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}
}
Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions Article de journal
Dans: EMBO J, vol. 15, no. 21, p. 5976-5987, 1996, ISBN: 8918475, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN
@article{,
title = {The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions},
author = {P Romby and J Caillet and C Ebel and C Sacerdot and M Graffe and F Eyermann and C Brunel and H Moine and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8918475},
isbn = {8918475},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {21},
pages = {5976-5987},
abstract = {Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.},
note = {0261-4189
Journal Article},
keywords = {Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic RNA Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 21-28, 1996, ISBN: 8786995, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support
@article{,
title = {The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic RNA},
author = {J C Paillart and E Skripkin and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8786995},
isbn = {8786995},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {21-28},
abstract = {The retroviral genome consists of two identical RNA molecules physically linked together close to their 5' end, in a region called the Dimer Linkage Structure (DLS). Recent findings suggest that dimerization is involved in encapsidation, regulation of translation and reverse transcription. Previous in vitro studies localized the DLS of HIV-1 in a region downstream of the splice donor (SD) site. More recently, we showed that dimerization of HIV-1 RNA also involves sequences upstream of the SD site. Modification interference experiments and site-directed mutagenesis were used to identify the nucleotides required in the dimerization process of HIV-1 RNA. Our results point out a self-complementary sequence located in a hairpin loop, between the Primer Binding Site (PBS) and the SD site, as the Dimerization Initiation Site.},
note = {0031-6865
Journal Article},
keywords = {Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Ng J D, Lorber B, Witz J, Théobald-Dietrich A, Kern D, Giege R
The crystallization of biological macromolecules from precipitates: evidence for Ostwald ripening. Article de journal
Dans: J Crystal Growth, vol. 168, no. 1-4, p. 50-62, 1996, ISBN: 10.1016/0022-0248(96)00362-4.
Résumé | Liens | BibTeX | Étiquettes: * Protein * Virus * Crystallization * Growth kinetics * Ostwald ripening, Unité ARN
@article{,
title = {The crystallization of biological macromolecules from precipitates: evidence for Ostwald ripening.},
author = {J D Ng and B Lorber and J Witz and A Théobald-Dietrich and D Kern and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/0022024896003624},
isbn = {10.1016/0022-0248(96)00362-4},
year = {1996},
date = {1996-01-01},
journal = {J Crystal Growth},
volume = {168},
number = {1-4},
pages = {50-62},
abstract = {Crystals were obtained by different methods under conditions where nucleation and growth occur from precipitated macromolecular material. The phenomenon was observed with compounds of different size and nature, such as thaumatin, concanavalin A, an α-amylase, a thermostable aspartyl-tRNA synthetase, the nucleo-protein complex between a tRNAAsp transcript and its cognate yeast aspartyl-tRNA synthetase, and tomato bushy stunt virus. In each system, after a rather rapid precipitation step at high supersaturation lasting one to several days, a few microcrystals appear after prolonged equilibration at constant temperature. With α-amylase, the virus and the thermostable synthetase, crystallization is accompanied by appearance of depletion zones around the growing crystals and growth of the largest crystals at the expense of the smaller ones. These features are evidences for crystal growth by Ostwald ripening. In the case of thaumatin, concanavalin A and the nucleo-protein complex, crystallization occurs by a phase transition mechanism since it is never accompanied by the disappearance of the smallest crystals. A careful analysis with thermostable aspartyl-tRNA synthetase indicates that its crystallization at 4°C under high supersaturation starts by a phase transition mechanism with the formation of small crystals within an amorphous protein precipitate. Ostwald ripening follows over a period of up to three/four months with a growth rate of about 0.8 Å/s that is 13 times slower than that of crystals growing at 20°C in the absence of precipitate without ripening. At the end of the ripening process at 4°C, only one unique synthetase crystal remains per microassay with dimensions as large as 1 mm.},
keywords = {* Protein * Virus * Crystallization * Growth kinetics * Ostwald ripening, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Michel F, Westhof E
Visualizing the logic behind RNA self-assembly Article de journal
Dans: Science, vol. 273, no. 5282, p. 1676-1677, 1996, ISBN: 8830411, (0036-8075 Comment Journal Article).
