Becker H D, Reinbolt J, Kreutzer R, Giege R, Kern D
Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes Article de journal
Dans: Biochemistry, vol. 36, no. 29, p. 8785-8797, 1997, ISBN: 9220965, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/genetics/*isolation & purification Blotting, Amino Acyl/metabolism Sequence Alignment Thermus thermophilus/*enzymology/genetics, Transfer, Unité ARN, Western Catalysis Isoenzymes/chemistry/*isolation & purification Kinetics Molecular Sequence Data Molecular Weight RNA
@article{,
title = {Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes},
author = {H D Becker and J Reinbolt and R Kreutzer and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9220965},
isbn = {9220965},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {29},
pages = {8785-8797},
abstract = {Two aspartyl-tRNA synthetases (AspRSs) were isolated from Thermus thermophilus HB8. Both are alpha2 dimers but differ in the length of their polypeptide chains (AspRS1, 68 kDa; and AspRS2, 51 kDa). Both chains start with Met and are deprived of common sequences to a significant extent. This rules out the possibility that AspRS2 is derived from AspRS1 by proteolysis, in agreement with specific recognition of each AspRS by the homologous antibodies. DNA probes derived from N-terminal amino acid sequences hybridize specifically to different genomic DNA fragments, revealing that the two AspRSs are encoded by distinct genes. Both enzymes are present in various strains from T. thermophilus and along the growth cycle of the bacteria, suggesting that they are constitutive. Kinetic investigations show that the two enzymes are specific for aspartic acid activation and tRNAAsp charging. tRNA aspartylation by the thermostable AspRSs is governed by thermodynamic parameters which values are similar to those measured for mesophilic aspartylation systems. Both thermophilic AspRSs are deprived of species specificity for tRNA aspartylation and exhibit N-terminal sequence signatures found in other AspRSs, suggesting that they are evolutionarily related to AspRSs from mesophilic prokaryotes and eukaryotes. Comparison of the efficiency of tRNA aspartylation by each enzyme under conditions approaching the physiological ones suggests that in vivo tRNAAsp charging is essentially ensured by AspRS1, although AspRS2 is the major species. The physiological significance of the two different AspRSs in T. thermophilus is discussed.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/genetics/*isolation & purification Blotting, Amino Acyl/metabolism Sequence Alignment Thermus thermophilus/*enzymology/genetics, Transfer, Unité ARN, Western Catalysis Isoenzymes/chemistry/*isolation & purification Kinetics Molecular Sequence Data Molecular Weight RNA},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Westhof E
RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin Article de journal
Dans: J Mol Biol, vol. 269, no. 3, p. 326-341, 1997, ISBN: 9199403, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry Base Composition *Computer Simulation Guanine/chemistry Hydrogen Bonding Models, Asp/*chemistry/metabolism Ribose/chemistry/metabolism Support, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Uridine/chemistry Water/*chemistry/metabolism, Transfer, Unité ARN
@article{,
title = {RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9199403},
isbn = {9199403},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {269},
number = {3},
pages = {326-341},
abstract = {The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.},
note = {0022-2836
Journal Article},
keywords = {Anticodon/*chemistry Base Composition *Computer Simulation Guanine/chemistry Hydrogen Bonding Models, Asp/*chemistry/metabolism Ribose/chemistry/metabolism Support, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Uridine/chemistry Water/*chemistry/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Westhof E
Rules governing the orientation of the 2'-hydroxyl group in RNA Article de journal
Dans: J Mol Biol, vol. 274, no. 1, p. 54-63, 1997, ISBN: 9398515, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/*chemistry/*metabolism Ribose/chemistry/metabolism Support, Carbohydrate Conformation Carbon/chemistry/metabolism Hydrogen Bonding Hydroxyl Radical/*chemistry/metabolism Proteins/genetics/metabolism RNA, Non-U.S. Gov't Water/metabolism, Transfer, Unité ARN
@article{,
title = {Rules governing the orientation of the 2'-hydroxyl group in RNA},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9398515},
isbn = {9398515},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {274},
number = {1},
pages = {54-63},
abstract = {Molecular dynamics simulations reveal that, in C3'-endo sugar puckers, only three orientations are accessible to the 2'-hydroxyl groups distinctive of RNA molecules: towards (i) the O3', (ii) the O4' of the same sugar, and (iii) the shallow groove base atoms. In the rarer C2'-endo sugar puckers, orientations towards the O3' atom of the same sugar are strongly favoured. Surprisingly, in helical regions, the frequently suggested intra-strand O2'-H(n).O4'(n+1) interaction is not found. This observation led to the detection of an axial C-H.O interaction between the C2'-H2'(n) group and the O4'(n+1) atom contributing to the stabilization of RNA helical regions. Subsequent analysis of crystallographic structures of both RNA and A-DNA helices fully supports this finding. Specific hydration patterns are also thought to play a significant role in the stabilization of RNA structures. In the shallow groove of RNA, known as a favourable RNA or protein-binding region, three well-defined hydration sites are located around the O2' atom. These hydration sites, occupied by water molecules exchanging with the bulk, constitute, after dehydration, anchor points for specific interactions between RNA and nucleic acids, proteins or drugs. Therefore, the fact that the 2'-hydroxyl group is not monopolised by axial stabilization, together with its water-like behaviour, facilitates complex formation involving RNA helical regions.},
note = {0022-2836
Journal Article},
keywords = {Asp/*chemistry/*metabolism Ribose/chemistry/metabolism Support, Carbohydrate Conformation Carbon/chemistry/metabolism Hydrogen Bonding Hydroxyl Radical/*chemistry/metabolism Proteins/genetics/metabolism RNA, Non-U.S. Gov't Water/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Théobald-Dietrich A, Kostyuk D, Kochetkov S N, Kisselev L, Giege R, Fasiolo F
Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides Article de journal
Dans: RNA, vol. 3, no. 8, p. 893-904, 1997, ISBN: 9257648, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN
@article{,
title = {Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides},
author = {R Aphasizhev and A Théobald-Dietrich and D Kostyuk and S N Kochetkov and L Kisselev and R Giege and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9257648},
isbn = {9257648},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {8},
pages = {893-904},
abstract = {The contribution of the ribose 2'-hydroxyls to RNA structure and function has been analyzed, but still remains controversial. In this work, we report the use of a mutant T7 RNA polymerase as a tool in RNA studies, applied to the aspartate and methionine tRNA aminoacylation systems from yeast. Our approach consists of determining the effect of substituting natural ribonucleotides by deoxyribonucleotides in RNA and, thereby, defining the subset of important 2'-hydroxyl groups. We show that deoxyribose-containing RNA can be folded in a global conformation similar to that of natural RNA. Melting curves of tRNAs, obtained by temperature-gradient gel electrophoresis, indicate that in deoxyribo-containing molecules, the thermal stability of the tertiary network drops down, whereas the stability of the secondary structure remains unaltered. Nuclease footprinting reveals a significant increase in the accessibility of both single- and double-stranded regions. As to the functionality of the deoxyribose-containing tRNAs, their in vitro aminoacylation efficiency indicates striking differential effects depending upon the nature of the substituted ribonucleotides. Strongest decrease in charging occurs for yeast initiator tRNA(Met) transcripts containing dG or dC residues and for yeast tRNA(Asp) transcripts with dU or dG. In the aspartate system, the decreased aminoacylation capacities can be correlated with the substitution of the ribose moieties of U11 and G27, disrupting two hydrogen bond contacts with the synthetase. Altogether, this suggests that specific 2'-hydroxyl groups in tRNAs can act as determinants specifying aminoacylation identity.},
note = {1355-8382
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Senger B, Fasiolo F
Importance of structural features for tRNA(Met) identity Article de journal
Dans: RNA, vol. 3, no. 5, p. 489-497, 1997, ISBN: 9149230, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Electrophoresis, Genetic Variation (Genetics), Met/*biosynthesis/*chemistry/isolation & purification Saccharomyces cerevisiae/genetics/metabolism Support, Non-U.S. Gov't Transcription, Polyacrylamide Gel Kinetics Magnesium Chloride Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {Importance of structural features for tRNA(Met) identity},
author = {R Aphasizhev and B Senger and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9149230},
isbn = {9149230},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {5},
pages = {489-497},
abstract = {We showed previously that the tRNA tertiary structure makes an important contribution to the identity of yeast tRNA(Met) (Senger B, Aphasizhev R, Walter P, Fasiolo F, 1995, J Mol Biol 249:45-58). To learn more about the role played by the tRNA framework, we analyzed the effect of some phosphodiester cleavages and 2'OH groups in tRNA binding and aminoacylation. The tRNA is inactivated provided the break occurs in the central core region responsible for the tertiary fold or in the anticodon stem/loop region. We also show that, for tRNA(Met) to bind, the anticodon loop, but not the anticodon stem, requires a ribosephosphate backbone. A tertiary mutant of yeast tRNA(Met) involving interactions from the D- and T-loop unique to the initiator species fails to be aminoacylated, but still binds to yeast methionyl-tRNA synthetase. In the presence of 10 mM MgCl2, the mutant transcript has a 3D fold significantly stabilized by about 30 degrees C over a wild-type transcript as deduced from the measure of their T(m) values. The k(cat) defect of the tRNA(Met) mutant may arise from a failure to overcome an increase of the free energetic cost of distorting the more stable tRNA structure and/or a tRNA based MetRS conformational change required for formation of transition state of aminoacylation.},
note = {1355-8382
Journal Article},
keywords = {Anticodon Base Sequence Electrophoresis, Genetic Variation (Genetics), Met/*biosynthesis/*chemistry/isolation & purification Saccharomyces cerevisiae/genetics/metabolism Support, Non-U.S. Gov't Transcription, Polyacrylamide Gel Kinetics Magnesium Chloride Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Friant S., Heyman T., Wilhelm M. L., Wilhelm F. X.
Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 441-9, 1996, (0305-1048 Journal Article).
Résumé | BibTeX | Étiquettes: Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer
@article{,
title = {Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon},
author = { S. Friant and T. Heyman and M. L. Wilhelm and F. X. Wilhelm},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {441-9},
abstract = {Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway.},
note = {0305-1048
Journal Article},
keywords = {Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
de Barros J. P. Pais, Keith G., Adlouni C. El, Glasser A. L., Mack G., Dirheimer G., Desgres J.
2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 8, p. 1489-96, 1996, (0305-1048 Journal Article).
Résumé | BibTeX | Étiquettes: &, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer
@article{,
title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver},
author = { J. P. Pais de Barros and G. Keith and C. El Adlouni and A. L. Glasser and G. Mack and G. Dirheimer and J. Desgres},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {8},
pages = {1489-96},
abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.},
note = {0305-1048
Journal Article},
keywords = {&, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Reinbolt J, Wakao H, Laalami S, Grunberg-Manago M, Romby P, Ehresmann B, Ehresmann C
Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking Article de journal
Dans: Biochemistry, vol. 35, no. 9, p. 2978-2984, 1996, ISBN: 8608135, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN
@article{,
title = {Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking},
author = {G Yusupova and J Reinbolt and H Wakao and S Laalami and M Grunberg-Manago and P Romby and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608135},
isbn = {8608135},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {9},
pages = {2978-2984},
abstract = {trans-Diamminedichloroplatinum(II) was used to induce reversible cross-links between Escherichia coli initiation factor 2 (IF-2) and fMet-tRNA(f)(Met). Two distinct cross-links between IF-2 and the initiator tRNA were produced. Analysis of the cross-linking regions on both RNA and protein moieties reveals that the T arm of the tRNA is in the proximity of a region of the C-terminal domain of IF-2 (residues Asn611-Arg645). This cross-link is well-correlated with the fact that the C-domain of IF-2 contains the fMet-tRNA binding site and that the cross-linked RNA fragment precisely maps in a region which is protected by IF-2 from chemical modification and enzymatic digestion. Rather unexpectedly, a second cross-link was characterized which involves the anticodon arm of fMet-tRNA(f)(Met) and the N-terminal part of IF-2 (residues Trp215-Arg237).},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Lanchy J M, Yusupov M, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids Article de journal
Dans: J Mol Biol, vol. 261, no. 3, p. 315-321, 1996, ISBN: 8780773, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support
@article{,
title = {Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids},
author = {G Yusupova and J M Lanchy and M Yusupov 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=8780773},
isbn = {8780773},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {261},
number = {3},
pages = {315-321},
abstract = {During reverse transcription of the genomic RNA of human immunodeficiency virus type 1 (HIV-1) into double-stranded DNA, reverse transcriptase (RT) must accommodate RNA-RNA, DNA-RNA, RNA-DNA and DNA-DNA hybrids as primer-template. In this study, we examined extension of RNA-tRNA3Lys, and DNA-tRNA3Lys complexes by HIV-1 RT. When the 3' end of tRNA3Lys is annealed to oligoribonucleotides, tRNA3Lys, but not the complementary RNAs, is extended by HIV-1 RT, indicating that tRNA3Lys is efficiently used as primer and RNA as template. An opposite primer usage is observed when tRNA3Lys is annealed to complementary oligodeoxyribonucleotides. In this case, the oligodeoxyribonucleotides are efficiently used as primer and tRNA3Lys as template. This result indicates that the nature of nucleic acid bound to tRNA3Lys determines which strand of the RNA-tRNA3Lys and DNA-tRNA3Lys hybrids is extended by HIV-1 RT. When an oligoribonucleotide is annealed to an unmodified transcript of tRNA3Lys, both nucleic acids are extended by HIV-1 RT, indicating that specific selection of tRNA3Lys as primer requires the post-transcriptional modifications of tRNA3Lys.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Skripkin E, Isel C, Marquet R, Ehresmann B, Ehresmann C
Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNA3(Lys) Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 509-514, 1996, ISBN: 8602365, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cross-Linking Reagents/*metabolism Ficusin/*metabolism HIV-1/*genetics Human Molecular Sequence Data Molecular Structure RNA, Lys/*genetics/metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*genetics/metabolism Support
@article{,
title = {Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNA3(Lys)},
author = {E Skripkin and C Isel and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602365},
isbn = {8602365},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {509-514},
abstract = {Initiation of reverse transcription is a crucial step of retroviral infection. In HIV-1, it involves hybridization of the 18 3'-terminal nucleotides of the primer tRNA3(Lys) to the primer binding site (PBS) of the viral RNA. Moreover, additional interactions between the two RNAs were recently evidenced [Isel et al. (1995) J. Mol. Biol. 247, 25269-25272]. To get further information on the topology of the viral RNA/tRNA3(Lys) complex, we used psoralen to induce RNA-RNA crosslinking. A defined intermolecular crosslinked complex was obtained. The crosslinked regions were characterized by RNase T1 digestion followed by bi-dimensional gel electrophoresis. The crosslinked residues (nucleotide mcm5S2U34 and U35 in the anticodon loop of tRNA3(Lys) and UCU154 in the viral RNA upstream of the PBS) were mapped using a retardation method coupled with random hydrolysis. The formation of this crosslink depends on the same elements that are required for the formation of the extended interactions between primer and template RNAs, i.e., the modified bases of the tRNA and a conserved A-rich loop located upstream of the PBS in the genomic RNA. Therefore, the present crosslinking data provide relevant information on the topology of the template/primer binary complex.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cross-Linking Reagents/*metabolism Ficusin/*metabolism HIV-1/*genetics Human Molecular Sequence Data Molecular Structure RNA, Lys/*genetics/metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Sissler M, Giege R, Florentz C
Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts Article de journal
Dans: EMBO J, vol. 15, no. 18, p. 5069-5076, 1996, ISBN: 8890180, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Arginine/*metabolism Base Sequence Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Arg/*chemistry/metabolism RNA, Asp/chemistry/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Fungal/*chemistry/metabolism RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts},
author = {M Sissler and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8890180},
isbn = {8890180},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {18},
pages = {5069-5076},
abstract = {Yeast arginyl-tRNA synthetase recognizes the non-modified wild-type transcripts derived from both yeast tRNA(Arg) and tRNA(Asp) with equal efficiency. It discriminates its cognate natural substrate, tRNA(Arg), from non-cognate tRNA(Asp) by a negative discrimination mechanism whereby a single methyl group acts as an anti-determinant. Considering these facts, recognition elements responsible for specific arginylation in yeast have been searched by studying the in vitro arginylation properties of a series of transcripts derived from yeast tRNA(Asp), considered as an arginine isoacceptor tRNA. In parallel, experiments on similar tRNA(Arg) transcripts were performed. Unexpectedly, in the tRNA(Arg) context, arginylation is basically linked to the presence of residue C35, whereas in the tRNA(Asp) context, it is deeply related to that of C36 and G37 but is insensitive to the nucleotide at position 35. Each of these nucleotides present in one host, is absent in the other host tRNA. Thus, arginine identity is dependent on two different specific recognition sets according to the tRNA framework investigated.},
note = {0261-4189
Journal Article},
keywords = {*Anticodon Arginine/*metabolism Base Sequence Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Arg/*chemistry/metabolism RNA, Asp/chemistry/metabolism Saccharomyces cerevisiae Support, FLORENTZ, Fungal/*chemistry/metabolism RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Fasiolo F
Yeast tRNA(Met) recognition by methionyl-tRNA synthetase requires determinants from the primary, secondary and tertiary structure: a review Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 597-604, 1996, ISBN: 8955903, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Anticodon Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Met/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {Yeast tRNA(Met) recognition by methionyl-tRNA synthetase requires determinants from the primary, secondary and tertiary structure: a review},
author = {B Senger and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955903},
isbn = {8955903},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {597-604},
abstract = {The primordial role of the CAU anticodon in methionine identity of the tRNA has been established by others nearly a decade ago in Escherichia coli and yeast tRNA(Met). We show here that the CAU triplet alone is unable to confer methionine acceptance to a tRNA. This requires the contribution of the discriminatory base A73 and the non-anticodon bases of the anticodon loop. To better understand the functional communication between the anticodon and the active site, we analysed the binding and aminoacylation of tRNA(Met) based anticodon and acceptor-stem minihelices and of tRNA(Met) chimeras where the central core region of yeast tRNA(Met) is replaced by that of unusual mitochondrial forms lacking either a D-stem or a T-stem. These studies suggest that the high selectivity of the anticodon bases in tRNA(Met) implies the L-conformation of the tRNA and the presence of a D-stem. The importance of a L-structure for recognition of tRNA(Met) was also deduced from mutations of tertiary interactions known to play a general role in tRNA(Met) folding.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acid Sequence Anticodon Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Met/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Hillenbrandt R, Sprinzl M, Giege R
Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu Article de journal
Dans: EMBO J, vol. 15, no. 3, p. 650-657, 1996, ISBN: 8599948, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN
@article{,
title = {Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu},
author = {J Rudinger and R Hillenbrandt and M Sprinzl and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8599948},
isbn = {8599948},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {3},
pages = {650-657},
