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2002
Goldschmidt V, Rigourd M, Ehresmann C, Grice S F Le, Ehresmann B, Marquet R
Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 277, no. 45, p. 43233-43242, 2002, ISBN: 12194974, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Primers DNA Replication HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Human Kinetics Polymerase Chain Reaction RNA, Genetic, Lys/genetics RNA, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN, Viral/*chemistry/*genetics/metabolism Support
@article{,
title = {Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription},
author = {V Goldschmidt and M Rigourd and C Ehresmann and S F Le Grice and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12194974},
isbn = {12194974},
year = {2002},
date = {2002-01-01},
journal = {J Biol Chem},
volume = {277},
number = {45},
pages = {43233-43242},
abstract = {Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition between the viral RNA (vRNA), tRNA(3)(Lys), which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between the HIV-1 RNA and tRNA(3)(Lys). Here, we compared the relative importance of the secondary structure elements of this complex in the initiation process. To this aim, we used the previously published three-dimensional model of the initiation complex to rationally introduce a series of deletions and substitutions in the vRNA. When necessary, we used chemical probing to check the structure of the tRNA(3)(Lys)-mutant vRNA complexes. For each of them, we measured the binding affinity of RT and the kinetics of initial extension of tRNA(3)(Lys) and of synthesis of the (-) strand strong stop DNA. Our results were overall in keeping with the three-dimensional model of the initiation complex. Surprisingly, we found that disruption of the intermolecular template-primer interactions, which are not directly recognized by RT, more severely affected reverse transcription than deletions or disruption of one of the intramolecular helices to which RT directly binds. Perturbations of the highly constrained junction between the intermolecular helix formed by the primer binding site and the 3' end of tRNA(3)(Lys) and the helix immediately upstream also had dramatic effects on the initiation of reverse transcription. Taken together, our results demonstrate the overwhelming importance of the overall three-dimensional structure of the initiation complex and identify structural elements that constitute promising targets for anti-initiation-specific drugs.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA Primers DNA Replication HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Human Kinetics Polymerase Chain Reaction RNA, Genetic, Lys/genetics RNA, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN, Viral/*chemistry/*genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition between the viral RNA (vRNA), tRNA(3)(Lys), which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between the HIV-1 RNA and tRNA(3)(Lys). Here, we compared the relative importance of the secondary structure elements of this complex in the initiation process. To this aim, we used the previously published three-dimensional model of the initiation complex to rationally introduce a series of deletions and substitutions in the vRNA. When necessary, we used chemical probing to check the structure of the tRNA(3)(Lys)-mutant vRNA complexes. For each of them, we measured the binding affinity of RT and the kinetics of initial extension of tRNA(3)(Lys) and of synthesis of the (-) strand strong stop DNA. Our results were overall in keeping with the three-dimensional model of the initiation complex. Surprisingly, we found that disruption of the intermolecular template-primer interactions, which are not directly recognized by RT, more severely affected reverse transcription than deletions or disruption of one of the intramolecular helices to which RT directly binds. Perturbations of the highly constrained junction between the intermolecular helix formed by the primer binding site and the 3' end of tRNA(3)(Lys) and the helix immediately upstream also had dramatic effects on the initiation of reverse transcription. Taken together, our results demonstrate the overwhelming importance of the overall three-dimensional structure of the initiation complex and identify structural elements that constitute promising targets for anti-initiation-specific drugs.
Brule F, Marquet R, Rong L, Wainberg M A, Roques B P, Grice S F Le, Ehresmann B, Ehresmann C
Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex Article de journal
Dans: RNA, vol. 8, no. 1, p. 8-15, 2002, ISBN: 11873759, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Genetic, Genetic Transcription, Lys/*chemistry/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*chemistry/genetics/metabolism Support
@article{,
title = {Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex},
author = {F Brule and R Marquet and L Rong and M A Wainberg and B P Roques and S F Le Grice and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11873759},
isbn = {11873759},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {1},
pages = {8-15},
abstract = {The conversion of the single-stranded RNA genome into double-stranded DNA by virus-coded reverse transcriptase (RT) is an essential step of the retrovirus life cycle. In human immunodeficiency virus type 1 (HIV-1), RT uses the cellular tRNA(Lys)3 to initiate the (-) strand DNA synthesis. Placement of the primer tRNA(Lys)3 involves binding of its 3'-terminal 18 nt to a complementary region of genomic RNA termed PBS. However, the PBS sequence is not the unique determinant of primer usage and additional contacts are important. This placement is believed to be achieved in vivo by the nucleocapsid domain of Gag or by the mature protein NCp. Up to now, structural information essentially arose from heat-annealed primer-template complexes (Isel et al., J Mol Biol, 1995, 247:236-250; Isel et al., EMBO J, 1999, 18:1038-1048). Here, we investigated the formation of the primer-template complex mediated by NCp and compared structural and functional properties of heat- and NCp-annealed complexes. We showed that both heat- and NCp-mediated procedures allow comparable high yields of annealing. Then, we investigated structural features of both kinds of complexes by enzymatic probing, and we compared their relative efficiency in (-) strong stop DNA synthesis. We did not find any significant differences between these complexes, suggesting that information derived from the heat-annealed complex can be transposed to the NCp-mediated complex and most likely to complexes formed in vivo.},
note = {1355-8382
Journal Article},
keywords = {Genetic, Genetic Transcription, Lys/*chemistry/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*chemistry/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
The conversion of the single-stranded RNA genome into double-stranded DNA by virus-coded reverse transcriptase (RT) is an essential step of the retrovirus life cycle. In human immunodeficiency virus type 1 (HIV-1), RT uses the cellular tRNA(Lys)3 to initiate the (-) strand DNA synthesis. Placement of the primer tRNA(Lys)3 involves binding of its 3'-terminal 18 nt to a complementary region of genomic RNA termed PBS. However, the PBS sequence is not the unique determinant of primer usage and additional contacts are important. This placement is believed to be achieved in vivo by the nucleocapsid domain of Gag or by the mature protein NCp. Up to now, structural information essentially arose from heat-annealed primer-template complexes (Isel et al., J Mol Biol, 1995, 247:236-250; Isel et al., EMBO J, 1999, 18:1038-1048). Here, we investigated the formation of the primer-template complex mediated by NCp and compared structural and functional properties of heat- and NCp-annealed complexes. We showed that both heat- and NCp-mediated procedures allow comparable high yields of annealing. Then, we investigated structural features of both kinds of complexes by enzymatic probing, and we compared their relative efficiency in (-) strong stop DNA synthesis. We did not find any significant differences between these complexes, suggesting that information derived from the heat-annealed complex can be transposed to the NCp-mediated complex and most likely to complexes formed in vivo.
2001
Carnicelli D., Brigotti M., Rizzi S., Keith G., Montanaro L., Sperti S.
Nucleotides U28-A42 and A37 in unmodified yeast tRNA(Trp) as negative identity elements for bovine tryptophanyl-tRNA synthetase Article de journal
Dans: FEBS Lett, vol. 492, no. 3, p. 238-41, 2001, (0014-5793 Journal Article).
Résumé | BibTeX | Étiquettes: Acid, Adenine/chemistry, Animals, Base, Cattle, cerevisiae/genetics, Conformation, Data, Fungal/genetics/metabolism, Gov't, Kinetics, Ligase/*metabolism, Molecular, Non-U.S., Nucleic, RNA, Saccharomyces, Sequence, Species, Specificity, Substrate, Support, Transfer, Trp/chemistry/*metabolism, Tryptophan-tRNA, Uridine/chemistry
@article{,
title = {Nucleotides U28-A42 and A37 in unmodified yeast tRNA(Trp) as negative identity elements for bovine tryptophanyl-tRNA synthetase},
author = { D. Carnicelli and M. Brigotti and S. Rizzi and G. Keith and L. Montanaro and S. Sperti},
year = {2001},
date = {2001-01-01},
journal = {FEBS Lett},
volume = {492},
number = {3},
pages = {238-41},
abstract = {Wild-type bovine and yeast tRNA(Trp) are efficiently aminoacylated by tryptophanyl-tRNA synthetase both from beef and from yeast. Upon loss of modified bases in the synthetic transcripts, mammalian tRNA(Trp) retains the double recognition by the two synthetases, while yeast tRNA(Trp) loses its substrate properties for the bovine enzyme and is recognised only by the cognate synthetase. By testing chimeric bovine-yeast transcripts with tryptophanyl-tRNA synthetase purified from beef pancreas, the nucleotides responsible for the loss of charging of the synthetic yeast transcript have been localised in the anticodon arm. A complete loss of charging akin to that observed with the yeast transcript requires substitution in the bovine backbone of G37 in the anticodon loop with yeast A37 and of C28-G42 in the anticodon stem with yeast U28-A42. Since A37 does not prevent aminoacylation of the wild-type yeast tRNA(Trp) by the beef enzyme, a negative combination apparently emerges in the synthetic transcript after unmasking of U28 by loss of pseudourydilation.},
note = {0014-5793
Journal Article},
keywords = {Acid, Adenine/chemistry, Animals, Base, Cattle, cerevisiae/genetics, Conformation, Data, Fungal/genetics/metabolism, Gov't, Kinetics, Ligase/*metabolism, Molecular, Non-U.S., Nucleic, RNA, Saccharomyces, Sequence, Species, Specificity, Substrate, Support, Transfer, Trp/chemistry/*metabolism, Tryptophan-tRNA, Uridine/chemistry},
pubstate = {published},
tppubtype = {article}
}
Wild-type bovine and yeast tRNA(Trp) are efficiently aminoacylated by tryptophanyl-tRNA synthetase both from beef and from yeast. Upon loss of modified bases in the synthetic transcripts, mammalian tRNA(Trp) retains the double recognition by the two synthetases, while yeast tRNA(Trp) loses its substrate properties for the bovine enzyme and is recognised only by the cognate synthetase. By testing chimeric bovine-yeast transcripts with tryptophanyl-tRNA synthetase purified from beef pancreas, the nucleotides responsible for the loss of charging of the synthetic yeast transcript have been localised in the anticodon arm. A complete loss of charging akin to that observed with the yeast transcript requires substitution in the bovine backbone of G37 in the anticodon loop with yeast A37 and of C28-G42 in the anticodon stem with yeast U28-A42. Since A37 does not prevent aminoacylation of the wild-type yeast tRNA(Trp) by the beef enzyme, a negative combination apparently emerges in the synthetic transcript after unmasking of U28 by loss of pseudourydilation.
Senger B, Despons L, Walter P, Jakubowski H, Fasiolo F
Yeast cytoplasmic and mitochondrial methionyl-tRNA synthetases: two structural frameworks for identical functions Article de journal
Dans: J Mol Biol, vol. 311, no. 1, p. 205-216, 2001, ISBN: 11469869, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Amino Acid Sequence Binding Sites Coenzyme A/metabolism Comparative Study Cysteine/genetics/metabolism Cytoplasm/*enzymology Genes, Fungal/genetics Genetic Complementation Test Homocysteine/genetics/metabolism Kinetics Methionine/metabolism Methionine-tRNA Ligase/*chemistry/genetics/*metabolism Mitochondria/*enzymology Molecular Sequence Data Mutation/genetics Protein Transport RNA, Met/genetics/metabolism Saccharomyces cerevisiae/cytology/*enzymology/genetics Sequence Alignment Structure-Activity Relationship Support, Non-P.H.S. Zinc/metabolism Zinc Fingers/genetics/physiology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Yeast cytoplasmic and mitochondrial methionyl-tRNA synthetases: two structural frameworks for identical functions},
author = {B Senger and L Despons and P Walter and H Jakubowski and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11469869},
isbn = {11469869},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {311},
number = {1},
pages = {205-216},
abstract = {The yeast Saccharomyces cerevisiae possesses two methionyl-tRNA synthetases (MetRS), one in the cytoplasm and the other in mitochondria. The cytoplasmic MetRS has a zinc-finger motif of the type Cys-X(2)-Cys-X(9)-Cys-X(2)-Cys in an insertion domain that divides the nucleotide-binding fold into two halves, whereas no such motif is present in the mitochondrial MetRS. Here, we show that tightly bound zinc atom is present in the cytoplasmic MetRS but not in the mitochondrial MetRS. To test whether the presence of a zinc-binding site is required for cytoplasmic functions of MetRS, we constructed a yeast strain in which cytoplasmic MetRS gene was inactivated and the mitochondrial MetRS gene was expressed in the cytoplasm. Provided that methionine-accepting tRNA is overexpressed, this strain was viable, indicating that mitochondrial MetRS was able to aminoacylate tRNA(Met) in the cytoplasm. Site-directed mutagenesis demonstrated that the zinc domain was required for the stability and consequently for the activity of cytoplasmic MetRS. Mitochondrial MetRS, like cytoplasmic MetRS, supported homocysteine editing in vivo in the yeast cytoplasm. Both MetRSs catalyzed homocysteine editing and aminoacylation of coenzyme A in vitro. Thus, identical synthetic and editing functions can be carried out in different structural frameworks of cytoplasmic and mitochondrial MetRSs.},
note = {0022-2836
Journal Article},
keywords = {Acylation Amino Acid Sequence Binding Sites Coenzyme A/metabolism Comparative Study Cysteine/genetics/metabolism Cytoplasm/*enzymology Genes, Fungal/genetics Genetic Complementation Test Homocysteine/genetics/metabolism Kinetics Methionine/metabolism Methionine-tRNA Ligase/*chemistry/genetics/*metabolism Mitochondria/*enzymology Molecular Sequence Data Mutation/genetics Protein Transport RNA, Met/genetics/metabolism Saccharomyces cerevisiae/cytology/*enzymology/genetics Sequence Alignment Structure-Activity Relationship Support, Non-P.H.S. Zinc/metabolism Zinc Fingers/genetics/physiology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The yeast Saccharomyces cerevisiae possesses two methionyl-tRNA synthetases (MetRS), one in the cytoplasm and the other in mitochondria. The cytoplasmic MetRS has a zinc-finger motif of the type Cys-X(2)-Cys-X(9)-Cys-X(2)-Cys in an insertion domain that divides the nucleotide-binding fold into two halves, whereas no such motif is present in the mitochondrial MetRS. Here, we show that tightly bound zinc atom is present in the cytoplasmic MetRS but not in the mitochondrial MetRS. To test whether the presence of a zinc-binding site is required for cytoplasmic functions of MetRS, we constructed a yeast strain in which cytoplasmic MetRS gene was inactivated and the mitochondrial MetRS gene was expressed in the cytoplasm. Provided that methionine-accepting tRNA is overexpressed, this strain was viable, indicating that mitochondrial MetRS was able to aminoacylate tRNA(Met) in the cytoplasm. Site-directed mutagenesis demonstrated that the zinc domain was required for the stability and consequently for the activity of cytoplasmic MetRS. Mitochondrial MetRS, like cytoplasmic MetRS, supported homocysteine editing in vivo in the yeast cytoplasm. Both MetRSs catalyzed homocysteine editing and aminoacylation of coenzyme A in vitro. Thus, identical synthetic and editing functions can be carried out in different structural frameworks of cytoplasmic and mitochondrial MetRSs.
Schiffer S, Helm M, Théobald-Dietrich A, Giege R, Marchfelder A
The plant tRNA 3' processing enzyme has a broad substrate spectrum Article de journal
Dans: Biochemistry, vol. 40, no. 28, p. 8264-8272, 2001, ISBN: 11444972, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Non-U.S. Gov't, Plant/genetics/*metabolism RNA, Post-Transcriptional RNA, Transfer, Tyr/genetics/*metabolism Substrate Specificity/genetics Support, Unité ARN
@article{,
title = {The plant tRNA 3' processing enzyme has a broad substrate spectrum},
author = {S Schiffer and M Helm and A Théobald-Dietrich and R Giege and A Marchfelder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11444972},
isbn = {11444972},
year = {2001},
date = {2001-01-01},
journal = {Biochemistry},
volume = {40},
number = {28},
pages = {8264-8272},
abstract = {To elucidate the minimal substrate for the plant nuclear tRNA 3' processing enzyme, we synthesized a set of tRNA variants, which were subsequently incubated with the nuclear tRNA 3' processing enzyme. Our experiments show that the minimal substrate for the nuclear RNase Z consists of the acceptor stem and T arm. The broad substrate spectrum of the nuclear RNase Z raises the possibility that this enzyme might have additional functions in the nucleus besides tRNA 3' processing. Incubation of tRNA variants with the plant mitochondrial enzyme revealed that the organellar counterpart of the nuclear enzyme has a much narrower substrate spectrum. The mitochondrial RNase Z only tolerates deletion of anticodon and variable arms and only with a drastic reduction in cleavage efficiency, indicating that the mitochondrial activity can only cleave bona fide tRNA substrates efficiently. Both enzymes prefer precursors containing short 3' trailers over extended 3' additional sequences. Determination of cleavage sites showed that the cleavage site is not shifted in any of the tRNA variant precursors.},
note = {0006-2960
Journal Article},
keywords = {Non-U.S. Gov't, Plant/genetics/*metabolism RNA, Post-Transcriptional RNA, Transfer, Tyr/genetics/*metabolism Substrate Specificity/genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
To elucidate the minimal substrate for the plant nuclear tRNA 3' processing enzyme, we synthesized a set of tRNA variants, which were subsequently incubated with the nuclear tRNA 3' processing enzyme. Our experiments show that the minimal substrate for the nuclear RNase Z consists of the acceptor stem and T arm. The broad substrate spectrum of the nuclear RNase Z raises the possibility that this enzyme might have additional functions in the nucleus besides tRNA 3' processing. Incubation of tRNA variants with the plant mitochondrial enzyme revealed that the organellar counterpart of the nuclear enzyme has a much narrower substrate spectrum. The mitochondrial RNase Z only tolerates deletion of anticodon and variable arms and only with a drastic reduction in cleavage efficiency, indicating that the mitochondrial activity can only cleave bona fide tRNA substrates efficiently. Both enzymes prefer precursors containing short 3' trailers over extended 3' additional sequences. Determination of cleavage sites showed that the cleavage site is not shifted in any of the tRNA variant precursors.
