism RNA, Unité ARN, Viral Models, Viral/*chemistry/genetics/metabolism Structure-Activity Relationship Support
@article{,
title = {Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA},
author = {B Felden and C Florentz and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199250},
isbn = {8199250},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {12},
pages = {1143-1157},
abstract = {A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicularly and mimicking a tRNA structure, and a fifth domain which makes the connection with the rest of the viral RNA. After recalling the different steps that led to the present structural knowledge of the BMV tRNA-like domain, we review its novel structural features revealed by the modelling and that did not appear in older versions of 3-D models of this structure. These features comprise additional base-pairs, hairpin loops, new tertiary long-range interactions, and a second pseudoknot. The main goal of this paper is to strengthen the validity of the model by establishing correlations between the putative 3-D conformation and the functional properties of the domain. For that, we show how the present structural model rationalises mutagenic and footprinting data that have established the importance of specific regions of the RNA for its recognition and aminoacylation by yeast tyrosyl-tRNA synthetase. We discuss further how the model corroborates mutational analyses performed to understand recognition of this RNA domain by the (ATP,CTP):tRNA nucleotidyl-transferase and by the viral replicase. The published mutants of the BMV tRNA-like domain fall into two classes. In one class, the mutants leave unchanged the overall architecture of the molecule, thereby affecting functions directly. In the second class, the overall architecture of the mutants is perturbed, and thus functions are affected indirectly.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Bromovirus/*genetics Computer Simulation Genome, FLORENTZ, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Promoter Regions (Genetics) RNA, Non-U.S. Gov't Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism RNA, Unité ARN, Viral Models, Viral/*chemistry/genetics/metabolism Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicularly and mimicking a tRNA structure, and a fifth domain which makes the connection with the rest of the viral RNA. After recalling the different steps that led to the present structural knowledge of the BMV tRNA-like domain, we review its novel structural features revealed by the modelling and that did not appear in older versions of 3-D models of this structure. These features comprise additional base-pairs, hairpin loops, new tertiary long-range interactions, and a second pseudoknot. The main goal of this paper is to strengthen the validity of the model by establishing correlations between the putative 3-D conformation and the functional properties of the domain. For that, we show how the present structural model rationalises mutagenic and footprinting data that have established the importance of specific regions of the RNA for its recognition and aminoacylation by yeast tyrosyl-tRNA synthetase. We discuss further how the model corroborates mutational analyses performed to understand recognition of this RNA domain by the (ATP,CTP):tRNA nucleotidyl-transferase and by the viral replicase. The published mutants of the BMV tRNA-like domain fall into two classes. In one class, the mutants leave unchanged the overall architecture of the molecule, thereby affecting functions directly. In the second class, the overall architecture of the mutants is perturbed, and thus functions are affected indirectly.
1992
Rudinger J, Puglisi J D, Putz J, Schatz D, Eckstein F, Florentz C, Giege R
Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 89, no. 13, p. 5882-5886, 1992, ISBN: 1631068, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase},
author = {J Rudinger and J D Puglisi and J Putz and D Schatz and F Eckstein and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1631068},
isbn = {1631068},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {13},
pages = {5882-5886},
abstract = {The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.},
note = {0027-8424
Journal Article},
keywords = {Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.
Rudinger J, Florentz C, Dreher T, Giege R
Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 8, p. 1865-1870, 1992, ISBN: 1579487, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support
@article{,
title = {Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA},
author = {J Rudinger and C Florentz and T Dreher and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579487},
isbn = {1579487},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {8},
pages = {1865-1870},
abstract = {Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.
Perret V, Florentz C, Puglisi J D, Giege R
Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities Article de journal
Dans: J Mol Biol, vol. 226, no. 2, p. 323-333, 1992, ISBN: 1640453, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Activation Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism RNA, Asp/metabolism/*ultrastructure RNA, FLORENTZ, Fungal/metabolism/ultrastructure RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure Saccharomyces cerevisiae Structure-Activity Relationship Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities},
author = {V Perret and C Florentz and J D Puglisi and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1640453},
isbn = {1640453},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {226},
number = {2},
pages = {323-333},
abstract = {The structure and function of in vitro transcribed tRNA(Asp) variants with inserted conformational features characteristic of yeast tRNA(Phe), such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA(Phe) were transplanted into the previous structural variants of tRNA(Asp). The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA(Phe), suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA(Asp) identity elements into yeast tRNA(Phe). This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Activation Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism RNA, Asp/metabolism/*ultrastructure RNA, FLORENTZ, Fungal/metabolism/ultrastructure RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure Saccharomyces cerevisiae Structure-Activity Relationship Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The structure and function of in vitro transcribed tRNA(Asp) variants with inserted conformational features characteristic of yeast tRNA(Phe), such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA(Phe) were transplanted into the previous structural variants of tRNA(Asp). The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA(Phe), suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA(Asp) identity elements into yeast tRNA(Phe). This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.
Frugier M, Florentz C, Giege R
Anticodon-independent aminoacylation of an RNA minihelix with valine Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 89, no. 9, p. 3990-3994, 1992, ISBN: 1570324, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support
@article{,
title = {Anticodon-independent aminoacylation of an RNA minihelix with valine},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1570324},
isbn = {1570324},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {9},
pages = {3990-3994},
abstract = {Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.},
note = {0027-8424
Journal Article},
keywords = {*Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.
Dreher T W, Tsai C H, Florentz C, Giege R
Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides Article de journal
Dans: Biochemistry, vol. 31, no. 38, p. 9183-9189, 1992, ISBN: 1390705, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support
@article{,
title = {Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides},
author = {T W Dreher and C H Tsai and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1390705},
isbn = {1390705},
year = {1992},
date = {1992-01-01},
journal = {Biochemistry},
volume = {31},
number = {38},
pages = {9183-9189},
abstract = {The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].},
note = {0006-2960
Journal Article},
keywords = {Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support},
pubstate = {published},
tppubtype = {article}
}
The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].