abstract = {During protein biosynthesis, all aminoacylated elongator tRNAs except selenocysteine-inserting tRNA Sec form ternary complexes with activated elongation factor. tRNA Sec is bound by its own translation factor, an elongation factor analogue, e.g. the SELB factor in prokaryotes. An apparent reason for this discrimination could be related to the unusual length of tRNA Sec amino acid-acceptor branch formed by 13 bp. However, it has been recently shown that an aspartylated minihelix of 13 bp derived from yeast tRNA Asp is an efficient substrate for Thermus thermophilus EF-Tu-GTP, suggesting that features other than the length of tRNA Sec prevent its recognition by EF-Tu-GTP. A stepwise mutational analysis of a minihelix derived from tRNA Sec in which sequence elements of tRNA Asp were introduced showed that the sequence of the amino acid- acceptor branch of Escherichia coli tRNA Sec contains a specific structural element that hinders its binding to T.thermophilus EF-Tu-GTP. This antideterminant is located in the 8th, 9th and 10th bp in the acceptor branch of tRNA Sec, corresponding to the last base pair in the amino acid acceptor stem and the two first pairs in the T-stem. The function of this C7.G66/G49.U65/C50.G64 box was tested by its transplantation into a minihelix derived from tRNA Asp, abolishing its recognition by EF-Tu-GTP. The specific role of this nucleotide combination is further supported by its absence in all known prokaryotic elongator tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
de Barros J P Pais, Keith G, Adlouni C El, Glasser A L, Mack G, Dirheimer G, Desgres J
2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 8, p. 1489-1496, 1996, ISBN: 8628682, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver},
author = {J P Pais de Barros and G Keith and C El Adlouni and A L Glasser and G Mack and G Dirheimer and J Desgres},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8628682},
isbn = {8628682},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {8},
pages = {1489-1496},
abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.},
note = {0305-1048
Journal Article},
keywords = {Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mazauric M H, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D
Dans: Eur J Biochem, vol. 241, no. 3, p. 814-826, 1996, ISBN: 8944770, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN
@article{,
title = {An example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus},
author = {M H Mazauric and J Reinbolt and B Lorber and C Ebel and G Keith and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8944770},
isbn = {8944770},
year = {1996},
date = {1996-01-01},
journal = {Eur J Biochem},
volume = {241},
number = {3},
pages = {814-826},
abstract = {Glycyl-tRNA synthetase (Gly-tRNA synthetase) from Thermus thermophilus was purified to homogeneity and with high yield using a five-step purification procedure in amounts sufficient to solve its crystallographic structure [Logan, D.T., Mazauric, M.-H., Kern, D. & Moras, D. (1995) EMBO J. 14, 4156-4167]. Molecular-mass determinations of the native and denatured protein indicate an oligomeric structure of the alpha 2 type consistent with that found for eukaryotic Gly-tRNA synthetases (yeast and Bombyx mori), but different from that of Gly-tRNA synthetases from mesophilic prokaryotes (Escherichia coli and Bacillus brevis) which are alpha 2 beta 2 tetramers. N-terminal sequencing of the polypeptide chain reveals significant identity, reaching 50% with those of the eukaryotic enzymes (B. mori, Homo sapiens, yeast and Caenorhabditis elegans) but no significant identity was found with both alpha and beta chains of the prokaryotic enzymes (E. coli, Haemophilus influenzae and Coxiella burnetii) albeit the enzyme is deprived of the N-terminal extension characterizing eukaryotic synthetases. Thus, the thermophilic Gly-tRNA synthetase combines strong structural homologies of eukaryotic Gly-tRNA synthetases with a feature of prokaryotic synthetases. Heat-stability measurements show that this synthetase keeps its ATP-PPi exchange and aminoacylation activities up to 70 degrees C. Glycyladenylate strongly protects the enzyme against thermal inactivation at higher temperatures. Unexpectedly, tRNA(Gly) does not induce protection. Cross-aminoacylations reveal that the thermophilic Gly-tRNA synthetase charges heterologous E. coli tRNA(gly(GCC)) and tRNA(Gly(GCC)) and yeast tRNA(Gly(GCC)) as efficiently as T. thermophilus tRNA(Gly). All these aminoacylation reactions are characterized by similar activation energies as deduced from Arrhenius plots. Therefore, contrary to the E. coli and H. sapiens Gly-tRNA synthetases, the prokaryotic thermophilic enzyme does not possess a strict species specificity. The results are discussed in the context of the three-dimensional structure of the synthetase and in the view of the particular evolution of the glycinylation systems.},
note = {0014-2956
Journal Article},
keywords = {Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Martin F, Reinbolt J, Dirheimer G, Gangloff J, Eriani G
Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity Article de journal
Dans: RNA, vol. 2, no. 9, p. 919-927, 1996, ISBN: 8809018, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN
@article{,
title = {Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity},
author = {F Martin and J Reinbolt and G Dirheimer and J Gangloff and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8809018},
isbn = {8809018},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {9},
pages = {919-927},
abstract = {Elements that confer identity to a tRNA in the cellular environment, where all aminoacyl-tRNA synthetases are competing for substrates, may be delineated by in vivo experiments using suppressor tRNAs. Here we describe the selection of active Escherichia coli tRNAAsp amber mutants and analyze their identity. Starting from a library containing randomly mutated tRNA(CUA)Asp genes, we isolated four amber suppressors presenting either lysine, alanine, or glutamine activity. Two of them, presenting mainly alanine or lysine activity, were further submitted to a second round of mutagenesis selection in order to improve their efficiency of suppression. Eleven suppressors were isolated, each containing two or three mutations. Ten presented identities of the two parental mutants, whereas one had switched from lysine to arginine identity. Analysis of the different mutants revealed (or confirmed for some nucleotides) their role as positive and/or negative determinants in AlaRS, LysRS, and ArgRS recognition. More generally, it appears that tRNAAsp presents identity characteristics closely related to those of tRNALys, as well as a structural basis for acquiring alanine or arginine identity upon moderate mutational changes; these consist of addition or suppression of the corresponding positive or negative determinants, as well as tertiary interactions. Failure to isolate aspartic acid-inserting suppressors is probably due to elimination of the important G34 identity element and its replacement by an antideterminant when changing the anticodon of the tRNAAsp to the CUA triplet.},
note = {1355-8382
Journal Article},
keywords = {Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Hillenbrandt R, Sprinzl M, Giege R
Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu Article de journal
Dans: EMBO J, vol. 15, no. 3, p. 650-657, 1996, ISBN: 8599948, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN
@article{,
title = {Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu},
author = {J Rudinger and R Hillenbrandt and M Sprinzl and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8599948},
isbn = {8599948},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {3},
pages = {650-657},
abstract = {During protein biosynthesis, all aminoacylated elongator tRNAs except selenocysteine-inserting tRNA Sec form ternary complexes with activated elongation factor. tRNA Sec is bound by its own translation factor, an elongation factor analogue, e.g. the SELB factor in prokaryotes. An apparent reason for this discrimination could be related to the unusual length of tRNA Sec amino acid-acceptor branch formed by 13 bp. However, it has been recently shown that an aspartylated minihelix of 13 bp derived from yeast tRNA Asp is an efficient substrate for Thermus thermophilus EF-Tu-GTP, suggesting that features other than the length of tRNA Sec prevent its recognition by EF-Tu-GTP. A stepwise mutational analysis of a minihelix derived from tRNA Sec in which sequence elements of tRNA Asp were introduced showed that the sequence of the amino acid- acceptor branch of Escherichia coli tRNA Sec contains a specific structural element that hinders its binding to T.thermophilus EF-Tu-GTP. This antideterminant is located in the 8th, 9th and 10th bp in the acceptor branch of tRNA Sec, corresponding to the last base pair in the amino acid acceptor stem and the two first pairs in the T-stem. The function of this C7.G66/G49.U65/C50.G64 box was tested by its transplantation into a minihelix derived from tRNA Asp, abolishing its recognition by EF-Tu-GTP. The specific role of this nucleotide combination is further supported by its absence in all known prokaryotic elongator tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
de Barros J P Pais, Keith G, Adlouni C El, Glasser A L, Mack G, Dirheimer G, Desgres J
2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 8, p. 1489-1496, 1996, ISBN: 8628682, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver},
author = {J P Pais de Barros and G Keith and C El Adlouni and A L Glasser and G Mack and G Dirheimer and J Desgres},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8628682},
isbn = {8628682},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {8},
pages = {1489-1496},
abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.},
note = {0305-1048
Journal Article},
keywords = {Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mazauric M H, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D
Dans: Eur J Biochem, vol. 241, no. 3, p. 814-826, 1996, ISBN: 8944770, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN
@article{,
title = {An example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus},
author = {M H Mazauric and J Reinbolt and B Lorber and C Ebel and G Keith and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8944770},
isbn = {8944770},
year = {1996},
date = {1996-01-01},
journal = {Eur J Biochem},
volume = {241},
number = {3},
pages = {814-826},