2000
Delagoutte B., Keith G., Moras D., Cavarelli J.
Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 56, no. Pt 4, p. 492-4, 2000, (0907-4449 Journal Article).
Résumé | BibTeX | Étiquettes: &, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray
@article{,
title = {Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes},
author = { B. Delagoutte and G. Keith and D. Moras and J. Cavarelli},
year = {2000},
date = {2000-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {56},
number = {Pt 4},
pages = {492-4},
abstract = {Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64},
note = {0907-4449
Journal Article},
keywords = {&, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64
Zenkova M A, Vlasov A V, Konevets D A, Sil'nikov V N, Giege R, Vlasov V V
[Chemical ribonucleases. 2. Design and hydrolytic properties RNase mimetics based on diazabicyclo[2.2.2]octane with various positive charges] Article de journal
Dans: Bioorg Khim, vol. 26, no. 9, p. 679-685, 2000, ISBN: 11036527, (0132-3423 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bicyclo Compounds, Heterocyclic/*chemical synthesis/chemistry Catalysis Cations, Lys/chemistry/genetics Ribonucleases/*chemistry Structure-Activity Relationship, Monovalent/chemistry Drug Design English Abstract Human Hydrolysis Imidazoles/*chemical synthesis/chemistry Magnesium/chemistry Mitochondria/chemistry Molecular Mimicry Point Mutation RNA, Transfer, Unité ARN
@article{,
title = {[Chemical ribonucleases. 2. Design and hydrolytic properties RNase mimetics based on diazabicyclo[2.2.2]octane with various positive charges]},
author = {M A Zenkova and A V Vlasov and D A Konevets and V N Sil'nikov and R Giege and V V Vlasov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11036527},
isbn = {11036527},
year = {2000},
date = {2000-01-01},
journal = {Bioorg Khim},
volume = {26},
number = {9},
pages = {679-685},
abstract = {A procedure was proposed allowing one to synthesize RNA mimics on the basis of conjugates of diazabicyclo[2.2.2]octane with imidazole bearing a varying number of positive charges (nDm series, where n is the number of positive charges at neutral pH, m is the code of an imidazole-containing fragment of the catalytic domain: 1, histamine; 2, histidine methyl ester). The hydrolytic activity of six compounds of this series was studied under physiological conditions using in vitro transcript of human mitochondrial tRNA(Lys) as a substrate. It was shown that the rate of RNA hydrolysis with nDm conjugates rises with an increase in the number of positive charges: an approximately 30-fold acceleration of hydrolysis was observed with an increase in the total charge of the construct from +2 to +4.},
note = {0132-3423
Journal Article},
keywords = {Bicyclo Compounds, Heterocyclic/*chemical synthesis/chemistry Catalysis Cations, Lys/chemistry/genetics Ribonucleases/*chemistry Structure-Activity Relationship, Monovalent/chemistry Drug Design English Abstract Human Hydrolysis Imidazoles/*chemical synthesis/chemistry Magnesium/chemistry Mitochondria/chemistry Molecular Mimicry Point Mutation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A procedure was proposed allowing one to synthesize RNA mimics on the basis of conjugates of diazabicyclo[2.2.2]octane with imidazole bearing a varying number of positive charges (nDm series, where n is the number of positive charges at neutral pH, m is the code of an imidazole-containing fragment of the catalytic domain: 1, histamine; 2, histidine methyl ester). The hydrolytic activity of six compounds of this series was studied under physiological conditions using in vitro transcript of human mitochondrial tRNA(Lys) as a substrate. It was shown that the rate of RNA hydrolysis with nDm conjugates rises with an increase in the number of positive charges: an approximately 30-fold acceleration of hydrolysis was observed with an increase in the total charge of the construct from +2 to +4.
Wittberger D, Berens C, Hammann C, Westhof E, Schroeder R
Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs Article de journal
Dans: J Mol Biol, vol. 300, no. 2, p. 339-352, 2000, ISBN: 10873469, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support
@article{,
title = {Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs},
author = {D Wittberger and C Berens and C Hammann and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10873469},
isbn = {10873469},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {300},
number = {2},
pages = {339-352},
abstract = {In order to evaluate uranyl photocleavage as a tool to identify and characterize structural and dynamic properties in RNA, we compared uranyl cleavage sites in five RNA molecules with known X-ray structures, namely the hammerhead and hepatitis delta virus ribozymes, the P4-P6 domain of the Tetrahymena group I intron, as well as tRNA(Phe) and tRNA(Asp) from yeast. Uranyl photocleavage was observed at specific positions in all molecules investigated. In order to characterize the sites, photocleavage was performed in the absence and in increasing amounts of MgCl(2). Uranyl photocleavage correlates well with sites of low calculated accessibility, suggesting that uranyl ions bind in tight RNA pockets formed by close approach of phosphate groups. RNA foldings require ion binding, usually magnesium ions. Thus, upon the adoption of the native structure, uranyl ions can no longer bind well except in flexible and open to the solvent regions that can undergo induced-fit without disrupting the native fold. Uranyl photocleavage was compared to N-ethyl-N-nitrosourea and lead-induced cleavages in the context of the three-dimensional X-ray structures. Overall, the regions protected from ENU attack are sites of uranyl cleavage, indicating sites of low accessibility which can form ion binding sites. On the contrary, lead cleavages occur at flexible and accessible sites and correlate with the unspecific cleavages prevalent in dynamic and open regions. Applied in a magnesium-dependent manner, and only in combination with other backbone probing agents such as N-ethyl-N-nitrosourea, lead and Fenton cleavage, uranyl probing has the potential to reveal high-affinity metal ion environments, as well as regions involved in conformational transitions.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support},
pubstate = {published},
tppubtype = {article}
}
In order to evaluate uranyl photocleavage as a tool to identify and characterize structural and dynamic properties in RNA, we compared uranyl cleavage sites in five RNA molecules with known X-ray structures, namely the hammerhead and hepatitis delta virus ribozymes, the P4-P6 domain of the Tetrahymena group I intron, as well as tRNA(Phe) and tRNA(Asp) from yeast. Uranyl photocleavage was observed at specific positions in all molecules investigated. In order to characterize the sites, photocleavage was performed in the absence and in increasing amounts of MgCl(2). Uranyl photocleavage correlates well with sites of low calculated accessibility, suggesting that uranyl ions bind in tight RNA pockets formed by close approach of phosphate groups. RNA foldings require ion binding, usually magnesium ions. Thus, upon the adoption of the native structure, uranyl ions can no longer bind well except in flexible and open to the solvent regions that can undergo induced-fit without disrupting the native fold. Uranyl photocleavage was compared to N-ethyl-N-nitrosourea and lead-induced cleavages in the context of the three-dimensional X-ray structures. Overall, the regions protected from ENU attack are sites of uranyl cleavage, indicating sites of low accessibility which can form ion binding sites. On the contrary, lead cleavages occur at flexible and accessible sites and correlate with the unspecific cleavages prevalent in dynamic and open regions. Applied in a magnesium-dependent manner, and only in combination with other backbone probing agents such as N-ethyl-N-nitrosourea, lead and Fenton cleavage, uranyl probing has the potential to reveal high-affinity metal ion environments, as well as regions involved in conformational transitions.
Wientges J, Putz J, Giege R, Florentz C, Schwienhorst A
Selection of viral RNA-derived tRNA-like structures with improved valylation activities Article de journal
Dans: Biochemistry, vol. 39, no. 20, p. 6207-6218, 2000, ISBN: 10821696, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 3' Untranslated Regions Acylation Anticodon/chemistry Base Sequence Cloning, FLORENTZ, Molecular Gene Library Kinetics Molecular Sequence Data Nucleic Acid Conformation Oligonucleotides/chemistry RNA, Non-U.S. Gov't Tymovirus/enzymology/genetics Valine-tRNA Ligase/chemistry Variation (Genetics), RNA Support, Transfer, Unité ARN, Val/*chemistry RNA, Viral/*chemistry Sequence Analysis
@article{,
title = {Selection of viral RNA-derived tRNA-like structures with improved valylation activities},
author = {J Wientges and J Putz and R Giege and C Florentz and A Schwienhorst},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10821696},
isbn = {10821696},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {20},
pages = {6207-6218},
abstract = {The tRNA-like structure (TLS) of turnip yellow mosaic virus (TYMV) RNA was previously shown to be efficiently charged by yeast valyl-tRNA synthetase (ValRS). This RNA has a noncanonical structure at its 3'-terminus but mimics a tRNA L-shaped fold, including an anticodon loop containing the major identity nucleotides for valylation, and a pseudoknotted amino acid accepting domain. Here we describe an in vitro selection experiment aimed (i) to verify the completeness of the valine identity set, (ii) to elucidate the impact of the pseudoknot on valylation, and (iii) to investigate whether functional communication exists between the two distal anticodon and amino acid accepting domains. Valylatable variants were selected from a pool of 2 x 10(13) RNA molecules derived from the TYMV TLS randomized in the anticodon loop nucleotides and in the length (1-6 nucleotides) and sequence of the pseudoknot loop L1. After nine rounds of selection by aminoacylation, 42 have been isolated. Among them, 17 RNAs could be efficiently charged by yeast ValRS. Their sequence revealed strong conservation of the second and the third anticodon triplet positions (A(56), C(55)) and the very 3'-end loop nucleotide C(53). A large variability of the other nucleotides of the loop was observed and no wild-type sequence was recovered. The selected molecules presented pseudoknot domains with loop L1 varying in size from 3-6 nucleotides and some sequence conservation, but did neither reveal the wild-type combination. All selected variants are 5-50 times more efficiently valylated than the wild-type TLS, suggesting that the natural viral sequence has emerged from a combination of evolutionary pressures among which aminoacylation was not predominant. This is in line with the role of the TLS in viral replication.},
note = {0006-2960
Journal Article},
keywords = {3' Untranslated Regions Acylation Anticodon/chemistry Base Sequence Cloning, FLORENTZ, Molecular Gene Library Kinetics Molecular Sequence Data Nucleic Acid Conformation Oligonucleotides/chemistry RNA, Non-U.S. Gov't Tymovirus/enzymology/genetics Valine-tRNA Ligase/chemistry Variation (Genetics), RNA Support, Transfer, Unité ARN, Val/*chemistry RNA, Viral/*chemistry Sequence Analysis},
pubstate = {published},
tppubtype = {article}
}
The tRNA-like structure (TLS) of turnip yellow mosaic virus (TYMV) RNA was previously shown to be efficiently charged by yeast valyl-tRNA synthetase (ValRS). This RNA has a noncanonical structure at its 3'-terminus but mimics a tRNA L-shaped fold, including an anticodon loop containing the major identity nucleotides for valylation, and a pseudoknotted amino acid accepting domain. Here we describe an in vitro selection experiment aimed (i) to verify the completeness of the valine identity set, (ii) to elucidate the impact of the pseudoknot on valylation, and (iii) to investigate whether functional communication exists between the two distal anticodon and amino acid accepting domains. Valylatable variants were selected from a pool of 2 x 10(13) RNA molecules derived from the TYMV TLS randomized in the anticodon loop nucleotides and in the length (1-6 nucleotides) and sequence of the pseudoknot loop L1. After nine rounds of selection by aminoacylation, 42 have been isolated. Among them, 17 RNAs could be efficiently charged by yeast ValRS. Their sequence revealed strong conservation of the second and the third anticodon triplet positions (A(56), C(55)) and the very 3'-end loop nucleotide C(53). A large variability of the other nucleotides of the loop was observed and no wild-type sequence was recovered. The selected molecules presented pseudoknot domains with loop L1 varying in size from 3-6 nucleotides and some sequence conservation, but did neither reveal the wild-type combination. All selected variants are 5-50 times more efficiently valylated than the wild-type TLS, suggesting that the natural viral sequence has emerged from a combination of evolutionary pressures among which aminoacylation was not predominant. This is in line with the role of the TLS in viral replication.
Tisne C, Rigourd M, Marquet R, Ehresmann C, Dardel F
Dans: RNA, vol. 6, no. 10, p. 1403-1412, 2000, ISBN: 11073216, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics/metabolism RNA, Genetic Transcription, Genetic/*genetics Virus Replication, Lys/*chemistry/genetics/metabolism Structure-Activity Relationship Support, MARQUET, Molecular Molecular Sequence Data Mutation/genetics Nuclear Magnetic Resonance, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/biosynthesis/genetics Escherichia coli/genetics *Genetic Engineering HIV-1/*genetics/physiology Human Iodine/metabolism Models
@article{,
title = {NMR and biochemical characterization of recombinant human tRNA(Lys)3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription},
author = {C Tisne and M Rigourd and R Marquet and C Ehresmann and F Dardel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073216},
isbn = {11073216},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1403-1412},
abstract = {Reverse transcription of HIV-1 viral RNA uses human tRNA(Lys)3 as a primer. Some of the modified nucleotides carried by this tRNA must play a key role in the initiation of this process, because unmodified tRNA produced in vitro is only marginally active as primer. To provide a better understanding of the contribution of base modifications in the initiation complex, we have designed a recombinant system that allows tRNA(Lys)3 expression in Escherichia coli. Because of their high level of overexpression, some modifications are incorporated at substoichiometric levels. We have purified the two major recombinant tRNA(Lys)3 subspecies, and their modified nucleotide contents have been characterized by a combination of NMR and biochemical techniques. Both species carry psis, Ds, T, t6A, and m7G. Differences are observed at position 34, within the anticodon. One fraction lacks the 5-methylaminomethyl group, whereas the other lacks the 2-thio group. Although the s2U34-containing recombinant tRNA is a less efficient primer, it presents most of the characteristics of the mammalian tRNA. On the other hand, the mnm5U34-containing tRNA has a strongly reduced activity. Our results demonstrate that the modifications that are absent in E. coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence DNA, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics/metabolism RNA, Genetic Transcription, Genetic/*genetics Virus Replication, Lys/*chemistry/genetics/metabolism Structure-Activity Relationship Support, MARQUET, Molecular Molecular Sequence Data Mutation/genetics Nuclear Magnetic Resonance, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/biosynthesis/genetics Escherichia coli/genetics *Genetic Engineering HIV-1/*genetics/physiology Human Iodine/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Reverse transcription of HIV-1 viral RNA uses human tRNA(Lys)3 as a primer. Some of the modified nucleotides carried by this tRNA must play a key role in the initiation of this process, because unmodified tRNA produced in vitro is only marginally active as primer. To provide a better understanding of the contribution of base modifications in the initiation complex, we have designed a recombinant system that allows tRNA(Lys)3 expression in Escherichia coli. Because of their high level of overexpression, some modifications are incorporated at substoichiometric levels. We have purified the two major recombinant tRNA(Lys)3 subspecies, and their modified nucleotide contents have been characterized by a combination of NMR and biochemical techniques. Both species carry psis, Ds, T, t6A, and m7G. Differences are observed at position 34, within the anticodon. One fraction lacks the 5-methylaminomethyl group, whereas the other lacks the 2-thio group. Although the s2U34-containing recombinant tRNA is a less efficient primer, it presents most of the characteristics of the mammalian tRNA. On the other hand, the mnm5U34-containing tRNA has a strongly reduced activity. Our results demonstrate that the modifications that are absent in E. coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process.