Liens | BibTeX | Étiquettes: Animals Base Composition Crystallography, Catalytic/*chemistry RNA, Protozoan/*chemistry Tetrahymena/genetics, Unité ARN, X-Ray Introns *Nucleic Acid Conformation RNA
@article{,
title = {Visualizing the logic behind RNA self-assembly},
author = {F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8830411},
isbn = {8830411},
year = {1996},
date = {1996-01-01},
journal = {Science},
volume = {273},
number = {5282},
pages = {1676-1677},
note = {0036-8075
Comment
Journal Article},
keywords = {Animals Base Composition Crystallography, Catalytic/*chemistry RNA, Protozoan/*chemistry Tetrahymena/genetics, Unité ARN, X-Ray Introns *Nucleic Acid Conformation RNA},
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}
}
Louise-May S, Auffinger P, Westhof E
RNA structure from molecular dynamics simulations Chapitre d'ouvrage
Dans: Sarma, R H; Sarma, M H (Ed.): Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995, vol. 2, p. 73-90, Adenine Press, 1996.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {RNA structure from molecular dynamics simulations},
author = {S Louise-May and P Auffinger and E Westhof},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books/about/Biological_structure_and_dynamics.html?id=SepqAAAAMAAJ&redir_esc=y},
year = {1996},
date = {1996-01-01},
booktitle = {Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995},
volume = {2},
pages = {73-90},
publisher = {Adenine Press},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Lentzen G, Moine H, Ehresmann C, Ehresmann B, Wintermeyer W
Structure of 4.5S RNA in the signal recognition particle of Escherichia coli as studied by enzymatic and chemical probing Article de journal
Dans: RNA, vol. 2, no. 3, p. 244-253, 1996, ISBN: 8608448, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Proteins/chemistry/metabolism Base Sequence Escherichia coli/*chemistry *Escherichia coli Proteins Hydroxyl Radical Lead Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Bacterial/*chemistry/metabolism Ribonucleases Signal Recognition Particle/*chemistry/metabolism Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Structure of 4.5S RNA in the signal recognition particle of Escherichia coli as studied by enzymatic and chemical probing},
author = {G Lentzen and H Moine and C Ehresmann and B Ehresmann and W Wintermeyer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608448},
isbn = {8608448},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {3},
pages = {244-253},
abstract = {The structure of 4.5S RNA, the Escherichia coli homologue of the signal recognition particle (SRP) RNA, alone and in the SRP complex with protein P48 (Ffh) was probed both enzymatically and chemically. The molecule is largely resistant against single strand-specific nucleases, indicating a highly base paired structure. Reactivity appears mainly in the apical tetraloop and in one of the conserved internal loops. Although some residues are found reactive toward dimethylsulphate and kethoxal in regions predicted to be unpaired by the phylogenetic secondary structure model of 4.5S RNA, generally the reactivity is low, and some residues in internal loops are not reactive at all. RNase V1 cleaves the RNA at multiple sites that coincide with predicted helices, although the cleavages show a pronounced asymmetry. The binding of protein P48 to 4.5S RNA results in a protection of residues in the apical part of the molecule homologous to eukaryotic SRP RNA (domain IV), whereas the cleavages in the conserved apical tetraloop are not protected. Hydroxyl radical treatment reveals an asymmetric pattern of backbone reactivity; in particular, the region encompassing nucleotides 60-82, i.e., the 3' part of the conserved domain IV, is protected. The data suggest that a bend in the domain IV region, most likely at the central asymmetric internal loop, is an important element of the tertiary structure of 4.5S RNA. Hyperchromicity and lead cleavage data are consistent with the model as they reveal the unfolding of a higher-order structure between 30 and 40 degrees C. Protection by protein P48 occurs in this region of the RNA and, more strongly, in the 5' part of domain IV (nt 26-50, most strongly from 35 to 49). It is likely that P48 binds to the outside of the bent form of 4.5S RNA.},
note = {1355-8382
Journal Article},
keywords = {Bacterial Proteins/chemistry/metabolism Base Sequence Escherichia coli/*chemistry *Escherichia coli Proteins Hydroxyl Radical Lead Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Bacterial/*chemistry/metabolism Ribonucleases Signal Recognition Particle/*chemistry/metabolism Support, Non-U.S. Gov't, 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}
}
Jaeger L, Michel F, Westhof E
The structure of group I ribozymes Chapitre d'ouvrage