abstract = {Glycyl-tRNA synthetase (Gly-tRNA synthetase) from Thermus thermophilus was purified to homogeneity and with high yield using a five-step purification procedure in amounts sufficient to solve its crystallographic structure [Logan, D.T., Mazauric, M.-H., Kern, D. & Moras, D. (1995) EMBO J. 14, 4156-4167]. Molecular-mass determinations of the native and denatured protein indicate an oligomeric structure of the alpha 2 type consistent with that found for eukaryotic Gly-tRNA synthetases (yeast and Bombyx mori), but different from that of Gly-tRNA synthetases from mesophilic prokaryotes (Escherichia coli and Bacillus brevis) which are alpha 2 beta 2 tetramers. N-terminal sequencing of the polypeptide chain reveals significant identity, reaching 50% with those of the eukaryotic enzymes (B. mori, Homo sapiens, yeast and Caenorhabditis elegans) but no significant identity was found with both alpha and beta chains of the prokaryotic enzymes (E. coli, Haemophilus influenzae and Coxiella burnetii) albeit the enzyme is deprived of the N-terminal extension characterizing eukaryotic synthetases. Thus, the thermophilic Gly-tRNA synthetase combines strong structural homologies of eukaryotic Gly-tRNA synthetases with a feature of prokaryotic synthetases. Heat-stability measurements show that this synthetase keeps its ATP-PPi exchange and aminoacylation activities up to 70 degrees C. Glycyladenylate strongly protects the enzyme against thermal inactivation at higher temperatures. Unexpectedly, tRNA(Gly) does not induce protection. Cross-aminoacylations reveal that the thermophilic Gly-tRNA synthetase charges heterologous E. coli tRNA(gly(GCC)) and tRNA(Gly(GCC)) and yeast tRNA(Gly(GCC)) as efficiently as T. thermophilus tRNA(Gly). All these aminoacylation reactions are characterized by similar activation energies as deduced from Arrhenius plots. Therefore, contrary to the E. coli and H. sapiens Gly-tRNA synthetases, the prokaryotic thermophilic enzyme does not possess a strict species specificity. The results are discussed in the context of the three-dimensional structure of the synthetase and in the view of the particular evolution of the glycinylation systems.},
note = {0014-2956
Journal Article},
keywords = {Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Martin F, Reinbolt J, Dirheimer G, Gangloff J, Eriani G
Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity Article de journal
Dans: RNA, vol. 2, no. 9, p. 919-927, 1996, ISBN: 8809018, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN
@article{,
title = {Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity},
author = {F Martin and J Reinbolt and G Dirheimer and J Gangloff and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8809018},
isbn = {8809018},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {9},
pages = {919-927},
abstract = {Elements that confer identity to a tRNA in the cellular environment, where all aminoacyl-tRNA synthetases are competing for substrates, may be delineated by in vivo experiments using suppressor tRNAs. Here we describe the selection of active Escherichia coli tRNAAsp amber mutants and analyze their identity. Starting from a library containing randomly mutated tRNA(CUA)Asp genes, we isolated four amber suppressors presenting either lysine, alanine, or glutamine activity. Two of them, presenting mainly alanine or lysine activity, were further submitted to a second round of mutagenesis selection in order to improve their efficiency of suppression. Eleven suppressors were isolated, each containing two or three mutations. Ten presented identities of the two parental mutants, whereas one had switched from lysine to arginine identity. Analysis of the different mutants revealed (or confirmed for some nucleotides) their role as positive and/or negative determinants in AlaRS, LysRS, and ArgRS recognition. More generally, it appears that tRNAAsp presents identity characteristics closely related to those of tRNALys, as well as a structural basis for acquiring alanine or arginine identity upon moderate mutational changes; these consist of addition or suppression of the corresponding positive or negative determinants, as well as tertiary interactions. Failure to isolate aspartic acid-inserting suppressors is probably due to elimination of the important G34 identity element and its replacement by an antideterminant when changing the anticodon of the tRNAAsp to the CUA triplet.},
note = {1355-8382
Journal Article},
keywords = {Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Isel C, Ehresmann C, Marquet R, Ehresmann B
Structural and functional evidence that initiation and elongation of HIV-1 reverse transcription are distinct processes Article de journal
Dans: Biochimie, vol. 78, no. 11-12, p. 1087-1096, 1996, ISBN: 9150889, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/*biosynthesis/*chemistry RNA, Base Sequence Comparative Study HIV-1/*genetics/*metabolism HIV-1 Reverse Transcriptase/*metabolism Human Molecular Sequence Data *Nucleic Acid Conformation RNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/biosynthesis/chemistry Retroviridae/metabolism Support
@article{,
title = {Structural and functional evidence that initiation and elongation of HIV-1 reverse transcription are distinct processes},
author = {J M Lanchy and C Isel and C Ehresmann and R Marquet and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9150889},
isbn = {9150889},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {11-12},
pages = {1087-1096},
abstract = {Retroviral reverse transcription starts with the extension of a cellular tRNA primer bound near the 5' end of the viral genomic RNA at a site called the primer binding site (PBS). Formation of the HIV-1 initiation complex between tRNA3(Lys), viral RNA and reverse transcriptase probably occurs during encapsidation of these components. tRNA3(Lys) is thought to be selectively packaged by interaction with the reverse transcriptase domain of the Pr160Gag-Pol precursor protein, then annealed to the PBS of viral RNA with the help of the nucleocapsid protein. tRNA3(Lys) and HIV-1 viral RNA form a highly-structured complex, with extended interactions between the two molecules. Two different modes of reverse transcription have been distinguished: initiation, a tRNA3(Lys)-specific and distributive mode of polymerization corresponding to the addition of the first five nucleotides, followed by elongation, a non-specific and processive mode of DNA synthesis. These two modes are reminiscent of the initiation and elongation processes previously observed with DNA-dependent RNA polymerases.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acyl/*biosynthesis/*chemistry RNA, Base Sequence Comparative Study HIV-1/*genetics/*metabolism HIV-1 Reverse Transcriptase/*metabolism Human Molecular Sequence Data *Nucleic Acid Conformation RNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/biosynthesis/chemistry Retroviridae/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Isel C, Lanchy J M, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys Article de journal
Dans: EMBO J, vol. 15, no. 4, p. 917-924, 1996, ISBN: 8631312, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Cell-Free System Gene Expression Regulation, Genetic *Virus Replication, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase RNA, Viral/metabolism RNA-Directed DNA Polymerase/*metabolism Support
@article{,
title = {Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys},
author = {C Isel and J M Lanchy 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=8631312},
isbn = {8631312},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {4},
pages = {917-924},
abstract = {Initiation of RNA-dependent DNA synthesis by retroviral reverse transcriptases is generally considered as unspecific. In the case of human immunodeficiency virus type 1 (HIV-1), the natural primer is tRNA3Lys. We recently found evidence of complex interactions between tRNA3Lys and HIV-1 RNA that may be involved in the priming process. In this study, we compare the ability of natural and unmodified synthetic tRNA3Lys and 18mer oligoribo- and oligodeoxyribonucleotides complementary to the viral primer binding site to initiate replication of HIV-1 RNA using either homologous or heterologous reverse transcriptases. We show that HIV-1 RNA, HIV-1 reverse transcriptase and primer tRNA3Lys form a specific initiation complex that differs from the unspecific elongation complex formed when an oligodeoxyribonucleotide is used as primer. Modified nucleosides of tRNA3Lys are required for efficient initiation and transition to elongation. Transition from initiation to elongation, but not initiation of reverse transcription itself, is facilitated by extended primer-template interactions. Elongation, but not initiation of reverse transcription, is inhibited by Mn2+, which further differentiates these two different functional states of reverse transcriptase. These results define initiation of reverse transcription as a target to block viral replication.},
note = {0261-4189
Journal Article},
keywords = {Cell-Free System Gene Expression Regulation, Genetic *Virus Replication, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase RNA, Viral/metabolism RNA-Directed DNA Polymerase/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Ehresmann B, Marquet R
Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 11-19, 1996, ISBN: 8786994, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding},
author = {C Isel 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=8786994},
isbn = {8786994},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {11-19},
abstract = {RNAs play a crucial and central role in a large variety of biological functions obviously linked to the wide variety of structures that they can adopt. Understanding the function of RNAs thus requires the knowledge of their two- and three-dimensional structures. We describe in detail the way to access the secondary structure of RNAs, by combining sequence comparison, secondary structure prediction by computer and, mainly, experimental data obtained by probing with chemicals and ribonucleases. These approaches were used to investigate secondary structure of the region containing the primer binding site of HIV-1 genomic RNA either free or involved in the binary complex with the replication primer tRNA(3Lys).},
note = {0031-6865
Journal Article},
keywords = {Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
Hubert N, Walczak R, Sturchler C, Myslinski E, Schuster C, Westhof E, Carbon P, Krol A
RNAs mediating cotranslational insertion of selenocysteine in eukaryotic selenoproteins Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 590-596, 1996, ISBN: 8955902, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/chemistry/metabolism Rats Schistosoma mansoni Selenocysteine/chemistry/*metabolism Support, Animals Base Sequence Cattle Escherichia coli Human Mice Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Proteins/chemistry/*metabolism RNA/chemistry/*metabolism RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN
@article{,
title = {RNAs mediating cotranslational insertion of selenocysteine in eukaryotic selenoproteins},
author = {N Hubert and R Walczak and C Sturchler and E Myslinski and C Schuster and E Westhof and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955902},
isbn = {8955902},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {590-596},
abstract = {Selenocysteine, a selenium-containing analog of cysteine, is found in the prokaryotic and eukaryotic kingdoms in active sites of enzymes involved in oxidation-reduction reactions. Its biosynthesis and cotranslational insertion into selenoproteins is performed by an outstanding mechanism, implying the participation of several gene products. The tRNA(Sec) is one of these. In eukaryotes, its transcription mode by RNA polymerase III differs from that of classical tRNA genes, both at the level of the promoter elements and transcription factors involved. In addition, enhanced transcription is afforded by a newly characterized zinc finger activator. Not only transcription of the gene, but also the tRNA(Sec) itself is atypical since its 2D and 3D structures exhibit features which set it apart from classical tRNAs. Decoding of eukaryotic selenocysteine UGA codons requires a stem-loop structure in the 3'UTR of mRNAs, the selenocysteine insertion sequence (SECIS) element. Structure probing and sequence comparisons led us to propose a 2D structure model for the SECIS element, containing a novel RNA motif composed of four consecutive non-Watson-Crick base-pairs. A 3D model, rationalizing the accessibility data, was elaborated by computer modeling. It yields indicative or suggestive evidence for the role that could play some conserved residues and/or structural features in SECIS function. These might act as signals for interaction with SBP, the SECIS binding protein that we have characterized.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acid-Specific/chemistry/metabolism Rats Schistosoma mansoni Selenocysteine/chemistry/*metabolism Support, Animals Base Sequence Cattle Escherichia coli Human Mice Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Proteins/chemistry/*metabolism RNA/chemistry/*metabolism RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Grosjean H, Edqvist J, Straby K B, Giege R
Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture Article de journal
Dans: J Mol Biol, vol. 255, no. 1, p. 67-85, 1996, ISBN: 8568876, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Isomerases/metabolism Microinjections Molecular Sequence Data Mutation *Nucleic Acid Conformation Oocytes Pentosyltransferases/metabolism RNA Processing, Asp/*chemistry/metabolism Ribonucleosides/biosynthesis/*metabolism Support, Non-U.S. Gov't Xenopus laevis tRNA Methyltransferases/*metabolism, Post-Transcriptional/*physiology RNA, Transfer, Unité ARN
@article{,
title = {Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture},
author = {H Grosjean and J Edqvist and K B Straby and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8568876},
isbn = {8568876},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {255},
number = {1},
pages = {67-85},
abstract = {Information is still quite limited concerning the structural requirements in tRNA molecules for their post-transcriptional maturation by base and ribose modification enzymes. To address this question, we have chosen as the model system yeast tRNAAsp that has a known three-dimensional structure and the in vivo modifying machinery of the Xenopus laevis oocyte able to act on microinjected tRNA precursors. We have systematically compared the modification pattern of wild-type tRNAAsp with that of a series of structural mutants (21 altogether) altered at single or multiple positions in the D-, T-and the anticodon branch, as well as in the variable region. The experimental system allowed us to analyze the effects of structural perturbations in tRNA on the enzymatic formation of modified nucleosides at 12 locations scattered over the tRNA cloverleaf. We found that the formation of m1G37 and psi 40 in the anticodon loop and stem and psi 13 in the D-stem, were extremely sensitive to 3D perturbations. In contrast, the formation of T54, psi 55 and m1A58 in the T-loop, m5C49 in the T-stem and m2G6 in the amino acid accepting stem were essentially insensitive to change in the overall tRNA architecture; these modified nucleosides were also formed in appropriate minimalist (stems and loops) tRNA domains. The formation of m2G26 at the junction between the anticodon and the D-stem, of Q34 and manQ34 in the anticodon loop were sensitive only to drastic structural perturbation of the tRNA. Altogether, these results reflect the existence of different modes of tRNA recognition by the many different modifying enzymes. A classification of this family of maturation enzymes into two major groups, according to their sensitivities to structural perturbations in tRNA, is proposed.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Isomerases/metabolism Microinjections Molecular Sequence Data Mutation *Nucleic Acid Conformation Oocytes Pentosyltransferases/metabolism RNA Processing, Asp/*chemistry/metabolism Ribonucleosides/biosynthesis/*metabolism Support, Non-U.S. Gov't Xenopus laevis tRNA Methyltransferases/*metabolism, Post-Transcriptional/*physiology RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gotte M, Marquet R, Isel C, Anderson V E, Keith G, Gross H J, Ehresmann C, Ehresmann B, Heumann H
Probing the higher order structure of RNA with peroxonitrous acid Article de journal
Dans: FEBS Lett, vol. 390, no. 2, p. 226-228, 1996, ISBN: 8706865, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Probing the higher order structure of RNA with peroxonitrous acid},
author = {M Gotte and R Marquet and C Isel and V E Anderson and G Keith and H J Gross and C Ehresmann and B Ehresmann and H Heumann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8706865},
isbn = {8706865},
year = {1996},
date = {1996-01-01},
journal = {FEBS Lett},
volume = {390},
number = {2},
pages = {226-228},
abstract = {Potassium peroxonitrite (ONOOK) and [Fe(EDTA)]2- were used to analyze the influence of chemically entirely different hydroxyl radical sources on tRNA cleavage profiles. [Fe(EDTA)]2- gives rise to hydroxyl radicals via a Fenton-like reaction during the oxidation of chelated Fe2+, while ONOOK generates hydroxyl radicals via its conjugate acid (ONOOH) when adding a stable alkaline solution of ONOOK in samples buffered at neutral pH. [Fe(EDTA)]2- is known to induce oxidative strand scission at sugar moieties thought to be solvent accessible, while those residues located in the 'inside' of structured RNAs are protected. Although ONOOH is neutral and significantly smaller than the metal complex, both reagents generate the same protection pattern on tRNAs, suggesting that access of the commonly formed hydroxyl radical, rather than access of its source, is the determining factor when probing the higher order structure of RNA. Strong difference in reactivity is only seen at the modified 2-thiouridine S34 of tRNA(Lys3) which shows hyperreactivity towards ONOOK treatment. This particular reaction may require interaction between the peroxonitrite anion and the thiocarbonyl group of the base, since hyperreactivity is not observed when probing the dethiolated tRNA(Lys3).},
note = {0014-5793
Journal Article},
keywords = {Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R, Florentz C, Kern D, Gangloff J, Eriani G, Moras D
Aspartate identity of transfer RNAs Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 605-623, 1996, ISBN: 8955904, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN
@article{,
title = {Aspartate identity of transfer RNAs},
author = {R Giege and C Florentz and D Kern and J Gangloff and G Eriani and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955904},
isbn = {8955904},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {605-623},
abstract = {Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R
Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 22, p. 12078-12081, 1996, ISBN: 8901535, (0027-8424 Comment Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: Amino Acyl/*physiology RNA, Base Sequence Evolution, Genetic Molecular Sequence Data Peptide Elongation Factors/metabolism Plant Viruses/*genetics RNA, Genetic Virus Replication, Molecular Models, Transfer, Unité ARN, Viral/biosynthesis Translation
@article{,
title = {Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries},
author = {R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8901535},
isbn = {8901535},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {22},
pages = {12078-12081},
note = {0027-8424
Comment
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acyl/*physiology RNA, Base Sequence Evolution, Genetic Molecular Sequence Data Peptide Elongation Factors/metabolism Plant Viruses/*genetics RNA, Genetic Virus Replication, Molecular Models, Transfer, Unité ARN, Viral/biosynthesis Translation},
pubstate = {published},
tppubtype = {article}
}
Friant S, Heyman T, Wilhelm M L, Wilhelm F X
Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 441-449, 1996, ISBN: 8602356, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA/genetics/*metabolism RNA, Met/genetics/*metabolism Retroelements/*genetics Saccharomyces cerevisiae Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon},
author = {S Friant and T Heyman and M L Wilhelm and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602356},
isbn = {8602356},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {441-449},
abstract = {Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA/genetics/*metabolism RNA, Met/genetics/*metabolism Retroelements/*genetics Saccharomyces cerevisiae Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Caprara M G, Lehnert V, Lambowitz A M, Westhof E
A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core Article de journal
Dans: Cell, vol. 87, no. 6, p. 1135-1145, 1996, ISBN: 8978617, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN
@article{,
title = {A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core},
author = {M G Caprara and V Lehnert and A M Lambowitz and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8978617},
isbn = {8978617},
year = {1996},
date = {1996-01-01},
journal = {Cell},
volume = {87},
number = {6},
pages = {1135-1145},
abstract = {The Neurospora crassa mitochondrial (mt) tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns, in addition to aminoacylating tRNA(Tyr). Here, we compared the CYT-18 binding sites in the N. crassa mt LSU and ND1 introns with that in N. crassa mt tRNA(Tyr) by constructing three-dimensional models based on chemical modification and RNA footprinting data. Remarkably, superimposition of the CYT-18 binding sites in the model structures revealed an extended three-dimensional overlap between the tRNA and the group I intron catalytic core. Our results provide insight into how an RNA-splicing factor can evolve from a cellular RNA-binding protein. Further, the structural similarities between group I introns and tRNAs are consistent with an evolutionary relationship and suggest a general mechanism for the evolution of complex catalytic RNAs.},
note = {0092-8674
Journal Article},
keywords = {Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Becker H D, Giege R, Kern D
Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus Article de journal
Dans: Biochemistry, vol. 35, no. 23, p. 7447-7458, 1996, ISBN: 8652522, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN
@article{,
title = {Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus},
author = {H D Becker and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8652522},
isbn = {8652522},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {23},
pages = {7447-7458},
abstract = {The aspartate identity of tRNA for AspRS from Thermus thermophilus has been investigated by kinetic analysis of the aspartylation reaction of different tRNA molecules and their variants as well as of tRNAPhe variants with transplanted aspartate identity elements. It is shown that G10, G34, U35, C36, C38, and G73 determine recognition and aspartylation of yeast and T.thermophilus tRNA(Asp) by the thermophilic AspRS. This set of nucleotides specifies also tRNA aspartylation in the homologous yeast and Escherichia coli systems. Structural considerations indicate that the major aspartate identity elements interact with amino acids conserved in all AspRSs. It follows that the structural features of tRNA and synthetase specifying aspartylation are mainly conserved in various structural contexts and in organisms adapted to different life conditions. Mutations of tRNA identity elements provoke drastic losses of charging in the heterologous system involving yeast tRNA(Asp) and T. thermophilus AspRS. In the homologous systems, the mutational effects are less pronounced. However, effects in E. coli and T. thermophilus exceed those in yeast which are particularly moderate, indicating variations in the individual contributions of identity elements for aspartylation in prokaryotes and eukaryotes. Analysis of multiple tRNA mutants reveals cooperativity between the cluster of determinants of the anticodon loop and the additional determinants G10 and G73 for efficient aspartylation in the thermophilic system, suggesting that conformational changes trigger formation of the functional tRNA/synthetase complex.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Westhof E