Schaub M, Krol A, Carbon P
Structural organization of Staf-DNA complexes Article de journal
Dans: Nucleic Acids Res, vol. 28, no. 10, p. 2114-2121, 2000, ISBN: 10773080, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Animals Base Sequence Binding Sites DNA-Binding Proteins/*chemistry/*metabolism Human Models, Amino Acid-Specific/*genetics Support, Genetic Trans-Activators/*chemistry/*metabolism Vertebrates Xenopus laevis Zinc Fingers, Molecular Molecular Sequence Data Nucleic Acid Conformation Plasmids/*chemistry/*metabolism Protein Conformation RNA, Non-U.S. Gov't Templates, Small Nuclear/*genetics RNA, Transfer, Unité ARN
@article{,
title = {Structural organization of Staf-DNA complexes},
author = {M Schaub and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10773080},
isbn = {10773080},
year = {2000},
date = {2000-01-01},
journal = {Nucleic Acids Res},
volume = {28},
number = {10},
pages = {2114-2121},
abstract = {The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the optimal Xenopus selenocysteine tRNA (xtRNA(Sec)) and human U6 snRNA (hU6) Staf motifs. Generation of a series of polypeptides containing increasing numbers of Staf zinc fingers tested in binding assays, by interference techniques and by binding site selection served to elucidate the mode of interaction between the zinc fingers and the Staf motifs. Our results provide strong evidence that zinc fingers 3-6 represent the minimal zinc finger region for high affinity binding to Staf motifs. Furthermore, we show that the binding of Staf is achieved through a broad spectrum of close contacts between zinc fingers 1-6 and xtRNA(Sec)or optimal sites or between zinc fingers 3-6 and the hU6 site. Extensive DNA major groove contacts contribute to the interaction with Staf that associates more closely with the non-template than with the template strand. Based on these findings and the structural information provided by the solved structures of other zinc finger-DNA complexes, we propose a model for the interaction between Staf zinc fingers and the xtRNA(Sec), optimal and hU6 sites.},
note = {1362-4962
Journal Article},
keywords = {Amino Acid Sequence Animals Base Sequence Binding Sites DNA-Binding Proteins/*chemistry/*metabolism Human Models, Amino Acid-Specific/*genetics Support, Genetic Trans-Activators/*chemistry/*metabolism Vertebrates Xenopus laevis Zinc Fingers, Molecular Molecular Sequence Data Nucleic Acid Conformation Plasmids/*chemistry/*metabolism Protein Conformation RNA, Non-U.S. Gov't Templates, Small Nuclear/*genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the optimal Xenopus selenocysteine tRNA (xtRNA(Sec)) and human U6 snRNA (hU6) Staf motifs. Generation of a series of polypeptides containing increasing numbers of Staf zinc fingers tested in binding assays, by interference techniques and by binding site selection served to elucidate the mode of interaction between the zinc fingers and the Staf motifs. Our results provide strong evidence that zinc fingers 3-6 represent the minimal zinc finger region for high affinity binding to Staf motifs. Furthermore, we show that the binding of Staf is achieved through a broad spectrum of close contacts between zinc fingers 1-6 and xtRNA(Sec)or optimal sites or between zinc fingers 3-6 and the hU6 site. Extensive DNA major groove contacts contribute to the interaction with Staf that associates more closely with the non-template than with the template strand. Based on these findings and the structural information provided by the solved structures of other zinc finger-DNA complexes, we propose a model for the interaction between Staf zinc fingers and the xtRNA(Sec), optimal and hU6 sites.
Sauter C, Lorber B, Cavarelli J, Moras D, Giege R
The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain Article de journal
Dans: J Mol Biol, vol. 299, no. 5, p. 1313-1324, 2000, ISBN: 10873455, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/chemistry/genetics/*metabolism Aspartate-tRNA Ligase/*chemistry/genetics/*metabolism Binding Sites Catalytic Domain Conserved Sequence/genetics Crystallization Crystallography, Asp/chemistry/genetics/*metabolism Rotation Sequence Deletion/genetics Support, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Movement Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Yeasts/*enzymology/genetics, SAUTER, Secondary RNA, Transfer, Unité ARN, X-Ray Models
@article{,
title = {The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain},
author = {C Sauter and B Lorber and J Cavarelli and D Moras and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10873455},
isbn = {10873455},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {299},
number = {5},
pages = {1313-1324},
abstract = {Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.},
note = {0022-2836
Journal Article},
keywords = {Anticodon/chemistry/genetics/*metabolism Aspartate-tRNA Ligase/*chemistry/genetics/*metabolism Binding Sites Catalytic Domain Conserved Sequence/genetics Crystallization Crystallography, Asp/chemistry/genetics/*metabolism Rotation Sequence Deletion/genetics Support, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Movement Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Yeasts/*enzymology/genetics, SAUTER, Secondary RNA, Transfer, Unité ARN, X-Ray Models},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.
Petyuk V A, Giege R, Vlasov V V, Zenkova M A
[Mechanism of oligonucleotide hybridization with the 3'-terminal region of yeast tRNA(Phe)] Article de journal
Dans: Mol Biol (Mosk), vol. 34, no. 5, p. 879-886, 2000, ISBN: 11033816, (0026-8984 Journal Article).
Liens | BibTeX | Étiquettes: Base Sequence DNA Primers Electrophoresis, Phe/chemistry/*genetics, Polyacrylamide Gel Nucleic Acid Conformation Nucleic Acid Hybridization RNA, Transfer, Unité ARN
@article{,
title = {[Mechanism of oligonucleotide hybridization with the 3'-terminal region of yeast tRNA(Phe)]},
author = {V A Petyuk and R Giege and V V Vlasov and M A Zenkova},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11033816},
isbn = {11033816},
year = {2000},
date = {2000-01-01},
journal = {Mol Biol (Mosk)},
volume = {34},
number = {5},
pages = {879-886},
note = {0026-8984
Journal Article},
keywords = {Base Sequence DNA Primers Electrophoresis, Phe/chemistry/*genetics, Polyacrylamide Gel Nucleic Acid Conformation Nucleic Acid Hybridization RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Petyuk V, Serikov R, Tolstikov V, Potapov V, Giege R, Zenkova M, Vlassov V
Invasion of strongly binding oligonucleotides into tRNA structure Article de journal
Dans: Nucleosides Nucleotides Nucleic Acids, vol. 19, no. 7, p. 1145-1158, 2000, ISBN: 10999254, (1525-7770 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 2-Aminopurine/*analogs & derivatives/chemistry 5-Methylcytosine Cytosine/analogs & derivatives/chemistry Deoxyuridine/*analogs & derivatives/chemistry Electrophoresis, Non-U.S. Gov't Time Factors Yeasts/chemistry, Phe/*chemistry/metabolism Support, Polyacrylamide Gel Kinetics Nucleic Acid Conformation Oligodeoxyribonucleotides/chemistry Oligonucleotides/*metabolism RNA, Transfer, Unité ARN
@article{,
title = {Invasion of strongly binding oligonucleotides into tRNA structure},
author = {V Petyuk and R Serikov and V Tolstikov and V Potapov and R Giege and M Zenkova and V Vlassov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10999254},
isbn = {10999254},
year = {2000},
date = {2000-01-01},
journal = {Nucleosides Nucleotides Nucleic Acids},
volume = {19},
number = {7},
pages = {1145-1158},
abstract = {Interaction of yeast tRNA(Phe) with oligodeoxyribonucleotides containing 5-methylcytosine, 2-aminoadenine, and 5-propynyl-2'-deoxyuridine was investigated. The modified oligonucleotides show increased binding capacity although the association rates are similar for the modified and natural oligonucleotides. The most pronounced increase in association constant (70 times) due to the incorporation of the strongly binding units was achieved in the case of oligonucleotide complementary to the sequence 65-76 of the tRNA(Phe).},
note = {1525-7770
Journal Article},
keywords = {2-Aminopurine/*analogs & derivatives/chemistry 5-Methylcytosine Cytosine/analogs & derivatives/chemistry Deoxyuridine/*analogs & derivatives/chemistry Electrophoresis, Non-U.S. Gov't Time Factors Yeasts/chemistry, Phe/*chemistry/metabolism Support, Polyacrylamide Gel Kinetics Nucleic Acid Conformation Oligodeoxyribonucleotides/chemistry Oligonucleotides/*metabolism RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Interaction of yeast tRNA(Phe) with oligodeoxyribonucleotides containing 5-methylcytosine, 2-aminoadenine, and 5-propynyl-2'-deoxyuridine was investigated. The modified oligonucleotides show increased binding capacity although the association rates are similar for the modified and natural oligonucleotides. The most pronounced increase in association constant (70 times) due to the incorporation of the strongly binding units was achieved in the case of oligonucleotide complementary to the sequence 65-76 of the tRNA(Phe).
Lanchy J M, Isel C, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis Article de journal
Dans: J Biol Chem, vol. 275, no. 16, p. 12306-12312, 2000, ISBN: 10766870, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Base Sequence *DNA Replication *Hiv-1 Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, Genetic, Lys/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/genetics/metabolism RNA-Directed DNA Polymerase/*metabolism Support
@article{,
title = {Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis},
author = {J M Lanchy and C Isel and G Keith and S F Le Grice and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10766870},
isbn = {10766870},
year = {2000},
date = {2000-01-01},
journal = {J Biol Chem},
volume = {275},
number = {16},
pages = {12306-12312},
abstract = {Initiation of human immunodeficiency virus-1 (HIV-1) reverse transcription requires formation of a complex containing the viral RNA (vRNA), tRNA(3)(Lys) and reverse transcriptase (RT). The vRNA and the primer tRNA(3)(Lys) form several intermolecular interactions in addition to annealing of the primer 3' end to the primer binding site (PBS). These interactions are crucial for the efficiency and the specificity of the initiation of reverse transcription. However, as they are located upstream of the PBS, they must unwind as DNA synthesis proceeds. Here, the dynamics of the complex during initiation of reverse transcription was followed by enzymatic probing. Our data revealed reciprocal effects of the tertiary structure of the vRNA.tRNA(3)(Lys) complex and reverse transcriptase (RT) at a distance from the polymerization site. The structure of the initiation complex allowed RT to interact with the template strand up to 20 nucleotides upstream from the polymerization site. Conversely, nucleotide addition by RT modified the tertiary structure of the complex at 10-14 nucleotides from the catalytic site. The viral sequences became exposed at the surface of the complex as they dissociated from the tRNA following primer extension. However, the counterpart tRNA sequences became buried inside the complex. Surprisingly, they became exposed when mutations prevented the intermolecular interactions in the initial complex, indicating that the fate of the tRNA depended on the tertiary structure of the initial complex.},
note = {0021-9258
Journal Article},
keywords = {*Anticodon Base Sequence *DNA Replication *Hiv-1 Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, Genetic, Lys/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/genetics/metabolism RNA-Directed DNA Polymerase/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Initiation of human immunodeficiency virus-1 (HIV-1) reverse transcription requires formation of a complex containing the viral RNA (vRNA), tRNA(3)(Lys) and reverse transcriptase (RT). The vRNA and the primer tRNA(3)(Lys) form several intermolecular interactions in addition to annealing of the primer 3' end to the primer binding site (PBS). These interactions are crucial for the efficiency and the specificity of the initiation of reverse transcription. However, as they are located upstream of the PBS, they must unwind as DNA synthesis proceeds. Here, the dynamics of the complex during initiation of reverse transcription was followed by enzymatic probing. Our data revealed reciprocal effects of the tertiary structure of the vRNA.tRNA(3)(Lys) complex and reverse transcriptase (RT) at a distance from the polymerization site. The structure of the initiation complex allowed RT to interact with the template strand up to 20 nucleotides upstream from the polymerization site. Conversely, nucleotide addition by RT modified the tertiary structure of the complex at 10-14 nucleotides from the catalytic site. The viral sequences became exposed at the surface of the complex as they dissociated from the tRNA following primer extension. However, the counterpart tRNA sequences became buried inside the complex. Surprisingly, they became exposed when mutations prevented the intermolecular interactions in the initial complex, indicating that the fate of the tRNA depended on the tertiary structure of the initial complex.
Helm M, Brule H, Friede D, Giege R, Putz D, Florentz C
Search for characteristic structural features of mammalian mitochondrial tRNAs Article de journal
Dans: RNA, vol. 6, no. 10, p. 1356-1379, 2000, ISBN: 11073213, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Animals Base Pairing Base Sequence *Computational Biology Escherichia coli/genetics Genome Human Molecular Sequence Data Multigene Family *Nucleic Acid Conformation RNA/*chemistry/genetics RNA Stability RNA, Amino Acid-Specific/*chemistry/genetics Regulatory Sequences, FLORENTZ, Non-U.S. Gov't Variation (Genetics), Nucleic Acid/genetics Support, Transfer, Unité ARN
@article{,
title = {Search for characteristic structural features of mammalian mitochondrial tRNAs},
author = {M Helm and H Brule and D Friede and R Giege and D Putz and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073213},
isbn = {11073213},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1356-1379},
abstract = {A number of mitochondrial (mt) tRNAs have strong structural deviations from the classical tRNA cloverleaf secondary structure and from the conventional L-shaped tertiary structure. As a consequence, there is a general trend to consider all mitochondrial tRNAs as "bizarre" tRNAs. Here, a large sequence comparison of the 22 tRNA genes within 31 fully sequenced mammalian mt genomes has been performed to define the structural characteristics of this specific group of tRNAs. Vertical alignments define the degree of conservation/variability of primary sequences and secondary structures and search for potential tertiary interactions within each of the 22 families. Further horizontal alignments ascertain that, with the exception of serine-specific tRNAs, mammalian mt tRNAs do fold into cloverleaf structures with mostly classical features. However, deviations exist and concern large variations in size of the D- and T-loops. The predominant absence of the conserved nucleotides G18G19 and T54T55C56, respectively in these loops, suggests that classical tertiary interactions between both domains do not take place. Classification of the tRNA sequences according to their genomic origin (G-rich or G-poor DNA strand) highlight specific features such as richness/poorness in mismatches or G-T pairs in stems and extremely low G-content or C-content in the D- and T-loops. The resulting 22 "typical" mammalian mitochondrial sequences built up a phylogenetic basis for experimental structural and functional investigations. Moreover, they are expected to help in the evaluation of the possible impacts of those point mutations detected in human mitochondrial tRNA genes and correlated with pathologies.},
note = {1355-8382
Journal Article},
keywords = {Acylation Animals Base Pairing Base Sequence *Computational Biology Escherichia coli/genetics Genome Human Molecular Sequence Data Multigene Family *Nucleic Acid Conformation RNA/*chemistry/genetics RNA Stability RNA, Amino Acid-Specific/*chemistry/genetics Regulatory Sequences, FLORENTZ, Non-U.S. Gov't Variation (Genetics), Nucleic Acid/genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A number of mitochondrial (mt) tRNAs have strong structural deviations from the classical tRNA cloverleaf secondary structure and from the conventional L-shaped tertiary structure. As a consequence, there is a general trend to consider all mitochondrial tRNAs as "bizarre" tRNAs. Here, a large sequence comparison of the 22 tRNA genes within 31 fully sequenced mammalian mt genomes has been performed to define the structural characteristics of this specific group of tRNAs. Vertical alignments define the degree of conservation/variability of primary sequences and secondary structures and search for potential tertiary interactions within each of the 22 families. Further horizontal alignments ascertain that, with the exception of serine-specific tRNAs, mammalian mt tRNAs do fold into cloverleaf structures with mostly classical features. However, deviations exist and concern large variations in size of the D- and T-loops. The predominant absence of the conserved nucleotides G18G19 and T54T55C56, respectively in these loops, suggests that classical tertiary interactions between both domains do not take place. Classification of the tRNA sequences according to their genomic origin (G-rich or G-poor DNA strand) highlight specific features such as richness/poorness in mismatches or G-T pairs in stems and extremely low G-content or C-content in the D- and T-loops. The resulting 22 "typical" mammalian mitochondrial sequences built up a phylogenetic basis for experimental structural and functional investigations. Moreover, they are expected to help in the evaluation of the possible impacts of those point mutations detected in human mitochondrial tRNA genes and correlated with pathologies.
Giege R, Felden B, Zenkova M A, Sil'nikov V N, Vlassov V V
Cleavage of RNA with synthetic ribonuclease mimics Article de journal
Dans: Methods Enzymol, vol. 318, p. 147-165, 2000, ISBN: 10889986, (0076-6879 Journal Article).