Dans: Eckstein, F; Lilley, M J (Ed.): Catalytic RNA (Nucleic Acids and Molecular Biology), vol. 10, p. 33-51, Springer, 1996.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {The structure of group I ribozymes},
author = {L Jaeger and F Michel and E Westhof},
editor = {F Eckstein and M J Lilley},
url = {http://books.google.fr/books/about/Catalytic_RNA.html?id=_n4TAQAAMAAJ&redir_esc=y},
year = {1996},
date = {1996-01-01},
booktitle = {Catalytic RNA (Nucleic Acids and Molecular Biology)},
volume = {10},
pages = {33-51},
publisher = {Springer},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
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}
}
Huttenhofer A, Westhof E, Bock A
Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SELB Article de journal
Dans: RNA, vol. 2, no. 4, p. 354-366, 1996, ISBN: 8634916, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Messenger/*chemistry Selenocysteine/*metabolism Solutions Sulfuric Acid Esters/chemistry Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SELB},
author = {A Huttenhofer and E Westhof and A Bock},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8634916},
isbn = {8634916},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {4},
pages = {354-366},
abstract = {On the basis of chemical probing data, the solution structures of RNA hairpins within fdhF and fdnG mRNAs in Escherichia coli, which both promote selenocysteine incorporation at UGA codons, were derived with the help of computer modeling. We find that these mRNA hairpins contain two separate structural domains that possibly also exert two different functions. The first domain is comprised of the UGA codon, which is included within a complex and distorted double-stranded region. Thereby, release factor 2 might be prevented from binding to the UGA codon to terminate protein synthesis. The second domain is located within the apical loop of the mRNA hairpin structures. This loop region exhibits a defined tertiary structure in which no base is involved in Watson-Crick interactions. The structure of the loop is such that, following a sharp turn after G22 (A22 in fdnG mRNA), bases G23 and U24 are exposed to the solvent on the deep groove side of the supporting helix. Residues C25 and U26 close the loop with a possible single H-bonding interaction between the first and last residues of the loop, 04(U26) and N6(A21). The bulge residues U17 and U18 (in fdhF mRNA), or Ul7 only in fdnG mRNA, point their Watson-Crick positions in the same direction as loop residues G23 and U24 do, and at the same time open up the deep groove at the top of the hairpin helix. Chemical probing data demonstrate that bases G23 and U24 in both mRNA hairpins, as well as residues U17 and Ul7/U18 (for fdhF mRNA) located in a bulge 5' to the loop, are involved directly in binding to special elongation factor SELB in both mRNAs. Therefore, SELB recognizes identical bases within both mRNA hairpins despite differences in their primary sequence, consistent with the derived 3D models for these mRNAs, which exhibit similar tertiary structures. Binding of SELB to the fdhF mRNA hairpin was estimated to proceed with an apparent Kd of 30 nM.},
note = {1355-8382
Journal Article},
keywords = {Messenger/*chemistry Selenocysteine/*metabolism Solutions Sulfuric Acid Esters/chemistry Support, Non-U.S. Gov't, Unité ARN},
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}
}
Friant S, Heyman T, Wilhelm F X, Wilhelm M
Role of RNA primers in initiation of minus-strand and plus-strand DNA synthesis of the yeast retrotransposon Ty1 Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 674-680, 1996, ISBN: 8955910, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *DNA Replication *DNA Transposable Elements DNA, Bacterial/*metabolism Support, Complementary/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA/*metabolism RNA, Non-U.S. Gov't, Unité ARN
@article{,
title = {Role of RNA primers in initiation of minus-strand and plus-strand DNA synthesis of the yeast retrotransposon Ty1},
author = {S Friant and T Heyman and F X Wilhelm and M Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955910},
isbn = {8955910},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {674-680},