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations Article de journal
Dans: Biophys J, vol. 71, no. 2, p. 940-954, 1996, ISBN: 8842234, (0006-3495 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8842234},
isbn = {8842234},
year = {1996},
date = {1996-01-01},
journal = {Biophys J},
volume = {71},
number = {2},
pages = {940-954},
abstract = {Multiple molecular dynamics trajectories of the solvated and neutralized 17-residue tRNA(Asp) anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16-A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base pairs, the noncanonical G30-U40 "wobble" base pair, and the psi 32-C38 pseudo-base pair is presented as well as that of two C--H. O hydrogen bonds found to contribute to the array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biological function. The set of multiple molecular dynamics trajectories obtained does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.},
note = {0006-3495
Journal Article},
keywords = {Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Stetor S R, Li X, Rausch J W, Howard K J, Ehresmann B, North T W, Wohrl B M, Goody R S, Wainberg M A, Grice S F
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 19, p. 10063-10068, 1996, ISBN: 8816751, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support
@article{,
title = {Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases},
author = {E J Arts and S R Stetor and X Li and J W Rausch and K J Howard and B Ehresmann and T W North and B M Wohrl and R S Goody and M A Wainberg and S F Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8816751},
isbn = {8816751},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {19},
pages = {10063-10068},
abstract = {Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Ghosh M, Jacques P S, Ehresmann B, Grice S F Le
Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication Article de journal
Dans: J Biol Chem, vol. 271, no. 15, p. 9054-9061, 1996, ISBN: 8621554, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication},
author = {E J Arts and M Ghosh and P S Jacques and B Ehresmann and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621554},
isbn = {8621554},
year = {1996},
date = {1996-01-01},
journal = {J Biol Chem},
volume = {271},
number = {15},
pages = {9054-9061},
abstract = {The mechanism for the initiation of reverse transcription in human immunodeficiency virus type 1 (HIV-1) was studied utilizing a unique reverse transcriptase (RT) mutant altered in its noncatalytic p51 subunit. This mutant (p66/p51Delta13) retains full DNA- and RNA-dependent DNA polymerase activity but has reduced affinity for tRNA3Lys, the cognate HIV primer. When the ability to support(-)-strand DNA synthesis on a viral RNA template was evaluated, this mutant initiated from an 18-nucleotide (nt) oligoribo- or oligodeoxyribonucleotide primer complementary to the primer binding site (pbs). However, it failed to do so from natural and synthetic versions of tRNA3Lys. tRNA-primed(-)-strand synthesis could, however, be rescued by substituting the 76-nt tRNA3Lys with 81- and 107-nt tRNA-DNA chimeras, i.e. tRNA3Lys extended by 5 and 31 deoxyribonucleotides complementary to the viral genome upstream of the pbs. These findings imply that through interactions involving its p51 subunit, RT may be required to disrupt additional tRNA-viral RNA duplexes outside the pbs to proceed into productive(-)-strand DNA synthesis. Alternatively, specific interactions between tRNA3Lys and HIV-1 RT may be necessary for efficient initiation of(-)-strand DNA synthesis.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Senger B, Rengers J U, Sprinzl M, Walter P, Nussbaum G, Fasiolo F
Conservation in evolution for a small monomeric phenylalanyl-tRNA synthetase of the tRNA(Phe) recognition nucleotides and initial aminoacylation site Article de journal
Dans: Biochemistry, vol. 35, no. 1, p. 117-123, 1996, ISBN: 8555164, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Non-U.S. Gov't Variation (Genetics), Nucleic Acid Substrate Specificity Support, Phe/*chemistry/*metabolism Saccharomyces cerevisiae/enzymology/genetics Sequence Homology, Transfer, Unité ARN
@article{,
title = {Conservation in evolution for a small monomeric phenylalanyl-tRNA synthetase of the tRNA(Phe) recognition nucleotides and initial aminoacylation site},
author = {R Aphasizhev and B Senger and J U Rengers and M Sprinzl and P Walter and G Nussbaum and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8555164},
isbn = {8555164},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {1},
pages = {117-123},
abstract = {We previously showed that yeast mitochondrial phenylalanyl-tRNA synthetase (MSF protein) is evolutionarily distant to the cytoplasmic counterpart based on a high degree of divergence in protein sequence, molecular mass, and quaternary structure. Using yeast cytoplasmic tRNA(Phe) which is efficiently aminoacylated by MSF protein, we report here the tRNA(Phe) primary site of aminoacylation and the identity determinants for MSF protein. As for the cytoplasmic phenylalanyl-tRNA synthetase (Sampson, J. R., Di Renzo, A. B., Behlen, L. S., & Uhlenbeck, O. C. (1989) Science 243, 1363-1366), MSF protein recognizes nucleotides from the anticodon and the acceptor end including base A73 and, as shown here, adjacent G1-C72 base pair or at least C72 base. This indicates that the way of tRNA(Phe) binding for the two phenylalanine enzymes is conserved in evolution. However, tRNA(Phe) tertiary structure seems more critical for the interaction with the cytoplasmic enzyme than with MSF protein, and unlike cytoplasmic phenylalanyl-tRNA synthetase, the small size of the monomeric MSF protein probably does not allow contacts with residue 20 at the top corner of the L molecule. We also show that MSF protein preferentially aminoacylates the terminal 2'-OH group of tRNA(Phe) but with a catalytic efficiency for tRNA(Phe)-CC-3'-deoxyadenosine reduced 100-fold from that of native tRNA(Phe), suggesting a role of the terminal 3'-OH in catalysis. The loss is only 1.5-fold when tRNA(Phe)-CC-3'-deoxyadenosine is aminoacylated by yeast cytoplasmic PheRS (Sprinzl, M., & Cramer, F. (1973) Nature 245, 3-5), indicating mechanistic differences between the two PheRS's active sites for the amino acid transfer step.},
note = {0006-2960
Journal Article},
keywords = {Non-U.S. Gov't Variation (Genetics), Nucleic Acid Substrate Specificity Support, Phe/*chemistry/*metabolism Saccharomyces cerevisiae/enzymology/genetics Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J., Keith G., Monko M., Kuligowska E., Dirheimer G., Szarkowski J. W., Przykorska A.
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-9, 1995, (0261-3166 Journal Article).
Résumé | BibTeX | Étiquettes: &, Acid, Asp/chemistry/genetics/metabolism, Base, Binding, Chloroplasts/*enzymology, Conformation, Data, Endonucleases/isolation, Fungal/chemistry/genetics/metabolism, Gov't, Molecular, Non-U.S., Nucleic, Phe/chemistry/genetics/metabolism, purification/*metabolism, RNA, RNA/chemistry/metabolism, Sequence, Sites, Specificity, Substrate, Support, Transfer, Triticum/*enzymology
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = { J. Gabryszuk and G. Keith and M. Monko and E. Kuligowska and G. Dirheimer and J. W. Szarkowski and A. Przykorska},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-9},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {&, Acid, Asp/chemistry/genetics/metabolism, Base, Binding, Chloroplasts/*enzymology, Conformation, Data, Endonucleases/isolation, Fungal/chemistry/genetics/metabolism, Gov't, Molecular, Non-U.S., Nucleic, Phe/chemistry/genetics/metabolism, purification/*metabolism, RNA, RNA/chemistry/metabolism, Sequence, Sites, Specificity, Substrate, Support, Transfer, Triticum/*enzymology},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-9, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska and G Dirheimer and J W Szarkowski and A Przykorska},
editor = {Editor},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-9},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-9, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska and G Dirheimer and J W Szarkowski and A Przykorska},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-9},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Vlassov V V, Zuber G, Felden B, Behr J P, Giege R
Cleavage of tRNA with imidazole and spermine imidazole constructs: a new approach for probing RNA structure Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 16, p. 3161-3167, 1995, ISBN: 7667092, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/*chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites Buffers Hydrolysis Imidazoles Molecular Probes Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/genetics/metabolism, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Spermine Support
@article{,
title = {Cleavage of tRNA with imidazole and spermine imidazole constructs: a new approach for probing RNA structure},
author = {V V Vlassov and G Zuber and B Felden and J P Behr and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7667092},
isbn = {7667092},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {16},
pages = {3161-3167},
abstract = {Hydrolysis of RNA in imidazole buffer and by spermine-imidazole conjugates has been investigated. The RNA models were yeast tRNA(Asp) and a transcript derived from the 3'-terminal sequence of tobacco mosaic virus RNA representing a minihelix capable of being enzymatically aminoacylated with histidine. Imidazole buffer and spermine-imidazole conjugates in the presence of free imidazole cleave phosphodiester bonds in the folded RNAs in a specific fashion. Imidazole buffer induces cleavages preferentially in single-stranded regions because nucleotides in these regions have more conformational freedom and can assume more easily the geometry needed for formation of the hydrolysis intermediate state. Spermine-imidazole constructs supplemented with free imidazole cleave tRNA(Asp) within single-stranded regions after pyrimidine residues with a marked preference for pyrimidine-A sequences. Hydrolysis patterns suggest a cleavage mechanism involving an attack by the imidazole residue of the electrostatically bound spermine-imidazole and by free imidazole at the most accessible single-stranded regions of the RNA. Cleavages in a viral RNA fragment recapitulating a tRNA-like domain were found in agreement with the model of this molecule that accounts for its functional properties, thus illustrating the potential of the imidazole-derived reagents as structural probes for solution mapping of RNAs. The cleavage reactions are simple to perform, provide information reflecting the state of the ribose-phosphate backbone of RNA and can be used for mapping single- and double-stranded regions in RNAs.},
note = {0305-1048