Liens | BibTeX | Étiquettes: Asp/chemistry Ribonuclease, Base Sequence Electrophoresis, Chemical Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization Phosphorylation Plasmids/metabolism RNA/chemistry/*metabolism RNA, Non-U.S. Gov't, Pancreatic/chemistry/pharmacology Ribonucleases/*chemistry/pharmacology Saccharomyces cerevisiae/genetics Spectrophotometry Support, Polyacrylamide Gel Genetic Techniques Hydrolysis Imidazoles/pharmacology Models, Transfer, Unité ARN
@article{,
title = {Cleavage of RNA with synthetic ribonuclease mimics},
author = {R Giege and B Felden and M A Zenkova and V N Sil'nikov and V V Vlassov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10889986},
isbn = {10889986},
year = {2000},
date = {2000-01-01},
journal = {Methods Enzymol},
volume = {318},
pages = {147-165},
note = {0076-6879
Journal Article},
keywords = {Asp/chemistry Ribonuclease, Base Sequence Electrophoresis, Chemical Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization Phosphorylation Plasmids/metabolism RNA/chemistry/*metabolism RNA, Non-U.S. Gov't, Pancreatic/chemistry/pharmacology Ribonucleases/*chemistry/pharmacology Saccharomyces cerevisiae/genetics Spectrophotometry Support, Polyacrylamide Gel Genetic Techniques Hydrolysis Imidazoles/pharmacology Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fechter P, Rudinger-Thirion J, Théobald-Dietrich A, Giege R
Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features Article de journal
Dans: Biochemistry, vol. 39, no. 7, p. 1725-1733, 2000, ISBN: 10677221, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon/chemistry/metabolism Base Sequence Escherichia coli/enzymology/genetics Heat Methanococcus/enzymology/genetics Molecular Mimicry Molecular Sequence Data Nucleic Acid Denaturation RNA Processing, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tyrosine/chemistry/*metabolism Tyrosine-tRNA Ligase/chemistry/*metabolism, Post-Transcriptional RNA, Transfer, Tyr/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Structure-Activity Relationship Support, Unité ARN
@article{,
title = {Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features},
author = {P Fechter and J Rudinger-Thirion and A Théobald-Dietrich and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10677221},
isbn = {10677221},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {7},
pages = {1725-1733},
abstract = {The specific aminoacylation of tRNA by yeast tyrosyl-tRNA synthetase does not rely on the presence of modified residues in tRNA(Tyr), although such residues stabilize its structure. Thus, the major tyrosine identity determinants were searched by the in vitro approach using unmodified transcripts produced by T7 RNA polymerase. On the basis of the tyrosylation efficiency of tRNA variants, the strongest determinants are base pair C1-G72 and discriminator residue A73 (the 5'-phosphoryl group on C1, however, is unimportant for tyrosylation). The three anticodon bases G34, U35, and A36 contribute also to the tyrosine identity, but to a lesser extent, with G34 having the most pronounced effect. Mutation of the GUA tyrosine anticodon into a CAU methionine anticodon, however, leads to a loss of tyrosylation efficiency similar to that obtained after mutation of the C1-G72 or A73 determinants. Transplantation of the six determinants into four different tRNA frameworks and activity assays on heterologous Escherichia coli and Methanococcus jannaschii tRNA(Tyr) confirmed the completeness of the tyrosine set and the eukaryotic character of the C1-G72 base pair. On the other hand, it was found that tyrosine identity in yeast does not rely on fine architectural features of the tRNA, in particular the size and sequence of the D-loop. Noticeable, yeast TyrRS efficiently charges a variant of E. coli tRNA(Tyr) with a large extra-region provided its G1-C72 base pair is changed to a C1-G72 base pair. Finally, tyrosylation activity is compatible with a +1 shift of the anticodon in the 3'-direction but is strongly inhibited if this shift occurs in the opposite 5'-direction.},
note = {0006-2960
Journal Article},
keywords = {Acylation Anticodon/chemistry/metabolism Base Sequence Escherichia coli/enzymology/genetics Heat Methanococcus/enzymology/genetics Molecular Mimicry Molecular Sequence Data Nucleic Acid Denaturation RNA Processing, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tyrosine/chemistry/*metabolism Tyrosine-tRNA Ligase/chemistry/*metabolism, Post-Transcriptional RNA, Transfer, Tyr/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Structure-Activity Relationship Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The specific aminoacylation of tRNA by yeast tyrosyl-tRNA synthetase does not rely on the presence of modified residues in tRNA(Tyr), although such residues stabilize its structure. Thus, the major tyrosine identity determinants were searched by the in vitro approach using unmodified transcripts produced by T7 RNA polymerase. On the basis of the tyrosylation efficiency of tRNA variants, the strongest determinants are base pair C1-G72 and discriminator residue A73 (the 5'-phosphoryl group on C1, however, is unimportant for tyrosylation). The three anticodon bases G34, U35, and A36 contribute also to the tyrosine identity, but to a lesser extent, with G34 having the most pronounced effect. Mutation of the GUA tyrosine anticodon into a CAU methionine anticodon, however, leads to a loss of tyrosylation efficiency similar to that obtained after mutation of the C1-G72 or A73 determinants. Transplantation of the six determinants into four different tRNA frameworks and activity assays on heterologous Escherichia coli and Methanococcus jannaschii tRNA(Tyr) confirmed the completeness of the tyrosine set and the eukaryotic character of the C1-G72 base pair. On the other hand, it was found that tyrosine identity in yeast does not rely on fine architectural features of the tRNA, in particular the size and sequence of the D-loop. Noticeable, yeast TyrRS efficiently charges a variant of E. coli tRNA(Tyr) with a large extra-region provided its G1-C72 base pair is changed to a C1-G72 base pair. Finally, tyrosylation activity is compatible with a +1 shift of the anticodon in the 3'-direction but is strongly inhibited if this shift occurs in the opposite 5'-direction.
Fagegaltier D, Hubert N, Yamada K, Mizutani T, Carbon P, Krol A
Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation Article de journal
Dans: EMBO J, vol. 19, no. 17, p. 4796-4805, 2000, ISBN: 10970870, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Animals Bacterial Proteins/chemistry/*metabolism/physiology Caenorhabditis elegans/genetics Drosophila/genetics Hela Cells Human Mice Molecular Sequence Data Peptide Elongation Factors/chemistry/*metabolism/physiology Protein Binding Proteins/*genetics RNA, Amino Acyl/metabolism Sequence Homology, Genetic/*physiology, Non-U.S. Gov't Translation, Transfer, Unité ARN
@article{,
title = {Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation},
author = {D Fagegaltier and N Hubert and K Yamada and T Mizutani and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10970870},
isbn = {10970870},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {17},
pages = {4796-4805},
abstract = {Decoding of UGA selenocysteine codons in eubacteria is mediated by the specialized elongation factor SelB, which conveys the charged tRNA(Sec) to the A site of the ribosome, through binding to the SECIS mRNA hairpin. In an attempt to isolate the eukaryotic homolog of SelB, a database search in this work identified a mouse expressed sequence tag containing the complete cDNA encoding a novel protein of 583 amino acids, which we called mSelB. Several lines of evidence enabled us to establish that mSelB is the bona fide mammalian elongation factor for selenoprotein translation: it binds GTP, recognizes the Sec-tRNA(Sec) in vitro and in vivo, and is required for efficient selenoprotein translation in vivo. In contrast to the eubacterial SelB, the recombinant mSelB alone is unable to bind specifically the eukaryotic SECIS RNA hairpin. However, complementation with HeLa cell extracts led to the formation of a SECIS-dependent complex containing mSelB and at least another factor. Therefore, the role carried out by a single elongation factor in eubacterial selenoprotein translation is devoted to two or more specialized proteins in eukaryotes.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Animals Bacterial Proteins/chemistry/*metabolism/physiology Caenorhabditis elegans/genetics Drosophila/genetics Hela Cells Human Mice Molecular Sequence Data Peptide Elongation Factors/chemistry/*metabolism/physiology Protein Binding Proteins/*genetics RNA, Amino Acyl/metabolism Sequence Homology, Genetic/*physiology, Non-U.S. Gov't Translation, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Decoding of UGA selenocysteine codons in eubacteria is mediated by the specialized elongation factor SelB, which conveys the charged tRNA(Sec) to the A site of the ribosome, through binding to the SECIS mRNA hairpin. In an attempt to isolate the eukaryotic homolog of SelB, a database search in this work identified a mouse expressed sequence tag containing the complete cDNA encoding a novel protein of 583 amino acids, which we called mSelB. Several lines of evidence enabled us to establish that mSelB is the bona fide mammalian elongation factor for selenoprotein translation: it binds GTP, recognizes the Sec-tRNA(Sec) in vitro and in vivo, and is required for efficient selenoprotein translation in vivo. In contrast to the eubacterial SelB, the recombinant mSelB alone is unable to bind specifically the eukaryotic SECIS RNA hairpin. However, complementation with HeLa cell extracts led to the formation of a SECIS-dependent complex containing mSelB and at least another factor. Therefore, the role carried out by a single elongation factor in eubacterial selenoprotein translation is devoted to two or more specialized proteins in eukaryotes.
Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn C S, Ehresmann C, Moras D
Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem Article de journal
Dans: Cell, vol. 103, no. 6, p. 877-884, 2000, ISBN: 11136973, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Amino Acid Activation Binding Sites Crystallography, Amino Acyl/chemistry/*metabolism Serine/metabolism Support, Molecular Mutation *Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Threonine/metabolism Threonine-tRNA Ligase/*chemistry/*genetics/metabolism Zinc/metabolism, ROMBY, Tertiary *RNA Editing RNA, Transfer, Unité ARN, X-Ray Kinetics Models
@article{,
title = {Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem},
author = {A Dock-Bregeon and R Sankaranarayanan and P Romby and J Caillet and M Springer and B Rees and C S Francklyn and C Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11136973},
isbn = {11136973},
year = {2000},
date = {2000-01-01},
journal = {Cell},
volume = {103},
number = {6},
pages = {877-884},
abstract = {Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.},
note = {0092-8674
Journal Article},
keywords = {Acylation Amino Acid Activation Binding Sites Crystallography, Amino Acyl/chemistry/*metabolism Serine/metabolism Support, Molecular Mutation *Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Threonine/metabolism Threonine-tRNA Ligase/*chemistry/*genetics/metabolism Zinc/metabolism, ROMBY, Tertiary *RNA Editing RNA, Transfer, Unité ARN, X-Ray Kinetics Models},
pubstate = {published},
tppubtype = {article}
}
Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.
Delagoutte B, Keith G, Moras D, Cavarelli J
Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 56, no. Pt 4, p. 492-494, 2000, ISBN: 10739930, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Arg/*chemistry/isolation & purification/*metabolism Saccharomyces cerevisiae/enzymology/genetics Support, Arginine-tRNA Ligase/*chemistry/isolation & purification/*metabolism Crystallization Crystallography, Fungal/chemistry/isolation & purification/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray RNA
@article{,
title = {Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes},
author = {B Delagoutte and G Keith and D Moras and J Cavarelli},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10739930},
isbn = {10739930},
year = {2000},
date = {2000-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {56},
number = {Pt 4},
pages = {492-494},
abstract = {Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64},
note = {0907-4449
Journal Article},
keywords = {Arg/*chemistry/isolation & purification/*metabolism Saccharomyces cerevisiae/enzymology/genetics Support, Arginine-tRNA Ligase/*chemistry/isolation & purification/*metabolism Crystallization Crystallography, Fungal/chemistry/isolation & purification/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray RNA},
pubstate = {published},
tppubtype = {article}
}
Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64
Brule F, Bec G, Keith G, Grice S F Le, Roques B P, Ehresmann B, Ehresmann C, Marquet R
In vitro evidence for the interaction of tRNA(3)(Lys) with U3 during the first strand transfer of HIV-1 reverse transcription Article de journal
Dans: Nucleic Acids Res, vol. 28, no. 2, p. 634-640, 2000, ISBN: 10606665, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence HIV-1 Reverse Transcriptase/*metabolism Nucleic Acid Conformation Polymerase Chain Reaction RNA, Genetic, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/chemistry/*metabolism Support
@article{,
title = {In vitro evidence for the interaction of tRNA(3)(Lys) with U3 during the first strand transfer of HIV-1 reverse transcription},
author = {F Brule and G Bec and G Keith and S F Le Grice and B P Roques and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10606665},
isbn = {10606665},
year = {2000},
date = {2000-01-01},
journal = {Nucleic Acids Res},
volume = {28},
number = {2},
pages = {634-640},
abstract = {Over the course of its evolution, HIV-1 has taken maximum advantage of its tRNA(3)(Lys)primer by utilizing it in several steps of reverse transcription. Here, we have identified a conserved nonanucleotide sequence in the U3 region of HIV-1 RNA that is complementary to the anticodon stem of tRNA(3)(Lys). In order to test its possible role in the first strand transfer reaction, we applied an assay using a donor RNA corresponding to the 5'-part and an acceptor RNA spanning the 3'-part of HIV-1 RNA. In addition, we constructed two acceptor RNAs in which the nonanucleotide sequence complementary to tRNA(3)(Lys)was either substituted (S) or deleted (Delta). We used either natural tRNA(3)(Lys)or an 18 nt DNA as primer and measured the efficiency of (-) strand strong stop DNA transfer in the presence of wild-type, S or Delta acceptor RNA. Mutations in U3 did not decrease the transfer efficiency when reverse transcription was primed with the 18mer DNA. However, they significantly reduced the strand transfer efficiency in the tRNA(3)(Lys)-primed reactions. This reduction was also observed in the presence of nucleocapsid protein. These results suggest that tRNA(3)(Lys)increases (-) strand strong stop transfer by interacting with the U3 region of the genomic RNA. Sequence comparisons suggest that such long range interactions also exist in other lentiviruses.},
note = {1362-4962
Journal Article},
keywords = {Base Sequence HIV-1 Reverse Transcriptase/*metabolism Nucleic Acid Conformation Polymerase Chain Reaction RNA, Genetic, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Over the course of its evolution, HIV-1 has taken maximum advantage of its tRNA(3)(Lys)primer by utilizing it in several steps of reverse transcription. Here, we have identified a conserved nonanucleotide sequence in the U3 region of HIV-1 RNA that is complementary to the anticodon stem of tRNA(3)(Lys). In order to test its possible role in the first strand transfer reaction, we applied an assay using a donor RNA corresponding to the 5'-part and an acceptor RNA spanning the 3'-part of HIV-1 RNA. In addition, we constructed two acceptor RNAs in which the nonanucleotide sequence complementary to tRNA(3)(Lys)was either substituted (S) or deleted (Delta). We used either natural tRNA(3)(Lys)or an 18 nt DNA as primer and measured the efficiency of (-) strand strong stop DNA transfer in the presence of wild-type, S or Delta acceptor RNA. Mutations in U3 did not decrease the transfer efficiency when reverse transcription was primed with the 18mer DNA. However, they significantly reduced the strand transfer efficiency in the tRNA(3)(Lys)-primed reactions. This reduction was also observed in the presence of nucleocapsid protein. These results suggest that tRNA(3)(Lys)increases (-) strand strong stop transfer by interacting with the U3 region of the genomic RNA. Sequence comparisons suggest that such long range interactions also exist in other lentiviruses.
Benas P, Bec G, Keith G, Marquet R, Ehresmann C, Ehresmann B, Dumas P
The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop Article de journal
Dans: RNA, vol. 6, no. 10, p. 1347-1355, 2000, ISBN: 11073212, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Anticodon/*chemistry/genetics Base Sequence Cattle Chickens/*genetics Crystallography, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Lys/*chemistry/genetics Rabbits Support, MARQUET, Molecular Molecular Sequence Data Nuclear Magnetic Resonance, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray HIV-1/*genetics Models
@article{,
title = {The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop},
author = {P Benas and G Bec and G Keith and R Marquet and C Ehresmann and B Ehresmann and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073212},
isbn = {11073212},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1347-1355},
abstract = {We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon.},
note = {1355-8382
Journal Article},
keywords = {Animals Anticodon/*chemistry/genetics Base Sequence Cattle Chickens/*genetics Crystallography, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Lys/*chemistry/genetics Rabbits Support, MARQUET, Molecular Molecular Sequence Data Nuclear Magnetic Resonance, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray HIV-1/*genetics Models},
pubstate = {published},
tppubtype = {article}
}
We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon.
Becker H D, Roy H, Moulinier L, Mazauric M H, Keith G, Kern D
Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase Article de journal
Dans: Biochemistry, vol. 39, no. 12, p. 3216-3230, 2000, ISBN: 10727213, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase},
author = {H D Becker and H Roy and L Moulinier and M H Mazauric and G Keith and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10727213},
isbn = {10727213},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {12},
pages = {3216-3230},
abstract = {Thermus thermophilus possesses two aspartyl-tRNA synthetases (AspRSs), AspRS1 and AspRS2, encoded by distinct genes. Alignment of the protein sequences with AspRSs of other origins reveals that AspRS1 possesses the structural features of eubacterial AspRSs, whereas AspRS2 is structurally related to the archaebacterial AspRSs. The structural dissimilarity between the two thermophilic AspRSs is correlated with functional divergences. AspRS1 aspartylates tRNA(Asp) whereas AspRS2 aspartylates tRNA(Asp), and tRNA(Asn) with similar efficiencies. Since Asp bound on tRNA(Asn) is converted into Asn by a tRNA-dependent aspartate amidotransferase, AspRS2 is involved in Asn-tRNA(Asn) formation. These properties relate functionally AspRS2 to archaebacterial AspRSs. The structural basis of the dual specificity of T. thermophilus tRNA(Asn) was investigated by comparing its sequence with those of tRNA(Asp) and tRNA(Asn) of strict specificity. It is shown that the thermophilic tRNA(Asn) contains the elements defining asparagine identity in Escherichia coli, part of which being also the major elements of aspartate identity, whereas minor elements of this identity are missing. The structural context that permits expression of aspartate and asparagine identities by tRNA(Asn) and how AspRS2 accommodates tRNA(Asp) and tRNA(Asn) will be discussed. This work establishes a distinct structure-function relationship of eubacterial and archaebacterial AspRSs. The structural and functional properties of the two thermophilic AspRSs will be discussed in the context of the modern and primitive pathways of tRNA aspartylation and asparaginylation and related to the phylogenetic connexion of T. thermophilus to eubacteria and archaebacteria.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Thermus thermophilus possesses two aspartyl-tRNA synthetases (AspRSs), AspRS1 and AspRS2, encoded by distinct genes. Alignment of the protein sequences with AspRSs of other origins reveals that AspRS1 possesses the structural features of eubacterial AspRSs, whereas AspRS2 is structurally related to the archaebacterial AspRSs. The structural dissimilarity between the two thermophilic AspRSs is correlated with functional divergences. AspRS1 aspartylates tRNA(Asp) whereas AspRS2 aspartylates tRNA(Asp), and tRNA(Asn) with similar efficiencies. Since Asp bound on tRNA(Asn) is converted into Asn by a tRNA-dependent aspartate amidotransferase, AspRS2 is involved in Asn-tRNA(Asn) formation. These properties relate functionally AspRS2 to archaebacterial AspRSs. The structural basis of the dual specificity of T. thermophilus tRNA(Asn) was investigated by comparing its sequence with those of tRNA(Asp) and tRNA(Asn) of strict specificity. It is shown that the thermophilic tRNA(Asn) contains the elements defining asparagine identity in Escherichia coli, part of which being also the major elements of aspartate identity, whereas minor elements of this identity are missing. The structural context that permits expression of aspartate and asparagine identities by tRNA(Asn) and how AspRS2 accommodates tRNA(Asp) and tRNA(Asn) will be discussed. This work establishes a distinct structure-function relationship of eubacterial and archaebacterial AspRSs. The structural and functional properties of the two thermophilic AspRSs will be discussed in the context of the modern and primitive pathways of tRNA aspartylation and asparaginylation and related to the phylogenetic connexion of T. thermophilus to eubacteria and archaebacteria.