abstract = {The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae is a long terminal repeat mobile genetic element that transposes through an RNA intermediate. Initiation of minus-strand and plus-strand DNA synthesis are two critical steps during reverse transcription of the retrotransposon genome. Initiation of minus-strand DNA synthesis of the Ty1 element is primed by the cytoplasmic initiator methionine tRNA base paired to the primer binding site near the 5' end of the genomic RNA. A structural probing study of the primer tRNA-Ty1 RNA binary complex reveals that besides interactions between the primer binding site and the last 10 nucleotides at the 3' end of the primer tRNA, three short regions of Ty1 RNA named box 0, box 1 and box 2.1 interact with the T and D stems and loops of the primer tRNA. Some in vivo results underline the functional importance of the nucleotide sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primer tRNA play a role in the reverse transcription pathway. Plus-strand DNA synthesis is initiated from an RNase H resistant oligoribonucleotide spanning a purine-rich sequence, the polypurine tract (PPT). Two sites of initiation located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the TyB (pol) gene in the integrase coding sequence (PPT2) have been identified in the genome of Ty1. The two PPTs have an identical sequence, TGGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand DNA synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0300-9084
Journal Article},
keywords = {*DNA Replication *DNA Transposable Elements DNA, Bacterial/*metabolism Support, Complementary/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA/*metabolism RNA, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, Westhof E, Giege R
Usefulness of functional and structural solution data for the modeling of tRNA-like structures Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 3-9, 1996, ISBN: 8786997, (0031-6865 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Models, Chemical Molecular Sequence Data RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry Solutions Support, Unité ARN
@article{,
title = {Usefulness of functional and structural solution data for the modeling of tRNA-like structures},
author = {B Felden and C Florentz and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8786997},
isbn = {8786997},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {3-9},
abstract = {Structures of large RNAs are not easily solved by X-ray crystallography or by NMR spectroscopy. This paper reviews the alternate methodology based on enzymatic and chemical mapping data collected on RNAs combined with graphical modeling for the construction of three-dimensional models. The different steps that lead to the establishment of the models are critically discussed. It is shown how the correctness of an RNA model can be strengthened by establishing correlations between the structure and the functionality of the molecule and its variants. Finally, the predictive potential of a model is discussed The approach is illustrated by results obtained on plant viral tRNA-like structures, and particularly on that of brome mosaic virus (BMV) RNA.},
note = {0031-6865
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Models, Chemical Molecular Sequence Data RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry Solutions Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
Skouri M, Lorber B, Giege R, Munch J P, Candau S J
Effect of macromolecular impurities on lysozyme solubility and crystallizability: dynamic light scattering, phase diagram, and crystal growth studies Article de journal
Dans: J Crystal Growth, vol. 152, no. 3, p. 209-220, 1995, ISBN: 10.1016/0022-0248(95)00051-8.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Effect of macromolecular impurities on lysozyme solubility and crystallizability: dynamic light scattering, phase diagram, and crystal growth studies},
author = {M Skouri and B Lorber and R Giege and J P Munch and S J Candau},
url = {http://www.sciencedirect.com/science/article/pii/0022024895000518},
isbn = {10.1016/0022-0248(95)00051-8},
year = {1995},
date = {1995-01-01},
journal = {J Crystal Growth},
volume = {152},
number = {3},
pages = {209-220},
abstract = {The effects of macromolecular impurities on protein solubility and crystallizability were investigated by dynamic light scattering and crystal growth experiments using hen egg-white lysozyme as the model protein. In the presence of traces of protein impurities, representing no more than 2% (w/w) of the total protein, the average diffusion coefficients of the macromolecular particles found in undersaturated lysozyme solutions are significantly lower than those measured with purest lysozyme preparations. This fact is explained by the simultaneous existence of individual molecules and of large size aggregates in contaminated solutions, as indicated by the bimodal light scattering autocorrelation function. Controlled contamination experiments in which ovalbumin or conalbumin were added to purest lysozyme indicate that aggregates result from heterogeneous association of lysozyme molecules with the structurally unrelated proteins. These aggregates might become starting points for heterogeneous nucleation leading to the growth of ill-shaped microcrystals. Aggregates in under- or supersaturated lysozyme solutions containing NaCl can be eliminated by filtration over microporous membranes. As a result the number of ill-shaped crystals diminishes drastically; that of well-shaped tetragonal crystals decreases also but their size increases.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Philippe C, Benard L, Portier C, Westhof E, Ehresmann B, Ehresmann C
Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15 Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 1, p. 18-28, 1995, ISBN: 7532857, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/genetics/metabolism RNA, Base Sequence Binding Sites/genetics Escherichia coli/*genetics/metabolism Models, Genetic, Messenger/genetics/metabolism Ribosomal Proteins/*chemistry/*genetics/metabolism Support, Molecular Molecular Sequence Data Mutation Protein Conformation RNA, Non-U.S. Gov't Thermodynamics *Translation, Unité ARN
@article{,
title = {Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15},
author = {C Philippe and L Benard and C Portier and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7532857},
isbn = {7532857},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {1},
pages = {18-28},
abstract = {The ribosomal protein S15 controls its own translation by binding to a mRNA region overlapping the ribosome binding site. That region of the mRNA can fold in two mutually exclusive conformations that are in dynamic equilibrium: a structure with two hairpins and a pseudoknot. A mutational analysis provided evidence for the existence and requirement of the pseudoknot for translational control in vivo and S15 recognition in vitro. In this study, we used chemical probing to analyze the structural consequences of mutations and their effect on the stem-loop/pseudoknot equilibrium. Interactions between S15 and the pseudoknot structure were further investigated by footprinting experiments. These data, combined with computer modelling and the previously published data on S15 binding and in vivo control, provide important clues on pseudoknot formation and S15 recognition. An unexpected result is that the relevant control element, here the pseudoknot form, can exist in a variety of topologically equivalent structures recognizable and shapable by S15. S15 sits on the deep groove of the co-axial stack and makes contacts with both stems, shielding the bridging adenine. The only specific sequence determinants are found in the helix common to the pseudoknot and the hairpin structures.},
note = {0305-1048
Journal Article},
keywords = {Bacterial/genetics/metabolism RNA, Base Sequence Binding Sites/genetics Escherichia coli/*genetics/metabolism Models, Genetic, Messenger/genetics/metabolism Ribosomal Proteins/*chemistry/*genetics/metabolism Support, Molecular Molecular Sequence Data Mutation Protein Conformation RNA, Non-U.S. Gov't Thermodynamics *Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
O'Connor M, Brunelli C A, Firpo M A, Gregory S T, Lieberman K R, Lodmell J S, Moine H, Ryk D I Van, Dahlberg A E
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-868, 1995, ISBN: 8722001, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: 16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN
@article{,
title = {Genetic probes of ribosomal RNA function},
author = {M O'Connor and C A Brunelli and M A Firpo and S T Gregory and K R Lieberman and J S Lodmell and H Moine and D I Van Ryk and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722001},
isbn = {8722001},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-868},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, 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}
}
Logan D T, Mazauric M H, Kern D, Moras D
Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus Article de journal
Dans: EMBO J, vol. 14, no. 17, p. 4156-4167, 1995, ISBN: 7556056, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Binding Sites Comparative Study Crystallography, Bacterial Glycine-tRNA Ligase/*chemistry/genetics/isolation & purification Macromolecular Systems Models, Molecular Molecular Sequence Data Polymerase Chain Reaction *Protein Structure, Non-U.S. Gov't Thermus thermophilus/*enzymology, Secondary Sequence Homology, Unité ARN, X-Ray/methods DNA Probes Genes
@article{,
title = {Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus},
author = {D T Logan and M H Mazauric and D Kern and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7556056},
isbn = {7556056},
year = {1995},
date = {1995-01-01},
journal = {EMBO J},
volume = {14},
number = {17},
pages = {4156-4167},