Journal Article},
keywords = {Asp/*chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites Buffers Hydrolysis Imidazoles Molecular Probes Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/genetics/metabolism, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Spermine Support},
pubstate = {published},
tppubtype = {article}
}
Sturchler-Pierrat C, Hubert N, Totsuka T, Mizutani T, Carbon P, Krol A
Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec) Article de journal
Dans: J Biol Chem, vol. 270, no. 31, p. 18570-18574, 1995, ISBN: 7629188, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN
@article{,
title = {Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec)},
author = {C Sturchler-Pierrat and N Hubert and T Totsuka 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=7629188},
isbn = {7629188},
year = {1995},
date = {1995-01-01},
journal = {J Biol Chem},
volume = {270},
number = {31},
pages = {18570-18574},
abstract = {Selenocysteine synthesis is achieved on a specific tRNA, tRNA(Sec), which is first charged with serine to yield seryl-tRNA(Sec). Eukaryotic tRNA(Sec) exhibits an aminoacyl acceptor stem with a unique length of 9 base pairs. Within this stem, two base pairs, G5a.U67b and U6.U67, drew our attention, whose non-Watson-Crick status is maintained in the course of evolution either through U6.U67 base conservation or base covariation at G5a.U67b. Single or double point mutations were performed, which modified the identity of either or both of the base pairs. Serylation by seryl-tRNA synthetase was unaffected by substitutions at either G5a.U67b or U6.U67. Instead, and quite surprisingly, changing G5a.U67b and U6.U67 to G5a-C67b/U6.G67 or G5a-C67b/C6-G67 gave rise to a tRNA(Sec) mutant exhibiting a gain of function in serylation. This finding sheds light on the negative influence born by a few base pairs in the acceptor stem of tRNA(Sec) on its serylation abilities. The tRNA(Sec) capacities to support selenocysteylation were next examined with regard to a possible role played by the two non-Watson-Crick base pairs and the unique length of the acceptor stem. It first emerges from our study that tRNA(Sec) transcribed in vitro is able to support selenocysteylation. Second, none of the point mutations engineered at G5a.U67b and/or U6.U67 significantly modified the selenocysteylation level. In contrast, reduction of the acceptor stem length to 8 base pairs led tRNA(Sec) to lose its ability to efficiently support selenocysteylation. Thus, our study provides strong evidence that the length of the acceptor stem is of prime importance for the serine to selenocysteine conversion step.},
note = {0021-9258
Journal Article},
keywords = {Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Aphasizhev R, Walter P, Fasiolo F
The presence of a D-stem but not a T-stem is essential for triggering aminoacylation upon anticodon binding in yeast methionine tRNA Article de journal
Dans: J Mol Biol, vol. 249, no. 1, p. 45-58, 1995, ISBN: 7776375, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Animals Anticodon/metabolism Base Sequence Caenorhabditis elegans Cattle Molecular Sequence Data Molecular Structure Mutation RNA, Met/chemistry/genetics/*metabolism Saccharomyces cerevisiae/*metabolism Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {The presence of a D-stem but not a T-stem is essential for triggering aminoacylation upon anticodon binding in yeast methionine tRNA},
author = {B Senger and R Aphasizhev and P Walter and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7776375},
isbn = {7776375},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {249},
number = {1},
pages = {45-58},
abstract = {Dissection of the yeast cytoplasmic initiator tRNA(Met) into two helical domains, the T psi C acceptor and anticodon minihelices, failed to show anminoacylation and binding of the acceptor minihelix by the yeast methionyl-tRNA synthetase (MetRS) even in the presence of the anticodon minihelix. In contrast, based on the measure of the inhibition constant Ki, the anticodon minihelix carrying the methionine anticodon CAU is specifically bound to the synthetase and with an affinity comparable to that of the full-length tRNA. The yeast tRNA(Met) acceptor and anticodon minihelices were covalently linked using the central core sequences of either bovine mitochondrial tRNA(Ser) (AGY) lacking a D-stem or initiator tRNA(Met) from Caenorhabditis elegans lacking a T-stem. Based on modeling studies of analogous constructs performed by others, we assume that the folding and distance between the anticodon and acceptor ends of these hybrid tRNAs are identical to that of canonical tRNA. The three-quarter molecule, which includes the T-stem, has aminoacylation activity significantly more than an acceptor minihelix, while the acceptor stem/anticodon-D stem biloop has near wild-type aminoacylation activity. These results suggest that the high selectivity of the anticodon bases in tRNA(Met) depends upon the tRNA L-shape conformation and the presence of a D-arm. Protein contacts with the D-arm phosphate backbone are required for connecting anticodon recognition with the active site. These interactions probably contribute to fine tune the position of the acceptor end in the active site, allowing entry into the transition state of aminoacylation upon anticodon binding. The importance of an L structure for recognition of tRNA(Met) by yeast MetRS was also deduced from mutations of tertiary interactions known to play a general role in tRNA folding.},
note = {0022-2836
Journal Article},
keywords = {Acylation Animals Anticodon/metabolism Base Sequence Caenorhabditis elegans Cattle Molecular Sequence Data Molecular Structure Mutation RNA, Met/chemistry/genetics/*metabolism Saccharomyces cerevisiae/*metabolism Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schuster C, Myslinski E, Krol A, Carbon P
Staf, a novel zinc finger protein that activates the RNA polymerase III promoter of the selenocysteine tRNA gene Article de journal
Dans: EMBO J, vol. 14, no. 15, p. 3777-3787, 1995, ISBN: 7641696, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Animals Base Sequence Cloning, Amino Acid-Specific/*genetics Recombinant Fusion Proteins/metabolism Sequence Analysis, DNA Sequence Homology, Messenger RNA, Molecular DNA/metabolism DNA-Binding Proteins/biosynthesis/genetics/*metabolism Gene Expression Genes, Non-U.S. Gov't Trans-Activation (Genetics)/*physiology Trans-Activators/biosynthesis/genetics/*metabolism Xenopus laevis *Zinc Fingers, Reporter Human Molecular Sequence Data Oocytes Promoter Regions (Genetics)/*genetics RNA Polymerase III/*genetics RNA, Transfer, Unité ARN
@article{,
title = {Staf, a novel zinc finger protein that activates the RNA polymerase III promoter of the selenocysteine tRNA gene},
author = {C Schuster 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=7641696},
isbn = {7641696},
year = {1995},
date = {1995-01-01},
journal = {EMBO J},
volume = {14},
number = {15},
pages = {3777-3787},
abstract = {The selenocysteine tRNA gene (tRNA(Sec)) is atypical. Though transcribed by RNA polymerase III like all other tRNA genes, its basal promoter elements are distinct and reside essentially upstream of the coding region. In addition, transcription from the basal promoter is activated by a 15 bp activator element. In this report we describe the cloning and functional characterization of Staf (selenocysteine tRNA gene transcription activating factor), a novel Xenopus laevis transcription factor which binds to the tRNA(Sec) activator element and mediates its activation properties. The 600 amino acid Staf protein contains seven zinc fingers and a separate acidic activation domain. Seven highly conserved regions were detected between Staf and human ZNF76, a protein of unknown function, thereby aiding in predicting the locations of the functional domains of Staf. With the use of a novel expression assay in X.laevis oocytes we succeeded in demonstrating that Staf can activate the RNA polymerase III promoter of the tRNA(Sec) gene. This constitutes the first demonstration of the capacity of a cloned factor to activate RNA polymerase III transcription in vivo.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Animals Base Sequence Cloning, Amino Acid-Specific/*genetics Recombinant Fusion Proteins/metabolism Sequence Analysis, DNA Sequence Homology, Messenger RNA, Molecular DNA/metabolism DNA-Binding Proteins/biosynthesis/genetics/*metabolism Gene Expression Genes, Non-U.S. Gov't Trans-Activation (Genetics)/*physiology Trans-Activators/biosynthesis/genetics/*metabolism Xenopus laevis *Zinc Fingers, Reporter Human Molecular Sequence Data Oocytes Promoter Regions (Genetics)/*genetics RNA Polymerase III/*genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mely Y, de Rocquigny H, Sorinas-Jimeno M, Keith G, Roques B P, Marquet R, Gerard D
Binding of the HIV-1 nucleocapsid protein to the primer tRNA(3Lys), in vitro, is essentially not specific Article de journal
Dans: J Biol Chem, vol. 270, no. 4, p. 1650-1656, 1995, ISBN: 7829498, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Capsid/*chemistry/*metabolism *Capsid Proteins Escherichia coli Gene Products, Amino Acyl/biosynthesis/chemistry/*metabolism Substrate Specificity Support, gag/*chemistry/*metabolism HIV-1/*metabolism Hydrogen-Ion Concentration Kinetics Magnesium Chloride/pharmacology Mathematics Models, Genetic Zinc Fingers, MARQUET, Non-U.S. Gov't Transcription, Theoretical Molecular Sequence Data Nucleic Acid Conformation Osmolar Concentration Protein Binding RNA, Transfer, Unité ARN
@article{,
title = {Binding of the HIV-1 nucleocapsid protein to the primer tRNA(3Lys), in vitro, is essentially not specific},
author = {Y Mely and H de Rocquigny and M Sorinas-Jimeno and G Keith and B P Roques and R Marquet and D Gerard},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7829498},
isbn = {7829498},
year = {1995},
date = {1995-01-01},
journal = {J Biol Chem},
volume = {270},
number = {4},
pages = {1650-1656},
abstract = {The nucleocapsid protein NCp7 of human immunodeficiency virus, type 1, is a key component in the viral life cycle. Since, the first common step of all reported NCp7 activities corresponds to a nucleic acid-binding step, the NCp7 binding parameters to the natural primer tRNA(3Lys) were investigated. Using NCp7 intrinsic fluorescence, we found that (i) in 0.1 M NaCl, NCp7 bound noncooperatively to tRNA(3Lys) with a Kobs = 3.2 x 10(6) M-1 association constant and a n = 6 binding site size, (ii) four ionic interactions were formed in the NCp7.tRNA(3Lys) complex, and (iii) nonelectrostatic factors provided about 60% of the binding energy. These binding parameters were not significantly altered when the natural tRNA(3Lys) was replaced by either an in vitro synthetic tRNA(3Lys) transcript, the heterologous yeast tRNA(Phe) or the structurally unrelated 5 S RNA from Escherichia coli. Moreover, the environment of the intrinsic fluorescent reporters (Trp37 and Trp61) was similar in the various complexes. Finally, experiments performed at low protein concentration provide no evidence of high affinity binding sites. Taken together, our data strongly suggested an essentially nonspecific binding of NCp7 to tRNA(3Lys) and thus did not seem to support a direct role of NCp7, per se, in the selection of tRNA(3Lys) from the pool of cellular tRNAs.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Sequence Capsid/*chemistry/*metabolism *Capsid Proteins Escherichia coli Gene Products, Amino Acyl/biosynthesis/chemistry/*metabolism Substrate Specificity Support, gag/*chemistry/*metabolism HIV-1/*metabolism Hydrogen-Ion Concentration Kinetics Magnesium Chloride/pharmacology Mathematics Models, Genetic Zinc Fingers, MARQUET, Non-U.S. Gov't Transcription, Theoretical Molecular Sequence Data Nucleic Acid Conformation Osmolar Concentration Protein Binding RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Martin F, Eriani G, Reinbolt J, Dirheimer G, Gangloff J