Becker H D, Min B, Jacobi C, Raczniak G, Pelaschier J, Roy H, Klein S, Kern D, Soll D
The heterotrimeric Thermus thermophilus Asp-tRNA(Asn) amidotransferase can also generate Gln-tRNA(Gln) Article de journal
Dans: FEBS Lett, vol. 476, no. 3, p. 140-144, 2000, ISBN: 10913601, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Cloning, Amino Acyl/*metabolism Recombinant Proteins/chemistry/genetics/metabolism Sequence Deletion Substrate Specificity Support, Bacterial Molecular Sequence Data Nitrogenous Group Transferases/chemistry/genetics/*metabolism Protein Structure, Bacterial/metabolism RNA, Molecular Escherichia coli/genetics Genes, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Quaternary RNA, Transfer, Unité ARN
@article{,
title = {The heterotrimeric Thermus thermophilus Asp-tRNA(Asn) amidotransferase can also generate Gln-tRNA(Gln)},
author = {H D Becker and B Min and C Jacobi and G Raczniak and J Pelaschier and H Roy and S Klein and D Kern and D Soll},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10913601},
isbn = {10913601},
year = {2000},
date = {2000-01-01},
journal = {FEBS Lett},
volume = {476},
number = {3},
pages = {140-144},
abstract = {Thermus thermophilus strain HB8 is known to have a heterodimeric aspartyl-tRNA(Asn) amidotransferase (Asp-AdT) capable of forming Asn-tRNA(Asn) [Becker, H.D. and Kern, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12832-12837]. Here we show that, like other bacteria, T. thermophilus possesses the canonical set of amidotransferase (AdT) genes (gatA, gatB and gatC). We cloned and sequenced these genes, and constructed an artificial operon for overexpression in Escherichia coli of the thermophilic holoenzyme. The overproduced T. thermophilus AdT can generate Gln-tRNA(Gln) as well as Asn-tRNA(Asn). Thus, the T. thermophilus tRNA-dependent AdT is a dual-specific Asp/Glu-AdT resembling other bacterial AdTs. In addition, we observed that removal of the 44 carboxy-terminal amino acids of the GatA subunit only inhibits the Asp-AdT activity, leaving the Glu-AdT activity of the mutant AdT unaltered; this shows that Asp-AdT and Glu-AdT activities can be mechanistically separated.},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Sequence Cloning, Amino Acyl/*metabolism Recombinant Proteins/chemistry/genetics/metabolism Sequence Deletion Substrate Specificity Support, Bacterial Molecular Sequence Data Nitrogenous Group Transferases/chemistry/genetics/*metabolism Protein Structure, Bacterial/metabolism RNA, Molecular Escherichia coli/genetics Genes, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Quaternary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Thermus thermophilus strain HB8 is known to have a heterodimeric aspartyl-tRNA(Asn) amidotransferase (Asp-AdT) capable of forming Asn-tRNA(Asn) [Becker, H.D. and Kern, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12832-12837]. Here we show that, like other bacteria, T. thermophilus possesses the canonical set of amidotransferase (AdT) genes (gatA, gatB and gatC). We cloned and sequenced these genes, and constructed an artificial operon for overexpression in Escherichia coli of the thermophilic holoenzyme. The overproduced T. thermophilus AdT can generate Gln-tRNA(Gln) as well as Asn-tRNA(Asn). Thus, the T. thermophilus tRNA-dependent AdT is a dual-specific Asp/Glu-AdT resembling other bacterial AdTs. In addition, we observed that removal of the 44 carboxy-terminal amino acids of the GatA subunit only inhibits the Asp-AdT activity, leaving the Glu-AdT activity of the mutant AdT unaltered; this shows that Asp-AdT and Glu-AdT activities can be mechanistically separated.
1999
Auxilien S., Keith G., Grice S. F. Le, Darlix J. L.
Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 274, no. 7, p. 4412-20, 1999, (0021-9258 Journal Article).
Résumé | BibTeX | Étiquettes: *RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism
@article{,
title = {Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription},
author = { S. Auxilien and G. Keith and S. F. Le Grice and J. L. Darlix},
year = {1999},
date = {1999-01-01},
journal = {J Biol Chem},
volume = {274},
number = {7},
pages = {4412-20},
abstract = {During HIV reverse transcription, (+) strand DNA synthesis is primed by an RNase H-resistant sequence, the polypurine tract, and continues as far as a 18-nt double-stranded RNA region corresponding to the 3' end of tRNALys,3 hybridized to the viral primer binding site (PBS). Before (+) strand DNA transfer, reverse transcriptase (RT) needs to unwind the double-stranded tRNA-PBS RNA in order to reverse-transcribe the 3' end of primer tRNALys,3. Since the detailed mechanism of (+) strand DNA transfer remains incompletely understood, we developed an in vitro system to closely examine this mechanism, composed of HIV 5' RNA, natural modified tRNALys,3, synthetic unmodified tRNALys,3 or oligonucleotides (RNA or DNA) complementary to the PBS, as well as the viral proteins RT and nucleocapsid protein (NCp7). Prior to (+) strand DNA transfer, RT stalls at the double-stranded tRNA-PBS RNA complex and is able to reverse-transcribe modified nucleosides of natural tRNALys,3. Modified nucleoside m1A-58 of natural tRNALys,3 is only partially effective as a stop signal, as RT can transcribe as far as the hyper-modified adenosine (ms2t6A-37) in the anticodon loop. m1A-58 is almost always transcribed into A, whereas other modified nucleosides are transcribed correctly, except for m7G-46, which is sometimes transcribed into T. In contrast, synthetic tRNALys,3, an RNA PBS primer, and a DNA PBS primer are completely reverse-transcribed. In the presence of an acceptor template, (+) strand DNA transfer is efficient only with templates containing natural tRNALys,3 or the RNA PBS primer. Sequence analysis of transfer products revealed frequent errors at the transfer site with synthetic tRNALys,3, not observed with natural tRNALys,3. Thus, modified nucleoside m1A-58, present in all retroviral tRNA primers, appears to be important for both efficacy and fidelity of (+) strand DNA transfer. We show that other factors such as the nature of the (-) PBS of the acceptor template and the RNase H activity of RT also influence the efficacy of (+) strand DNA transfer.},
note = {0021-9258
Journal Article},
keywords = {*RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism},
pubstate = {published},
tppubtype = {article}
}
During HIV reverse transcription, (+) strand DNA synthesis is primed by an RNase H-resistant sequence, the polypurine tract, and continues as far as a 18-nt double-stranded RNA region corresponding to the 3' end of tRNALys,3 hybridized to the viral primer binding site (PBS). Before (+) strand DNA transfer, reverse transcriptase (RT) needs to unwind the double-stranded tRNA-PBS RNA in order to reverse-transcribe the 3' end of primer tRNALys,3. Since the detailed mechanism of (+) strand DNA transfer remains incompletely understood, we developed an in vitro system to closely examine this mechanism, composed of HIV 5' RNA, natural modified tRNALys,3, synthetic unmodified tRNALys,3 or oligonucleotides (RNA or DNA) complementary to the PBS, as well as the viral proteins RT and nucleocapsid protein (NCp7). Prior to (+) strand DNA transfer, RT stalls at the double-stranded tRNA-PBS RNA complex and is able to reverse-transcribe modified nucleosides of natural tRNALys,3. Modified nucleoside m1A-58 of natural tRNALys,3 is only partially effective as a stop signal, as RT can transcribe as far as the hyper-modified adenosine (ms2t6A-37) in the anticodon loop. m1A-58 is almost always transcribed into A, whereas other modified nucleosides are transcribed correctly, except for m7G-46, which is sometimes transcribed into T. In contrast, synthetic tRNALys,3, an RNA PBS primer, and a DNA PBS primer are completely reverse-transcribed. In the presence of an acceptor template, (+) strand DNA transfer is efficient only with templates containing natural tRNALys,3 or the RNA PBS primer. Sequence analysis of transfer products revealed frequent errors at the transfer site with synthetic tRNALys,3, not observed with natural tRNALys,3. Thus, modified nucleoside m1A-58, present in all retroviral tRNA primers, appears to be important for both efficacy and fidelity of (+) strand DNA transfer. We show that other factors such as the nature of the (-) PBS of the acceptor template and the RNase H activity of RT also influence the efficacy of (+) strand DNA transfer.
Perreau V. M., Keith G., Holmes W. M., Przykorska A., Santos M. A., Tuite M. F.
The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal
Dans: J Mol Biol, vol. 293, no. 5, p. 1039-53, 1999, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.
@article{,
title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure},
author = { V. M. Perreau and G. Keith and W. M. Holmes and A. Przykorska and M. A. Santos and M. F. Tuite},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {293},
number = {5},
pages = {1039-53},
abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.},
note = {0022-2836
Journal Article},
keywords = {*Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.},
pubstate = {published},
tppubtype = {article}
}
In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.
Wolfson A D, Khvorova A M, Sauter C, Florentz C, Giege R
Mimics of yeast tRNAAsp and their recognition by aspartyl-tRNA synthetase Article de journal
Dans: Biochemistry, vol. 38, no. 37, p. 11926-11932, 1999, ISBN: 10508395, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/*chemistry/metabolism Base Sequence Catalysis Cloning, Asp/*chemistry/genetics/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Molecular Enzyme Activation/genetics Genetic Engineering Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, SAUTER, Site-Directed Plasmids/chemical synthesis RNA, Transfer, Unité ARN
@article{,
title = {Mimics of yeast tRNAAsp and their recognition by aspartyl-tRNA synthetase},
author = {A D Wolfson and A M Khvorova and C Sauter and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10508395},
isbn = {10508395},
year = {1999},
date = {1999-01-01},
journal = {Biochemistry},
volume = {38},
number = {37},
pages = {11926-11932},
abstract = {Assuming that the L-shaped three-dimensional structure of tRNA is an architectural framework allowing the proper presentation of identity nucleotides to aminoacyl-tRNA synthetases implies that altered and/or simplified RNA architectures can fulfill this role and be functional substrates of these enzymes, provided they contain correctly located identity elements. In this work, this paradigm was submitted to new experimental verification. Yeast aspartyl-tRNA synthetase was the model synthetase, and the extent to which the canonical structural framework of cognate tRNAAsp can be altered without losing its ability to be aminoacylated was investigated. Three novel architectures recognized by the synthetase were found. The first resembles that of metazoan mitochondrial tRNASer lacking the D-arm. The second lacks both the D- and T-arms, and the 5'-strand of the amino acid acceptor arm. The third structure is a construct in which the acceptor and anticodon helices are joined by two connectors. Aspartylation specificity of these RNAs is verified by the loss of aminoacylation activity upon mutation of the putative identity residues. Kinetic data indicate that the first two architectures are mimics of the whole tRNAAsp molecule, while the third one behaves as an aspartate minihelix mimic. Results confirm the primordial role of the discriminator nucleotide G73 in aspartylation and demonstrate that neither a helical structure in the acceptor domain nor the presence of a D- or T-arm is mandatory for specific aspartylation, but that activity relies on the presence of the cognate aspartate GUC sequence in the anticodon loop.},
note = {0006-2960
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/*chemistry/metabolism Base Sequence Catalysis Cloning, Asp/*chemistry/genetics/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Molecular Enzyme Activation/genetics Genetic Engineering Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, SAUTER, Site-Directed Plasmids/chemical synthesis RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Assuming that the L-shaped three-dimensional structure of tRNA is an architectural framework allowing the proper presentation of identity nucleotides to aminoacyl-tRNA synthetases implies that altered and/or simplified RNA architectures can fulfill this role and be functional substrates of these enzymes, provided they contain correctly located identity elements. In this work, this paradigm was submitted to new experimental verification. Yeast aspartyl-tRNA synthetase was the model synthetase, and the extent to which the canonical structural framework of cognate tRNAAsp can be altered without losing its ability to be aminoacylated was investigated. Three novel architectures recognized by the synthetase were found. The first resembles that of metazoan mitochondrial tRNASer lacking the D-arm. The second lacks both the D- and T-arms, and the 5'-strand of the amino acid acceptor arm. The third structure is a construct in which the acceptor and anticodon helices are joined by two connectors. Aspartylation specificity of these RNAs is verified by the loss of aminoacylation activity upon mutation of the putative identity residues. Kinetic data indicate that the first two architectures are mimics of the whole tRNAAsp molecule, while the third one behaves as an aspartate minihelix mimic. Results confirm the primordial role of the discriminator nucleotide G73 in aspartylation and demonstrate that neither a helical structure in the acceptor domain nor the presence of a D- or T-arm is mandatory for specific aspartylation, but that activity relies on the presence of the cognate aspartate GUC sequence in the anticodon loop.
Sil'nikov V N, Luk'ianchuk N P, Shishkin G V, Giege R, Vlasov V V
[Imidazole compounds simulated active center of ribonuclease A. Synthesis and RNA cleaving activity] Article de journal
Dans: Dokl Akad Nauk, vol. 364, no. 5, p. 690-694, 1999, ISBN: 10347826, (0869-5652 Journal Article).
Liens | BibTeX | Étiquettes: Base Sequence Binding Sites *Imidazoles/chemical synthesis/chemistry/metabolism Molecular Sequence Data RNA, Pancreatic/*chemistry/metabolism Substrate Specificity, Phe/*metabolism Ribonuclease, Transfer, Unité ARN
@article{,
title = {[Imidazole compounds simulated active center of ribonuclease A. Synthesis and RNA cleaving activity]},
author = {V N Sil'nikov and N P Luk'ianchuk and G V Shishkin and R Giege and V V Vlasov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10347826},
isbn = {10347826},
year = {1999},
date = {1999-01-01},
journal = {Dokl Akad Nauk},
volume = {364},
number = {5},
pages = {690-694},
note = {0869-5652
Journal Article},
keywords = {Base Sequence Binding Sites *Imidazoles/chemical synthesis/chemistry/metabolism Molecular Sequence Data RNA, Pancreatic/*chemistry/metabolism Substrate Specificity, Phe/*metabolism Ribonuclease, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schaub M, Myslinski E, Krol A, Carbon P
Maximization of selenocysteine tRNA and U6 small nuclear RNA transcriptional activation achieved by flexible utilization of a Staf zinc finger Article de journal
Dans: J Biol Chem, vol. 274, no. 35, p. 25042-25050, 1999, ISBN: 10455183, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Animals Binding Sites/genetics DNA/genetics DNA-Binding Proteins/*genetics Human Hydroxyl Radical/metabolism Microinjections Molecular Sequence Data Mutation Oocytes Peptide Fragments/immunology Promoter Regions (Genetics) Protein Binding RNA, Amino Acid-Specific/*genetics Sequence Homology Support, Genetic Trans-Activation (Genetics)/*genetics Trans-Activators/*genetics Transcription Factors/genetics Xenopus Zinc Fingers/*genetics, Non-U.S. Gov't Templates, Small Nuclear/*genetics RNA, Transfer, Unité ARN
@article{,
title = {Maximization of selenocysteine tRNA and U6 small nuclear RNA transcriptional activation achieved by flexible utilization of a Staf zinc finger},
author = {M Schaub and E Myslinski and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10455183},
isbn = {10455183},
year = {1999},
date = {1999-01-01},
journal = {J Biol Chem},
volume = {274},
number = {35},
pages = {25042-25050},
abstract = {Transcriptional activators Staf and Oct-1 play critical roles in the activation of small nuclear RNA (snRNA) and snRNA-type gene transcription. Recently, we established that Staf binding to the human U6 snRNA (hU6) and Xenopus selenocysteine tRNA (xtRNA(Sec)) genes requires different sets of the seven C2-H2 zinc fingers. In this work, using a combination of oocyte microinjection, electrophoretic mobility shift assays, and missing nucleoside experiments with wild-type and mutant promoters, we demonstrate that the hU6 gene requires zinc fingers 2-7 for Staf binding and Oct-1 for maximal transcriptional activity. In contrast, the xtRNA(Sec) gene needs the binding of the seven Staf zinc fingers, but not Oct-1, for optimal transcriptional capacity. Mutation in the binding site for Staf zinc finger 1 in the tRNA(Sec) promoter reduced both Staf binding and transcriptional activity. Conversely, introduction of a zinc finger 1 binding site in the hU6 promoter increased Staf binding but interfered with the simultaneous Staf and Oct-1 binding, thus reducing transcriptional activity. Collectively, these results show that the differential utilization of Staf zinc finger 1 represents a new, critical determinant of the transcriptional activation mechanism for the Xenopus tRNA(Sec) and human U6 snRNA genes.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Sequence Animals Binding Sites/genetics DNA/genetics DNA-Binding Proteins/*genetics Human Hydroxyl Radical/metabolism Microinjections Molecular Sequence Data Mutation Oocytes Peptide Fragments/immunology Promoter Regions (Genetics) Protein Binding RNA, Amino Acid-Specific/*genetics Sequence Homology Support, Genetic Trans-Activation (Genetics)/*genetics Trans-Activators/*genetics Transcription Factors/genetics Xenopus Zinc Fingers/*genetics, Non-U.S. Gov't Templates, Small Nuclear/*genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Transcriptional activators Staf and Oct-1 play critical roles in the activation of small nuclear RNA (snRNA) and snRNA-type gene transcription. Recently, we established that Staf binding to the human U6 snRNA (hU6) and Xenopus selenocysteine tRNA (xtRNA(Sec)) genes requires different sets of the seven C2-H2 zinc fingers. In this work, using a combination of oocyte microinjection, electrophoretic mobility shift assays, and missing nucleoside experiments with wild-type and mutant promoters, we demonstrate that the hU6 gene requires zinc fingers 2-7 for Staf binding and Oct-1 for maximal transcriptional activity. In contrast, the xtRNA(Sec) gene needs the binding of the seven Staf zinc fingers, but not Oct-1, for optimal transcriptional capacity. Mutation in the binding site for Staf zinc finger 1 in the tRNA(Sec) promoter reduced both Staf binding and transcriptional activity. Conversely, introduction of a zinc finger 1 binding site in the hU6 promoter increased Staf binding but interfered with the simultaneous Staf and Oct-1 binding, thus reducing transcriptional activity. Collectively, these results show that the differential utilization of Staf zinc finger 1 represents a new, critical determinant of the transcriptional activation mechanism for the Xenopus tRNA(Sec) and human U6 snRNA genes.
Schaub M, Krol A, Carbon P
Flexible zinc finger requirement for binding of the transcriptional activator staf to U6 small nuclear RNA and tRNA(Sec) promoters Article de journal
Dans: J Biol Chem, vol. 274, no. 34, p. 24241-24249, 1999, ISBN: 10446199, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Animals Binding Sites DNA-Binding Proteins/chemistry/*metabolism Deoxyribonuclease I/pharmacology Human Molecular Sequence Data *Promoter Regions (Genetics) RNA, Amino Acid-Specific/*genetics Support, Non-U.S. Gov't Trans-Activators/chemistry/*metabolism Xenopus *Zinc Fingers, Small Nuclear/*genetics RNA, Transfer, Unité ARN
@article{,
title = {Flexible zinc finger requirement for binding of the transcriptional activator staf to U6 small nuclear RNA and tRNA(Sec) promoters},
author = {M Schaub and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10446199},
isbn = {10446199},
year = {1999},
date = {1999-01-01},
journal = {J Biol Chem},
volume = {274},
number = {34},
pages = {24241-24249},
abstract = {The transactivator Staf, which contains seven zinc finger motifs, exerts its effect on gene expression by binding to specific targets in small nuclear RNA (snRNA) and snRNA-type gene promoters. In this work, binding site selection allowed us to identify the 21-base pair ATTACCCATAATGCATYGCGG sequence as the high affinity consensus binding site for Staf. It shows a high sequence divergence with Staf-responsive elements in the Xenopus selenocysteine tRNA (tRNA(Sec)) and human U6 snRNA promoters. By using a combination of approaches, we analyzed the interaction of wild-type and truncated Staf zinc finger domains with the consensus, Xenopus tRNA(Sec), and human U6 sites. Two main conclusions emerged from our data. First, the data clearly indicate that zinc finger 7 does not establish base-specific contacts in Staf-DNA complexes. The second conclusion concerns zinc finger 1, which is required for the binding to the Xenopus tRNA(Sec) site but is dispensable in the case of the human U6 site. Taking into account the sequence differences in the two sites, these findings demonstrate that Staf utilizes zinc finger 1 in a rather flexible manner, illustrating how a protein can interact with DNAs containing targets of different sequences.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Sequence Animals Binding Sites DNA-Binding Proteins/chemistry/*metabolism Deoxyribonuclease I/pharmacology Human Molecular Sequence Data *Promoter Regions (Genetics) RNA, Amino Acid-Specific/*genetics Support, Non-U.S. Gov't Trans-Activators/chemistry/*metabolism Xenopus *Zinc Fingers, Small Nuclear/*genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The transactivator Staf, which contains seven zinc finger motifs, exerts its effect on gene expression by binding to specific targets in small nuclear RNA (snRNA) and snRNA-type gene promoters. In this work, binding site selection allowed us to identify the 21-base pair ATTACCCATAATGCATYGCGG sequence as the high affinity consensus binding site for Staf. It shows a high sequence divergence with Staf-responsive elements in the Xenopus selenocysteine tRNA (tRNA(Sec)) and human U6 snRNA promoters. By using a combination of approaches, we analyzed the interaction of wild-type and truncated Staf zinc finger domains with the consensus, Xenopus tRNA(Sec), and human U6 sites. Two main conclusions emerged from our data. First, the data clearly indicate that zinc finger 7 does not establish base-specific contacts in Staf-DNA complexes. The second conclusion concerns zinc finger 1, which is required for the binding to the Xenopus tRNA(Sec) site but is dispensable in the case of the human U6 site. Taking into account the sequence differences in the two sites, these findings demonstrate that Staf utilizes zinc finger 1 in a rather flexible manner, illustrating how a protein can interact with DNAs containing targets of different sequences.
Sankaranarayanan R, Dock-Bregeon A C, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D
The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site Article de journal
Dans: Cell, vol. 97, no. 3, p. 371-381, 1999, ISBN: 10319817, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site},
author = {R Sankaranarayanan and A C Dock-Bregeon and P Romby and J Caillet and M Springer and B Rees and C Ehresmann and B Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10319817},
isbn = {10319817},
year = {1999},
date = {1999-01-01},
journal = {Cell},
volume = {97},
number = {3},
pages = {371-381},
abstract = {E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.
Rudinger-Thirion J, Giege R, Felden B
Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu Article de journal
Dans: RNA, vol. 5, no. 8, p. 989-992, 1999, ISBN: 10445873, (1355-8382 Letter).
Liens | BibTeX | Étiquettes: Ala/metabolism RNA, Amino Acyl/*metabolism Support, Bacterial/*metabolism RNA, Base Sequence Escherichia coli/*genetics Guanosine Triphosphate/metabolism Models, Genetic Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/*metabolism Time Factors, Transfer, Unité ARN
@article{,
title = {Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu},
author = {J Rudinger-Thirion and R Giege and B Felden},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10445873},
isbn = {10445873},
year = {1999},
date = {1999-01-01},
journal = {RNA},
volume = {5},
number = {8},
pages = {989-992},
note = {1355-8382
Letter},
keywords = {Ala/metabolism RNA, Amino Acyl/*metabolism Support, Bacterial/*metabolism RNA, Base Sequence Escherichia coli/*genetics Guanosine Triphosphate/metabolism Models, Genetic Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/*metabolism Time Factors, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger-Thirion J, Giege R
The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS Article de journal
Dans: RNA, vol. 5, no. 4, p. 495-502, 1999, ISBN: 10199566, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics RNA, Amino Acyl-tRNA Ligases/*genetics/metabolism Anticodon/genetics Aspartic Acid/genetics/metabolism Base Sequence Escherichia coli/genetics Fungi/*enzymology/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/genetics Selenocysteine/genetics/metabolism Support, Bacterial/genetics RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS},
author = {J Rudinger-Thirion and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10199566},
isbn = {10199566},
year = {1999},
date = {1999-01-01},
journal = {RNA},
volume = {5},
number = {4},
pages = {495-502},
abstract = {The wild-type transcript of Escherichia coli tRNASec, characterized by a peculiar core architecture and a large variable region, was shown to be aspartylatable by yeast AspRS. Similar activities were found for tRNASec mutants with methionine, leucine, and tryptophan anticodons. The charging efficiency of these molecules was found comparable to that of a minihelix derived from tRNAAsp and is accounted for by the presence of the discriminator residue G73, which is a major aspartate identity determinant. Introducing the aspartate identity elements from the anticodon loop (G34, U35, C36, C38) into tRNASec transforms this molecule into an aspartate acceptor with kinetic properties identical to tRNAAsp. Expression of the aspartate identity set in tRNASec is independent of the size of its variable region. The functional study was completed by footprinting experiments with four different nucleases as structural probes. Protection patterns by AspRS of transplanted tRNASec and tRNAAsp were found similar. They are modified, particularly in the anticodon loop, upon changing the aspartate anticodon into that of methionine. Altogether, it appears that recognition of a tRNA by AspRS is more governed by the presence of the aspartate identity set than by the structural framework that carries this set.},
note = {1355-8382
Journal Article},
keywords = {Amino Acid-Specific/*genetics RNA, Amino Acyl-tRNA Ligases/*genetics/metabolism Anticodon/genetics Aspartic Acid/genetics/metabolism Base Sequence Escherichia coli/genetics Fungi/*enzymology/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/genetics Selenocysteine/genetics/metabolism Support, Bacterial/genetics RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The wild-type transcript of Escherichia coli tRNASec, characterized by a peculiar core architecture and a large variable region, was shown to be aspartylatable by yeast AspRS. Similar activities were found for tRNASec mutants with methionine, leucine, and tryptophan anticodons. The charging efficiency of these molecules was found comparable to that of a minihelix derived from tRNAAsp and is accounted for by the presence of the discriminator residue G73, which is a major aspartate identity determinant. Introducing the aspartate identity elements from the anticodon loop (G34, U35, C36, C38) into tRNASec transforms this molecule into an aspartate acceptor with kinetic properties identical to tRNAAsp. Expression of the aspartate identity set in tRNASec is independent of the size of its variable region. The functional study was completed by footprinting experiments with four different nucleases as structural probes. Protection patterns by AspRS of transplanted tRNASec and tRNAAsp were found similar. They are modified, particularly in the anticodon loop, upon changing the aspartate anticodon into that of methionine. Altogether, it appears that recognition of a tRNA by AspRS is more governed by the presence of the aspartate identity set than by the structural framework that carries this set.
Petyuk V A, Zenkova M A, Giege R, Vlassov V V
Hybridization of antisense oligonucleotides with the 3'part of tRNA(Phe) Article de journal
Dans: FEBS Lett, vol. 444, no. 2-3, p. 217-221, 1999, ISBN: 10050762, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/*genetics RNA, Base Sequence Electrophoresis, Calf Thymus/metabolism Support, Fungal/genetics RNA, Non-U.S. Gov't, Phe/*genetics Ribonuclease H, Polyacrylamide Gel Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization/*genetics Oligodeoxyribonucleotides/genetics Oligonucleotides, Transfer, Unité ARN
@article{,
title = {Hybridization of antisense oligonucleotides with the 3'part of tRNA(Phe)},
author = {V A Petyuk and M A Zenkova and R Giege and V V Vlassov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10050762},
isbn = {10050762},
year = {1999},
date = {1999-01-01},
journal = {FEBS Lett},
volume = {444},
number = {2-3},
pages = {217-221},
abstract = {The interaction of antisense oligodeoxyribonucleotides with yeast tRNA(Phe) was investigated. 14-15-mers complementary to the 3'-terminal sequence including the ACCA end bind to the tRNA under physiological conditions. At low oligonucleotide concentrations the binding occurs at the unique complementary site. At higher oligonucleotide concentrations, the second oligonucleotide molecule binds to the complex due to non-perfect duplex formation in the T-loop stabilized by stacking between the two bound oligonucleotides. In these complexes the acceptor stem is open and the 5'-terminal sequence of the tRNA is accessible for binding of a complementary oligonucleotide. The results prove that the efficient binding of oligonucleotides to the 3'-terminal sequence of the tRNA occurs through initial binding to the single-stranded sequence ACCA followed by invasion in the acceptor stem and strand displacement.},
note = {0014-5793
Journal Article},
keywords = {Antisense/*genetics RNA, Base Sequence Electrophoresis, Calf Thymus/metabolism Support, Fungal/genetics RNA, Non-U.S. Gov't, Phe/*genetics Ribonuclease H, Polyacrylamide Gel Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization/*genetics Oligodeoxyribonucleotides/genetics Oligonucleotides, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The interaction of antisense oligodeoxyribonucleotides with yeast tRNA(Phe) was investigated. 14-15-mers complementary to the 3'-terminal sequence including the ACCA end bind to the tRNA under physiological conditions. At low oligonucleotide concentrations the binding occurs at the unique complementary site. At higher oligonucleotide concentrations, the second oligonucleotide molecule binds to the complex due to non-perfect duplex formation in the T-loop stabilized by stacking between the two bound oligonucleotides. In these complexes the acceptor stem is open and the 5'-terminal sequence of the tRNA is accessible for binding of a complementary oligonucleotide. The results prove that the efficient binding of oligonucleotides to the 3'-terminal sequence of the tRNA occurs through initial binding to the single-stranded sequence ACCA followed by invasion in the acceptor stem and strand displacement.
Petyuk V, Zenkova M, Giege R, Vlassov V
Interaction of complementary oligonucleotides with the 3'-end of yeast tRNA(Phe) Article de journal
Dans: Nucleosides Nucleotides, vol. 18, no. 6-7, p. 1459-1461, 1999, ISBN: 10474225, (0732-8311 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Non-U.S. Gov't, Nucleic Acid Conformation RNA, Phe/*chemistry Saccharomyces cerevisiae/*genetics Support, Transfer, Unité ARN
@article{,
title = {Interaction of complementary oligonucleotides with the 3'-end of yeast tRNA(Phe)},
author = {V Petyuk and M Zenkova and R Giege and V Vlassov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10474225},
isbn = {10474225},
year = {1999},
date = {1999-01-01},
journal = {Nucleosides Nucleotides},
volume = {18},
number = {6-7},
pages = {1459-1461},
abstract = {Interaction of yeast tRNA(Phe) with oligodeoxyribonucleotides (ONs), complementary to the nucleotides 62-76 was investigated. Results of gel-mobility shift assay and RNase A probing evidence that the ONs containing the sequence complementary to the tRNA ACCA end can easily invade the hairpin structure under physiological conditions. The limiting step of association process is the tRNA unfolding.},
note = {0732-8311
Journal Article},
keywords = {Non-U.S. Gov't, Nucleic Acid Conformation RNA, Phe/*chemistry Saccharomyces cerevisiae/*genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Interaction of yeast tRNA(Phe) with oligodeoxyribonucleotides (ONs), complementary to the nucleotides 62-76 was investigated. Results of gel-mobility shift assay and RNase A probing evidence that the ONs containing the sequence complementary to the tRNA ACCA end can easily invade the hairpin structure under physiological conditions. The limiting step of association process is the tRNA unfolding.
Perreau V M, Keith G, Holmes W M, Przykorska A, Santos M A, Tuite M F
The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal
Dans: J Mol Biol, vol. 293, no. 5, p. 1039-1053, 1999, ISBN: 10547284, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry/*genetics/metabolism Base Sequence Candida albicans/*genetics Evolution, Fungal/chemistry/genetics/metabolism RNA, Molecular Genetic Code/genetics Imidazoles/metabolism Lead/metabolism Methylation Mutation/genetics *Nucleic Acid Conformation Nucleosides/genetics/metabolism RNA, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. tRNA Methyltransferases/metabolism, Ser/*chemistry/*genetics/metabolism Ribonucleases/metabolism Saccharomyces cerevisiae/genetics Solutions Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure},
author = {V M Perreau and G Keith and W M Holmes and A Przykorska and M A Santos and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10547284},
isbn = {10547284},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {293},
number = {5},
pages = {1039-1053},
abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.},
note = {0022-2836
Journal Article},
keywords = {Anticodon/*chemistry/*genetics/metabolism Base Sequence Candida albicans/*genetics Evolution, Fungal/chemistry/genetics/metabolism RNA, Molecular Genetic Code/genetics Imidazoles/metabolism Lead/metabolism Methylation Mutation/genetics *Nucleic Acid Conformation Nucleosides/genetics/metabolism RNA, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. tRNA Methyltransferases/metabolism, Ser/*chemistry/*genetics/metabolism Ribonucleases/metabolism Saccharomyces cerevisiae/genetics Solutions Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.
1998
Friant S., Heyman T., Bystrom A. S., Wilhelm M., Wilhelm F. X.
Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo Article de journal
Dans: Mol Cell Biol, vol. 18, no. 2, p. 799-806, 1998, (0270-7306 Journal Article).
Résumé | BibTeX | Étiquettes: *Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer
@article{,
title = {Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo},
author = { S. Friant and T. Heyman and A. S. Bystrom and M. Wilhelm and F. X. Wilhelm},
year = {1998},
date = {1998-01-01},
journal = {Mol Cell Biol},
volume = {18},
number = {2},
pages = {799-806},
abstract = {Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet).},
note = {0270-7306
Journal Article},
keywords = {*Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet).