Genetic selection for active E.coli amber tRNA(Asn) exclusively led to glutamine inserting suppressors Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 5, p. 779-784, 1995, ISBN: 7708493, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asn/*genetics Support, Base Sequence Escherichia coli/*genetics *Genes, ERIANI, Insertional RNA, Non-U.S. Gov't, Suppressor Glutamine/*genetics Molecular Sequence Data Mutagenesis, Transfer, Unité ARN
@article{,
title = {Genetic selection for active E.coli amber tRNA(Asn) exclusively led to glutamine inserting suppressors},
author = {F Martin and G Eriani and J Reinbolt and G Dirheimer and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7708493},
isbn = {7708493},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {5},
pages = {779-784},
abstract = {Suppressor tRNAs are useful tools for determining identity elements which define recognition of tRNAs in vivo by their cognate aminoacyl-tRNA synthetases. This study was aimed at the isolation of active amber tRNA(Asn). Nineteen mutated tRNA(Asn)CUA having amber suppressor activity were selected by an in vivo genetic screen, and all exclusively inserted glutamine. From analysis of the different mutations it is concluded that glutamine accepting activity was obtained upon reducing the interaction strength between the first base pair of the tRNA(Asn)CUA by direct or indirect effects. Failure to isolate tRNA(Asn)CUA suppressors charged with asparagine as well as other evolutionary related amino acids is discussed.},
note = {0305-1048
Journal Article},
keywords = {Asn/*genetics Support, Base Sequence Escherichia coli/*genetics *Genes, ERIANI, Insertional RNA, Non-U.S. Gov't, Suppressor Glutamine/*genetics Molecular Sequence Data Mutagenesis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kreutzer R, Kern D, Giege R, Rudinger J
Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 22, p. 4598-4602, 1995, ISBN: 8524648, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence Cloning, Genetic, Molecular Comparative Study Escherichia coli Kinetics Models, Phe/biosynthesis/chemistry/*metabolism Thermus thermophilus/*enzymology/*genetics *Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism Protein Binding RNA, Transfer, Unité ARN
@article{,
title = {Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction},
author = {R Kreutzer and D Kern and R Giege and J Rudinger},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8524648},
isbn = {8524648},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {22},
pages = {4598-4602},
abstract = {The phosphates of the tRNA(Phe) transcript from Thermus thermophilus interacting with the cognate synthetase were determined by footprinting. Backbone bond protection against cleavage by iodine of the phosphorothioate-containing transcripts was found in the anticodon stem-loop, the D stem-loop and the acceptor stem and weak protection was also seen in the variable loop. Most of the protected phosphates correspond to regions around known identity elements of tRNA(Phe). Enhancement of cleavage at certain positions indicates bending of tRNAPhe upon binding to the enzyme. When applied to the three-dimensional model of tRNA(Phe) from yeast the majority of the protections occur on the D loop side of the molecule, revealing that phenylalanyl-tRNA synthetase has a rather complex and novel pattern of interaction with tRNAPhe, differing from that of other known class II aminoacyl-tRNA synthetases.},
note = {0305-1048
Journal Article},
keywords = {Base Composition Base Sequence Cloning, Genetic, Molecular Comparative Study Escherichia coli Kinetics Models, Phe/biosynthesis/chemistry/*metabolism Thermus thermophilus/*enzymology/*genetics *Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism Protein Binding RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Keith G, Ehresmann B, Marquet R
Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer) Article de journal
Dans: J Mol Biol, vol. 247, no. 2, p. 236-250, 1995, ISBN: 7707372, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Conserved Sequence HIV-1/*genetics Models, Genetic, Lys/*genetics/metabolism RNA, MARQUET, Molecular Molecular Probes Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/*genetics/metabolism Structure-Activity Relationship Support
@article{,
title = {Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer)},
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=7707372},
isbn = {7707372},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {247},
number = {2},
pages = {236-250},
abstract = {Reverse transcription of human immunodeficiency virus type-1 (HIV-1) genomic RNA is primed by tRNA(3Lys), whose 3' end 18 nucleotides are complementary to the viral primer binding site (PBS). We used chemical and enzymatic probes to test the conformation of the viral RNA and tRNA(3Lys), in their free form and in the HIV-1 RNA/tRNA(3Lys) binary complex. Extensive reactivity changes were observed in both molecules upon formation of the binary complex. In the viral RNA, reactivity changes occurred up to 69 nucleotides upstream and 72 nucleotides downstream of the PBS. A secondary structure model of the HIV-1 RNA/tRNA(3Lys) complex accounting for all probing data has been constructed. It reveals an unexpectedly complex and compact pseudoknot-like structure in which most of the anticodon loop, the 3' strand of the anticodon stem and the 5' part of the variable loop of tRNA(3Lys) interact with viral sequences 12 to 39 nucleotides upstream of the PBS. The core of the binary complex is a complex junction formed by two single-stranded sequences of tRNA(3Lys), an intramolecular viral helix, an intramolecular tRNA helix, and two intermolecular helices formed by the template/primer interaction. This junction probably highly constrains the tertiary structure of the HIV-1 RNA/tRNA(3Lys) complex. Compared to the structure of the free molecules, only the D arm of tRNA(3Lys) and a small viral stem-loop downstream of the PBS are unaffected in the binary complex. Sequence comparison reveals that the main characteristics of the binary complex model are conserved among all HIV-1 isolates.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Binding Sites Conserved Sequence HIV-1/*genetics Models, Genetic, Lys/*genetics/metabolism RNA, MARQUET, Molecular Molecular Probes Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/*genetics/metabolism Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Przykorska A, Monko M, Kuligowska E, Sturchler C, Krol A, Dirheimer G, Szarkowski J W, Keith G
Native bovine selenocysteine tRNA(Sec) secondary structure as probed by two plant single-strand-specific nucleases Article de journal
Dans: Gene, vol. 161, no. 2, p. 259-263, 1995, ISBN: 7665090, (0378-1119 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry/*genetics Support, Animals Anticodon/chemistry/genetics Base Sequence Cattle Comparative Study Endonucleases Liver/chemistry Molecular Sequence Data Molecular Structure *Nucleic Acid Conformation Plants/enzymology RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN
@article{,
title = {Native bovine selenocysteine tRNA(Sec) secondary structure as probed by two plant single-strand-specific nucleases},
author = {J Gabryszuk and A Przykorska and M Monko and E Kuligowska and C Sturchler and A Krol and G Dirheimer and J W Szarkowski and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7665090},
isbn = {7665090},
year = {1995},
date = {1995-01-01},
journal = {Gene},
volume = {161},
number = {2},
pages = {259-263},
abstract = {Two single-strand-specific nucleases, discovered in plants, have been used to investigate the secondary and tertiary structures of the native bovine liver selenocysteine tRNA(Sec). To check the possible influence of nucleotide modifications on these structures, we compared the results obtained with the fully modified tRNA to the unmodified transcript prepared by in vitro T7 transcription of the Xenopus laevis tRNA(Sec) gene. We found that the structures in solution of the native tRNA(Sec) and the transcript are very similar despite some differences in accessibility to the enzymatic probes. Indeed, the modified anticodon-loop of native bovine tRNA(Sec), containing 5-methylcarboxymethyluridine (mcm5U34) and N6-isopentenyladenosine (i6A37), is less accessible to Rn nuclease than that of the transcript: the intensity of bands representing cuts at A36 and A38 is much lower as compared to those of the transcript, whereas no cuts were found at the level of i6A37 in the anticodon loop of the native molecule. Surprisingly, the variable arm of the native molecule has been found to be more susceptible to single-strand-specific nuclease action, suggesting a looser structure of the variable arm in native bovine tRNA(Sec) than in the transcript.},
note = {0378-1119
Journal Article},
keywords = {Amino Acid-Specific/*chemistry/*genetics Support, Animals Anticodon/chemistry/genetics Base Sequence Cattle Comparative Study Endonucleases Liver/chemistry Molecular Sequence Data Molecular Structure *Nucleic Acid Conformation Plants/enzymology RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-119, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska and G Dirheimer and J W Szarkowski and A Przykorska},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-119},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Eriani G, Cavarelli J, Martin F, Ador L, Rees B, Thierry J C, Gangloff J, Moras D
The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site Article de journal
Dans: J Mol Evol, vol. 40, no. 5, p. 499-508, 1995, ISBN: 7783225, (0022-2844 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Species Specificity Structure-Activity Relationship, Asp/metabolism Saccharomyces cerevisiae/enzymology Sequence Alignment Sequence Homology, ERIANI, Molecular Molecular Sequence Data Protein Binding Protein Conformation RNA, Transfer, Transfer/metabolism RNA, Unité ARN
@article{,
title = {The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site},
author = {G Eriani and J Cavarelli and F Martin and L Ador and B Rees and J C Thierry and J Gangloff and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7783225},
isbn = {7783225},
year = {1995},
date = {1995-01-01},
journal = {J Mol Evol},
volume = {40},
number = {5},
pages = {499-508},
abstract = {Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203-306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel beta-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2' hydroxyl whereas the class II enzymes prefer the 3' hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.},
note = {0022-2844
Journal Article},
keywords = {Amino Acid Species Specificity Structure-Activity Relationship, Asp/metabolism Saccharomyces cerevisiae/enzymology Sequence Alignment Sequence Homology, ERIANI, Molecular Molecular Sequence Data Protein Binding Protein Conformation RNA, Transfer, Transfer/metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}