Gabus C., Ficheux D., Rau M., Keith G., Sandmeyer S., Darlix J. L.
The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7 Article de journal
Dans: EMBO J, vol. 17, no. 16, p. 4873-80, 1998, (0261-4189 Journal Article).
Résumé | BibTeX | Étiquettes: *Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S.
@article{,
title = {The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7},
author = { C. Gabus and D. Ficheux and M. Rau and G. Keith and S. Sandmeyer and J. L. Darlix},
year = {1998},
date = {1998-01-01},
journal = {EMBO J},
volume = {17},
number = {16},
pages = {4873-80},
abstract = {Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.},
note = {0261-4189
Journal Article},
keywords = {*Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S.},
pubstate = {published},
tppubtype = {article}
}
Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.
1997
Friant S., Heyman T., Poch O., Wilhelm M., Wilhelm F. X.
Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex Article de journal
Dans: Yeast, vol. 13, no. 7, p. 639-45, 1997, (0749-503x Journal Article).
Résumé | BibTeX | Étiquettes: *Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics
@article{,
title = {Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex},
author = { S. Friant and T. Heyman and O. Poch and M. Wilhelm and F. X. Wilhelm},
year = {1997},
date = {1997-01-01},
journal = {Yeast},
volume = {13},
number = {7},
pages = {639-45},
abstract = {In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.},
note = {0749-503x
Journal Article},
keywords = {*Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics},
pubstate = {published},
tppubtype = {article}
}
In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.
Vlassov V, Abramova T, Godovikova T, Giege R, Silnikov V
Sequence-specific cleavage of yeast tRNA(Phe) with oligonucleotides conjugated to a diimidazole construct Article de journal
Dans: Antisense Nucleic Acid Drug Dev, vol. 7, no. 1, p. 39-42, 1997, ISBN: 9055037, (1087-2906 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/chemical synthesis/metabolism/*pharmacology RNA, Base Sequence Imidazoles/*chemistry Molecular Sequence Data Oligonucleotides, Fungal/*drug effects RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/pharmacology Support, Phe/chemistry/*drug effects/*metabolism Ribonuclease, Transfer, Unité ARN
@article{,
title = {Sequence-specific cleavage of yeast tRNA(Phe) with oligonucleotides conjugated to a diimidazole construct},
author = {V Vlassov and T Abramova and T Godovikova and R Giege and V Silnikov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9055037},
isbn = {9055037},
year = {1997},
date = {1997-01-01},
journal = {Antisense Nucleic Acid Drug Dev},
volume = {7},
number = {1},
pages = {39-42},
abstract = {Oligonucleotide derivatives conjugated to a chemical construction with two histamine residues imitating the catalytic center of ribonuclease A have been synthesized. In experiments with the conjugates complementary to the 3'-end and to the variable loop and the T loop of yeast tRNA(Phe), it was shown that the compounds can accomplish sequence-specific cleavage of the target RNA in physiologic conditions.},
note = {1087-2906
Journal Article},
keywords = {Antisense/chemical synthesis/metabolism/*pharmacology RNA, Base Sequence Imidazoles/*chemistry Molecular Sequence Data Oligonucleotides, Fungal/*drug effects RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/pharmacology Support, Phe/chemistry/*drug effects/*metabolism Ribonuclease, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Oligonucleotide derivatives conjugated to a chemical construction with two histamine residues imitating the catalytic center of ribonuclease A have been synthesized. In experiments with the conjugates complementary to the 3'-end and to the variable loop and the T loop of yeast tRNA(Phe), it was shown that the compounds can accomplish sequence-specific cleavage of the target RNA in physiologic conditions.
Vlassov A V, Andrievskaya O A, Kanyshkova T G, Baranovsky A G, Naumov V A, Breusov A A, Giege R, Buneva V N, Nevinsky G A
RNA-hydrolyzing antibodies from peripheral blood of patients with lupus erythematosus Article de journal
Dans: Biochemistry (Mosc), vol. 62, no. 5, p. 474-479, 1997, ISBN: 9275287, (0006-2979 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antibodies, Catalytic/*blood Human Hydrolysis Lupus Erythematosus, Lys/chemistry/*metabolism, Systemic/blood/*immunology Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {RNA-hydrolyzing antibodies from peripheral blood of patients with lupus erythematosus},
author = {A V Vlassov and O A Andrievskaya and T G Kanyshkova and A G Baranovsky and V A Naumov and A A Breusov and R Giege and V N Buneva and G A Nevinsky},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9275287},
isbn = {9275287},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry (Mosc)},
volume = {62},
number = {5},
pages = {474-479},
abstract = {Experiments and hydrolysis of substrates with known spatial structures (such as yeast tRNAPhe, as well as normal and mutant tRNALys from human mitochondria produced by transcription of the appropriate DNA species, that is, RNA genes) were performed to study the ribonuclease activity of antibodies isolated from blood sera of patients with systemic lupus erythematosus (SLE). The antibody preparations contained two types of ribonuclease activities: the first corresponded to the specificity of ribonuclease A and was found during hydrolysis at low salt concentrations, whereas the second was stimulated by Mg2+ and displayed unique specificity toward double-stranded regions of the substrate. The possible use of the antibody preparations as tools for structural studies of conformational differences between RNA molecules was examined. In experiments with unmodified and mutant tRNALys species differing in one base found in the T-loop, we found that hydrolysis with SLE antibodies can detect small local structural changes in RNA under physiological conditions.},
note = {0006-2979
Journal Article},
keywords = {Antibodies, Catalytic/*blood Human Hydrolysis Lupus Erythematosus, Lys/chemistry/*metabolism, Systemic/blood/*immunology Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Experiments and hydrolysis of substrates with known spatial structures (such as yeast tRNAPhe, as well as normal and mutant tRNALys from human mitochondria produced by transcription of the appropriate DNA species, that is, RNA genes) were performed to study the ribonuclease activity of antibodies isolated from blood sera of patients with systemic lupus erythematosus (SLE). The antibody preparations contained two types of ribonuclease activities: the first corresponded to the specificity of ribonuclease A and was found during hydrolysis at low salt concentrations, whereas the second was stimulated by Mg2+ and displayed unique specificity toward double-stranded regions of the substrate. The possible use of the antibody preparations as tools for structural studies of conformational differences between RNA molecules was examined. In experiments with unmodified and mutant tRNALys species differing in one base found in the T-loop, we found that hydrolysis with SLE antibodies can detect small local structural changes in RNA under physiological conditions.
Sissler M, Eriani G, Martin F, Giege R, Florentz C
Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 24, p. 4899-4906, 1997, ISBN: 9396794, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/chemistry Arginine-tRNA Ligase/classification/*metabolism Aspartate-tRNA Ligase/classification/*metabolism Base Sequence DNA Footprinting Escherichia coli Fungal Proteins/classification/*metabolism Models, Arg/chemistry/*metabolism RNA, Asp/chemistry/*metabolism Recombinant Fusion Proteins/metabolism Saccharomyces cerevisiae/metabolism Stereoisomerism Substrate Specificity Support, ERIANI, FLORENTZ, Fungal/chemistry/*metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase},
author = {M Sissler and G Eriani and F Martin and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9396794},
isbn = {9396794},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {24},
pages = {4899-4906},
abstract = {Gene cloning, overproduction and an efficient purification protocol of yeast arginyl-tRNA synthetase (ArgRS) as well as the interaction patterns of this protein with cognate tRNAArgand non-cognate tRNAAspare described. This work was motivated by the fact that the in vitro transcript of tRNAAspis of dual aminoacylation specificity and is not only aspartylated but also efficiently arginylated. The crystal structure of the complex between class II aspartyl-tRNA synthetase (AspRS) and tRNAAsp, as well as early biochemical data, have shown that tRNAAspis recognized by its variable region side. Here we show by footprinting with enzymatic and chemical probes that transcribed tRNAAspis contacted by class I ArgRS along the opposite D arm side, as is homologous tRNAArg, but with idiosyncratic interaction patterns. Besides protection, footprints also show enhanced accessibility of the tRNAs to the structural probes, indicative of conformational changes in the complexed tRNAs. These different patterns are interpreted in relation to the alternative arginine identity sets found in the anticodon loops of tRNAArgand tRNAAsp. The mirror image alternative interaction patterns of unmodified tRNAAspwith either class I ArgRS or class II AspRS, accounting for the dual identity of this tRNA, are discussed in relation to the class defining features of the synthetases. This study indicates that complex formation between unmodified tRNAAspand either ArgRS and AspRS is solely governed by the proteins.},
note = {0305-1048
Journal Article},
keywords = {Anticodon/chemistry Arginine-tRNA Ligase/classification/*metabolism Aspartate-tRNA Ligase/classification/*metabolism Base Sequence DNA Footprinting Escherichia coli Fungal Proteins/classification/*metabolism Models, Arg/chemistry/*metabolism RNA, Asp/chemistry/*metabolism Recombinant Fusion Proteins/metabolism Saccharomyces cerevisiae/metabolism Stereoisomerism Substrate Specificity Support, ERIANI, FLORENTZ, Fungal/chemistry/*metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gene cloning, overproduction and an efficient purification protocol of yeast arginyl-tRNA synthetase (ArgRS) as well as the interaction patterns of this protein with cognate tRNAArgand non-cognate tRNAAspare described. This work was motivated by the fact that the in vitro transcript of tRNAAspis of dual aminoacylation specificity and is not only aspartylated but also efficiently arginylated. The crystal structure of the complex between class II aspartyl-tRNA synthetase (AspRS) and tRNAAsp, as well as early biochemical data, have shown that tRNAAspis recognized by its variable region side. Here we show by footprinting with enzymatic and chemical probes that transcribed tRNAAspis contacted by class I ArgRS along the opposite D arm side, as is homologous tRNAArg, but with idiosyncratic interaction patterns. Besides protection, footprints also show enhanced accessibility of the tRNAs to the structural probes, indicative of conformational changes in the complexed tRNAs. These different patterns are interpreted in relation to the alternative arginine identity sets found in the anticodon loops of tRNAArgand tRNAAsp. The mirror image alternative interaction patterns of unmodified tRNAAspwith either class I ArgRS or class II AspRS, accounting for the dual identity of this tRNA, are discussed in relation to the class defining features of the synthetases. This study indicates that complex formation between unmodified tRNAAspand either ArgRS and AspRS is solely governed by the proteins.
Senger B, Auxilien S, Englisch U, Cramer F, Fasiolo F
The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase Article de journal
Dans: Biochemistry, vol. 36, no. 27, p. 8269-8275, 1997, ISBN: 9204872, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Base Sequence Escherichia coli/genetics Inosine/*chemistry/metabolism Isoleucine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Fungal/chemistry/metabolism RNA, Ile/*chemistry/metabolism Saccharomyces cerevisiae/*genetics Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase},
author = {B Senger and S Auxilien and U Englisch and F Cramer and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9204872},
isbn = {9204872},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {27},
pages = {8269-8275},
abstract = {Earlier work by two independent groups has established the fact that anticodons GAU and LAU of Escherichia coli tRNAIle isoacceptors play a critical role in the tRNA identity. Yeast possesses two isoleucine transfer RNAs, a major one with anticodon IAU and a minor one with anticodon PsiAPsi which are derived from the post-transcriptional modification of AAU and UAU gene sequences, respectively. We present direct evidence which reveals that inosine is a positive determinant for yeast isoleucyl-tRNA synthetase. We also show that yeast tRNAMet with guanosine at the wobble position becomes aminoacylated with isoleucine while methionine acceptance is lost. As inosine and guanosine share the 6-keto and the N-1 hydrogen groups, this suggests that these hydrogen donor and acceptor groups are determinants for isoleucine specificity. The role of the minor tRNAIle anticodon pseudouridines in tRNA isoleucylation could not be tested directly but was deduced from a 40-fold decrease in the activity of the unmodified transcript. The presence of the NHCO structure in guanosine, inosine, pseudouridine, and lysidine suggests a unifying model of wobble base recognition by the yeast and E. coli isoleucyl-tRNA synthetase. In contrast to lysidine which switches the identity of the tRNA from methionine to isoleucine [Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., & Yokoyama, S. (1988) Nature 336, 179-181], pseudouridine-34 does not modify the specificity of the yeast minor tRNAIle since U-34 is a strong negative determinant for yeast MetRS. Therefore, the major role of Psi-34 (in combination with Psi-36 or not) is likely in isoleucine AUA codon specificity and translational fidelity.},
note = {0006-2960
Journal Article},
keywords = {Acylation Anticodon Base Sequence Escherichia coli/genetics Inosine/*chemistry/metabolism Isoleucine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Fungal/chemistry/metabolism RNA, Ile/*chemistry/metabolism Saccharomyces cerevisiae/*genetics Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Earlier work by two independent groups has established the fact that anticodons GAU and LAU of Escherichia coli tRNAIle isoacceptors play a critical role in the tRNA identity. Yeast possesses two isoleucine transfer RNAs, a major one with anticodon IAU and a minor one with anticodon PsiAPsi which are derived from the post-transcriptional modification of AAU and UAU gene sequences, respectively. We present direct evidence which reveals that inosine is a positive determinant for yeast isoleucyl-tRNA synthetase. We also show that yeast tRNAMet with guanosine at the wobble position becomes aminoacylated with isoleucine while methionine acceptance is lost. As inosine and guanosine share the 6-keto and the N-1 hydrogen groups, this suggests that these hydrogen donor and acceptor groups are determinants for isoleucine specificity. The role of the minor tRNAIle anticodon pseudouridines in tRNA isoleucylation could not be tested directly but was deduced from a 40-fold decrease in the activity of the unmodified transcript. The presence of the NHCO structure in guanosine, inosine, pseudouridine, and lysidine suggests a unifying model of wobble base recognition by the yeast and E. coli isoleucyl-tRNA synthetase. In contrast to lysidine which switches the identity of the tRNA from methionine to isoleucine [Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., & Yokoyama, S. (1988) Nature 336, 179-181], pseudouridine-34 does not modify the specificity of the yeast minor tRNAIle since U-34 is a strong negative determinant for yeast MetRS. Therefore, the major role of Psi-34 (in combination with Psi-36 or not) is likely in isoleucine AUA codon specificity and translational fidelity.
Rudinger J, Felden B, Florentz C, Giege R
Strategy for RNA recognition by yeast histidyl-tRNA synthetase Article de journal
Dans: Bioorg Med Chem, vol. 5, no. 6, p. 1001-1009, 1997, ISBN: 9222493, (0968-0896 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/metabolism RNA, Base Sequence Histidine-tRNA Ligase/*metabolism Molecular Sequence Data RNA, FLORENTZ, Fungal/*metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN, Viral/metabolism Saccharomyces cerevisiae/*enzymology Substrate Specificity Support
@article{,
title = {Strategy for RNA recognition by yeast histidyl-tRNA synthetase},
author = {J Rudinger and B Felden and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9222493},
isbn = {9222493},
year = {1997},
date = {1997-01-01},
journal = {Bioorg Med Chem},
volume = {5},
number = {6},
pages = {1001-1009},
abstract = {Histidine aminoacylation systems are of interest because of the structural diversity of the RNA substrates recognized by histidyl-tRNA synthetases. Among tRNAs participating in protein synthesis, those specific for histidine all share an additional residue at their 5'-extremities. On the other hand, tRNA-like domains at the 3'--termini of some plant viruses can also be charged by histidyl-tRNA synthetases, although they are not actors in protein synthesis. This is the case for the RNAs from tobacco mosaic virus and its satellite virus but also those of turnip yellow and brome mosaic viruses. All these RNAs have intricate foldings at their 3'-termini differing from that of canonical tRNAs and share a pseudoknotted domain which is the prerequisite for their folding into structures mimicking the overall L-shape of tRNAs. This paper gives an overview on tRNA identity and rationalizes the apparently contradictory structural and aminoacylation features of histidine-specific tRNAs and tRNA-like structures. The discussion mainly relies on histidylation data obtained with the yeast synthetase, but the conclusions are of a more universal nature. In canonical tRNA(His), the major histidine identity element is the 'minus' 1 residue, since its removal impairs histidylation and conversely its addition to a non-cognate tRNA(Asp) confers histidine identity to the transplanted molecule. Optimal expression of histidine identity depends on the chemical nature of the -1 residue and is further increased and/or modulated by the discriminator base N73 and by residues in the anticodon. In the viral tRNA-like domains, the major identity determinant -1 is mimicked by a residue from the single-stranded L1 regions of the different pseudoknots. The consequences of this mimicry for the function of minimalist RNAs derived from tRNA-like domains are discussed. The characteristics of the histidine systems illustrate well the view that the core of the amino acid accepting RNAs is a scaffold that allows proper presentation of identity nucleotides to their amino acid identity counterparts in the synthetase and that different types of scaffoldings are possible.},
note = {0968-0896
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acyl/metabolism RNA, Base Sequence Histidine-tRNA Ligase/*metabolism Molecular Sequence Data RNA, FLORENTZ, Fungal/*metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN, Viral/metabolism Saccharomyces cerevisiae/*enzymology Substrate Specificity Support},
pubstate = {published},
tppubtype = {article}
}
Histidine aminoacylation systems are of interest because of the structural diversity of the RNA substrates recognized by histidyl-tRNA synthetases. Among tRNAs participating in protein synthesis, those specific for histidine all share an additional residue at their 5'-extremities. On the other hand, tRNA-like domains at the 3'--termini of some plant viruses can also be charged by histidyl-tRNA synthetases, although they are not actors in protein synthesis. This is the case for the RNAs from tobacco mosaic virus and its satellite virus but also those of turnip yellow and brome mosaic viruses. All these RNAs have intricate foldings at their 3'-termini differing from that of canonical tRNAs and share a pseudoknotted domain which is the prerequisite for their folding into structures mimicking the overall L-shape of tRNAs. This paper gives an overview on tRNA identity and rationalizes the apparently contradictory structural and aminoacylation features of histidine-specific tRNAs and tRNA-like structures. The discussion mainly relies on histidylation data obtained with the yeast synthetase, but the conclusions are of a more universal nature. In canonical tRNA(His), the major histidine identity element is the 'minus' 1 residue, since its removal impairs histidylation and conversely its addition to a non-cognate tRNA(Asp) confers histidine identity to the transplanted molecule. Optimal expression of histidine identity depends on the chemical nature of the -1 residue and is further increased and/or modulated by the discriminator base N73 and by residues in the anticodon. In the viral tRNA-like domains, the major identity determinant -1 is mimicked by a residue from the single-stranded L1 regions of the different pseudoknots. The consequences of this mimicry for the function of minimalist RNAs derived from tRNA-like domains are discussed. The characteristics of the histidine systems illustrate well the view that the core of the amino acid accepting RNAs is a scaffold that allows proper presentation of identity nucleotides to their amino acid identity counterparts in the synthetase and that different types of scaffoldings are possible.
Putz J, Wientges J, Sissler M, Giege R, Florentz C, Schwienhorst A
Rapid selection of aminoacyl-tRNAs based on biotinylation of alpha-NH2 group of charged amino acids Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 9, p. 1862-1863, 1997, ISBN: 9162902, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acids/*chemistry Biotin/*chemistry Polymerase Chain Reaction RNA, Amino Acyl/chemistry/*isolation & purification Support, FLORENTZ, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Rapid selection of aminoacyl-tRNAs based on biotinylation of alpha-NH2 group of charged amino acids},
author = {J Putz and J Wientges and M Sissler and R Giege and C Florentz and A Schwienhorst},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9162902},
isbn = {9162902},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {9},
pages = {1862-1863},
abstract = {A rapid selection procedure to separate low amounts of aminoacylated tRNAs from large pools of inactive variants is described. The procedure involves a three-step protocol. After initial aminoacylation of a tRNA pool, N-hydroxysuccinimide ester chemistry is applied to biotinylate the alpha-NH2 group of the amino acid bound to the 3'-end of a tRNA. The biotin tag is used to capture the derivatized tRNAs on streptavidin-conjugated magnetic beads. Variants bound to the solid phase can be amplified by RT-PCR and transcription, providing tRNAs for subsequent selection rounds.},
note = {0305-1048
Journal Article},
keywords = {Amino Acids/*chemistry Biotin/*chemistry Polymerase Chain Reaction RNA, Amino Acyl/chemistry/*isolation & purification Support, FLORENTZ, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A rapid selection procedure to separate low amounts of aminoacylated tRNAs from large pools of inactive variants is described. The procedure involves a three-step protocol. After initial aminoacylation of a tRNA pool, N-hydroxysuccinimide ester chemistry is applied to biotinylate the alpha-NH2 group of the amino acid bound to the 3'-end of a tRNA. The biotin tag is used to capture the derivatized tRNAs on streptavidin-conjugated magnetic beads. Variants bound to the solid phase can be amplified by RT-PCR and transcription, providing tRNAs for subsequent selection rounds.
Ng J D, Kuznetsov Y G, Malkin A J, Keith G, Giege R, McPherson A
Visualization of RNA crystal growth by atomic force microscopy Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 13, p. 2582-2588, 1997, ISBN: 9185567, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Atomic Force RNA, Crystallization *Microscopy, Fungal/*chemistry RNA, Non-U.S. Gov't Temperature, Phe/*chemistry Saccharomyces cerevisiae/genetics Support, Transfer, Unité ARN
@article{,
title = {Visualization of RNA crystal growth by atomic force microscopy},
author = {J D Ng and Y G Kuznetsov and A J Malkin and G Keith and R Giege and A McPherson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9185567},
isbn = {9185567},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {13},
pages = {2582-2588},
abstract = {The crystallization of transfer RNA (tRNA) was investigated using atomic force microscopy (AFM) over the temperature range from 4 to 16 degrees C, and this produced the first in situ AFM images of developing nucleic acid crystals. The growth of the (110) face of hexagonal yeast tRNAPhe crystals was observed to occur at steps on vicinal hillocks generated by multiple screw dislocation sources in the temperature range of 13.5-16 degrees C. Two-dimensional nucleation begins to dominate at 13.5 degrees C, with the appearance of three-dimensional nuclei at 12 degrees C. The changes in growth mechanisms are correlated with variations in supersaturation which is higher in the low temperature range. Growth of tRNA crystals was characterized by a strong anisotropy in the tangential step movement and transformation of growth modes on single crystals were directly observed by AFM over the narrow temperature range utilized. Finally, lattice resolution images of the molecular structure of surface layers were recorded. The implications of the strong temperature dependence of tRNAPhe crystal growth are discussed in view of improving and better controlling crystallization of nucleic acids.},
note = {0305-1048
Journal Article},
keywords = {Atomic Force RNA, Crystallization *Microscopy, Fungal/*chemistry RNA, Non-U.S. Gov't Temperature, Phe/*chemistry Saccharomyces cerevisiae/genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The crystallization of transfer RNA (tRNA) was investigated using atomic force microscopy (AFM) over the temperature range from 4 to 16 degrees C, and this produced the first in situ AFM images of developing nucleic acid crystals. The growth of the (110) face of hexagonal yeast tRNAPhe crystals was observed to occur at steps on vicinal hillocks generated by multiple screw dislocation sources in the temperature range of 13.5-16 degrees C. Two-dimensional nucleation begins to dominate at 13.5 degrees C, with the appearance of three-dimensional nuclei at 12 degrees C. The changes in growth mechanisms are correlated with variations in supersaturation which is higher in the low temperature range. Growth of tRNA crystals was characterized by a strong anisotropy in the tangential step movement and transformation of growth modes on single crystals were directly observed by AFM over the narrow temperature range utilized. Finally, lattice resolution images of the molecular structure of surface layers were recorded. The implications of the strong temperature dependence of tRNAPhe crystal growth are discussed in view of improving and better controlling crystallization of nucleic acids.
Isel C, Ehresmann C, Keith G, Ehresmann B, Marquet R
Two step synthesis of (-) strong-stop DNA by avian and murine reverse transcriptases in vitro Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 3, p. 545-552, 1997, ISBN: 9016594, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Cattle DNA Primers DNA, Avian/*enzymology Rna RNA, MARQUET, Murine/*enzymology Mice Myeloblastosis Virus, Non-U.S. Gov't, Pro RNA, Transfer, Trp RNA-Directed DNA Polymerase/*metabolism Support, Unité ARN, Viral/*biosynthesis Leukemia Virus
@article{,
title = {Two step synthesis of (-) strong-stop DNA by avian and murine reverse transcriptases in vitro},
author = {C Isel and C Ehresmann and G Keith and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9016594},
isbn = {9016594},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {3},
pages = {545-552},
abstract = {Retroviral reverses transcriptases (RTs) are RNA- and DNA-dependent DNA polymerases that use a tRNA bound at the so-called primer binding site (PBS) located near the 5'end of the genomic RNA as primer. Thus, RTs must be able to accommodate both RNA and DNA in the primer strand. To test whether the natural primer confers some advantages to the priming process, we compared initiation of reverse transcription of avian and murine retroviral RNAs, using either their natural tRNA primer, tRNATrp and tRNAPro, respectively, or synthetic 18mer oligodeoxyribonucleotides (ODNs) and oligoribonucleotides (ORNs) complementary to their PBS. In both retroviral systems, the initial extension of ODNs was fast and processive. The initial extension of ORNs, tRNATrp and tRNAPro was much slower and distributive, giving rise to the transient accumulation of short pausing products. Synthesis of (-) strong-stop DNA was delayed when using ORNs and tRNAs, compared to ODNs. Even though ORNs and tRNAs were initially extended at the same rate, the short pausing products were more rapidly extended when using the tRNA primers. As a consequence, synthesis of (-) strong-stop DNA was much more efficient with tRNA primers, compared to ORNs. Taken together, these results suggest that the tRNA-primed synthesis of (-) strong-stop DNA is a two-step process, as already observed for HIV-1. The initiation mode corresponds to the initial non-processive nucleotide addition and extension of the short pausing products. It is more efficient with the natural primers than with ORNs. Initiation is followed by a more processive and unspecific elongation mode. Elongation is observed when the primer strand is DNA, i.e. when using the ODNs as primers or when the ORN and tRNA primers have been extended by a sufficient number (depending on the retroviral system) of deoxyribonucleotides.},
note = {0305-1048
Journal Article},
keywords = {Animals Cattle DNA Primers DNA, Avian/*enzymology Rna RNA, MARQUET, Murine/*enzymology Mice Myeloblastosis Virus, Non-U.S. Gov't, Pro RNA, Transfer, Trp RNA-Directed DNA Polymerase/*metabolism Support, Unité ARN, Viral/*biosynthesis Leukemia Virus},
pubstate = {published},
tppubtype = {article}
}
Retroviral reverses transcriptases (RTs) are RNA- and DNA-dependent DNA polymerases that use a tRNA bound at the so-called primer binding site (PBS) located near the 5'end of the genomic RNA as primer. Thus, RTs must be able to accommodate both RNA and DNA in the primer strand. To test whether the natural primer confers some advantages to the priming process, we compared initiation of reverse transcription of avian and murine retroviral RNAs, using either their natural tRNA primer, tRNATrp and tRNAPro, respectively, or synthetic 18mer oligodeoxyribonucleotides (ODNs) and oligoribonucleotides (ORNs) complementary to their PBS. In both retroviral systems, the initial extension of ODNs was fast and processive. The initial extension of ORNs, tRNATrp and tRNAPro was much slower and distributive, giving rise to the transient accumulation of short pausing products. Synthesis of (-) strong-stop DNA was delayed when using ORNs and tRNAs, compared to ODNs. Even though ORNs and tRNAs were initially extended at the same rate, the short pausing products were more rapidly extended when using the tRNA primers. As a consequence, synthesis of (-) strong-stop DNA was much more efficient with tRNA primers, compared to ORNs. Taken together, these results suggest that the tRNA-primed synthesis of (-) strong-stop DNA is a two-step process, as already observed for HIV-1. The initiation mode corresponds to the initial non-processive nucleotide addition and extension of the short pausing products. It is more efficient with the natural primers than with ORNs. Initiation is followed by a more processive and unspecific elongation mode. Elongation is observed when the primer strand is DNA, i.e. when using the ODNs as primers or when the ORN and tRNA primers have been extended by a sufficient number (depending on the retroviral system) of deoxyribonucleotides.
Friant S, Heyman T, Poch O, Wilhelm M, Wilhelm F X
Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex Article de journal
Dans: Yeast, vol. 13, no. 7, p. 639-645, 1997, ISBN: 9200813, (0749-503x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Molecular Structure RNA, Fungal/genetics RNA, Met/*chemistry/*genetics Sequence Alignment *Sequence Analysis, Non-U.S. Gov't Yeasts/*genetics, RNA Support, Transfer, Unité ARN
@article{,
title = {Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex},
author = {S Friant and T Heyman and O Poch and M Wilhelm and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9200813},
isbn = {9200813},
year = {1997},
date = {1997-01-01},
journal = {Yeast},
volume = {13},
number = {7},
pages = {639-645},
abstract = {In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.},
note = {0749-503x
Journal Article},
keywords = {Amino Acid Sequence Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Molecular Structure RNA, Fungal/genetics RNA, Met/*chemistry/*genetics Sequence Alignment *Sequence Analysis, Non-U.S. Gov't Yeasts/*genetics, RNA Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.
Becker H F, Motorin Y, Sissler M, Florentz C, Grosjean H
Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the T psi-loop of yeast tRNAs Article de journal
Dans: J Mol Biol, vol. 274, no. 4, p. 505-518, 1997, ISBN: 9417931, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/metabolism Saccharomyces cerevisiae/genetics Substrate Specificity Support, Base Sequence Conserved Sequence Intramolecular Lyases/metabolism Models, FLORENTZ, Fungal/*chemistry/metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/*metabolism RNA, Non-U.S. Gov't Uridine/*analogs & derivatives/chemistry/metabolism tRNA Methyltransferases/metabolism, SISSLER, Transfer, Transfer/*chemistry/*metabolism RNA, Unité ARN
@article{,
title = {Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the T psi-loop of yeast tRNAs},
author = {H F Becker and Y Motorin and M Sissler and C Florentz and H Grosjean},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9417931},
isbn = {9417931},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {274},
number = {4},
pages = {505-518},
abstract = {Almost all transfer RNA molecules sequenced so far contain two universal modified nucleosides at positions 54 and 55, respectively: ribothymidine (T54) and pseudouridine (psi 55). To identify the tRNA elements recognized by tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase from the yeast Saccharomyces cerevisiae, a set of 43 yeast tRNA(Asp) mutants were used. Some variants contained point mutations, while the others included progressive reductions in size down to a tRNA minisubstrate consisting of the T psi-loop with only one G.C base-pair as stem (9-mer). All substrates (full-sized tRNA(Asp) and various minihelices) were produced in vitro by T7 transcription and tested using yeast extract (S100) as a source of enzymatic activities and S-adenosyl-L-methionine as a methyl donor. The results indicate that the minimal substrate for enzymatic formation of psi 55 is a stem/loop structure with only four G.C base-pairs in the stem, while a longer stem is required for efficient T54 formation. None of the conserved nucleotides (G53, C56, A58 and C61) and U54 for psi 55 or U55 for T54 formation can be replaced by any of the other three canonical nucleotides. Yeast tRNA:m5uridine-54 methyltransferase additionally requires the presence of a pyrimidine-60 in the loop. Interestingly, in a tRNA(Asp) variant in which the T psi-loop was permuted with the anticodon-loop, the new U32 and U33 residues derived from the T psi-loop were quantitatively converted to T32 and psi 33, respectively. Structural mapping of this variant with ethylnitrosourea confirmed that the intrinsic characteristic structure of the T psi-loop was conserved upon permutation and that the displaced anticodon-loop did not acquire a T psi-loop structure. These results demonstrate that a local conformation rather than the exact location of the U-U sequence within the tRNA architecture is the important identity determinant for recognition by yeast tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase.},
note = {0022-2836
Journal Article},
keywords = {Asp/chemistry/metabolism Saccharomyces cerevisiae/genetics Substrate Specificity Support, Base Sequence Conserved Sequence Intramolecular Lyases/metabolism Models, FLORENTZ, Fungal/*chemistry/metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/*metabolism RNA, Non-U.S. Gov't Uridine/*analogs & derivatives/chemistry/metabolism tRNA Methyltransferases/metabolism, SISSLER, Transfer, Transfer/*chemistry/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Almost all transfer RNA molecules sequenced so far contain two universal modified nucleosides at positions 54 and 55, respectively: ribothymidine (T54) and pseudouridine (psi 55). To identify the tRNA elements recognized by tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase from the yeast Saccharomyces cerevisiae, a set of 43 yeast tRNA(Asp) mutants were used. Some variants contained point mutations, while the others included progressive reductions in size down to a tRNA minisubstrate consisting of the T psi-loop with only one G.C base-pair as stem (9-mer). All substrates (full-sized tRNA(Asp) and various minihelices) were produced in vitro by T7 transcription and tested using yeast extract (S100) as a source of enzymatic activities and S-adenosyl-L-methionine as a methyl donor. The results indicate that the minimal substrate for enzymatic formation of psi 55 is a stem/loop structure with only four G.C base-pairs in the stem, while a longer stem is required for efficient T54 formation. None of the conserved nucleotides (G53, C56, A58 and C61) and U54 for psi 55 or U55 for T54 formation can be replaced by any of the other three canonical nucleotides. Yeast tRNA:m5uridine-54 methyltransferase additionally requires the presence of a pyrimidine-60 in the loop. Interestingly, in a tRNA(Asp) variant in which the T psi-loop was permuted with the anticodon-loop, the new U32 and U33 residues derived from the T psi-loop were quantitatively converted to T32 and psi 33, respectively. Structural mapping of this variant with ethylnitrosourea confirmed that the intrinsic characteristic structure of the T psi-loop was conserved upon permutation and that the displaced anticodon-loop did not acquire a T psi-loop structure. These results demonstrate that a local conformation rather than the exact location of the U-U sequence within the tRNA architecture is the important identity determinant for recognition by yeast tRNA:m5uridine-54 methyltransferase and tRNA:pseudouridine-55 synthase.