abstract = {The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not possess the proline previously believed to be an essential class II invariant. Nevertheless, crucial contacts with the active site of the other monomer involving motif 1 are conserved and a more comprehensive description of class II now becomes possible. Each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Binding Sites Comparative Study Crystallography, Bacterial Glycine-tRNA Ligase/*chemistry/genetics/isolation & purification Macromolecular Systems Models, Molecular Molecular Sequence Data Polymerase Chain Reaction *Protein Structure, Non-U.S. Gov't Thermus thermophilus/*enzymology, Secondary Sequence Homology, Unité ARN, X-Ray/methods DNA Probes Genes},
pubstate = {published},
tppubtype = {article}
}
Laouedj A, Schenk C, Pfohl-Leszkowicz A, Keith G, Schontz D, Guillemaut P, Rether B
Detection of DNA adducts in declining hop plants grown on fields formerly treated with heptachlor, a persistent insecticide Article de journal
Dans: Environ Pollut, vol. 90, no. 3, p. 409-414, 1995, ISBN: 15091476, (0269-7491 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Detection of DNA adducts in declining hop plants grown on fields formerly treated with heptachlor, a persistent insecticide},
author = {A Laouedj and C Schenk and A Pfohl-Leszkowicz and G Keith and D Schontz and P Guillemaut and B Rether},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15091476},
isbn = {15091476},
year = {1995},
date = {1995-01-01},
journal = {Environ Pollut},
volume = {90},
number = {3},
pages = {409-414},
abstract = {Hop decline was observed in Alsace, eastern France, in reparcelled sugar beet fields formerly abundantly treated with an insecticide, heptachlor. Leaves were collected from 'declining hops' grown in an heptachlor-contaminated area and from 'healthy hops' grown in a soil not contaminated by heptachlor. These two samples came from hop vines treated with other usual pesticides. 'Control' hop leaves came from soil neither treated with pesticide nor contaminated with heptachlor. Hypermodified nucleotides (DNA adducts) were detected using the (32)P-postlabelling method. No detectable DNA adducts were found in the 'control' specimen, whereas eight adducts were detected in the 'healthy hops' specimen, probably due to the usual pesticide treatment. However, 16 adducts, nine of which were new adducts, could be detected in the 'declining hops' specimen. It may therefore be supposed that the presence of these hypermodified nucleotides perturbs gene expression and so contributes to the hop decline. In addition, to confirm the genotoxicity of heptachlor, it is shown that it induces DNA adducts in bean-cell suspension culture as well. Finally, it is proposed, in the case of alternate cultures scheduled in fields which were formerly treated with pesticides, adapted to other cultures, that particular attention should be given to the history of the soils.},
note = {0269-7491
Journal Article},
keywords = {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}
}
Keith G
Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography Article de journal
Dans: Biochimie, vol. 77, no. 1-2, p. 142-144, 1995, ISBN: 7599271, (0300-9084 Journal Article).
Liens | BibTeX | Étiquettes: *Chromatography, Thin Layer Purines/chemistry Pyrimidines/chemistry RNA, Transfer/chemistry Ribonucleases/metabolism Ribonucleotides/*chemistry, Unité ARN
@article{,
title = {Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography},
author = {G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7599271},
isbn = {7599271},
year = {1995},
date = {1995-01-01},
journal = {Biochimie},
volume = {77},
number = {1-2},
pages = {142-144},
note = {0300-9084
Journal Article},
keywords = {*Chromatography, Thin Layer Purines/chemistry Pyrimidines/chemistry RNA, Transfer/chemistry Ribonucleases/metabolism Ribonucleotides/*chemistry, 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}
}
Heyman T, Agoutin B, Friant S, Wilhelm F X, Wilhelm M L
Dans: J Mol Biol, vol. 253, no. 2, p. 291-303, 1995, ISBN: 7563090, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes
@article{,
title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},
author = {T Heyman and B Agoutin and S Friant and F X Wilhelm and M L Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7563090},
isbn = {7563090},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {291-303},
abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes},
pubstate = {published},
tppubtype = {article}
}
Gaspin C, Westhof E
An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints Article de journal
Dans: J Mol Biol, vol. 254, no. 2, p. 163-174, 1995, ISBN: 7490740, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Algorithms Base Sequence Endoribonucleases/*chemistry Escherichia coli/chemistry Introns Models, Bacterial/*chemistry RNA, Catalytic/*chemistry Ribonuclease P *Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN
@article{,
title = {An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints},
author = {C Gaspin and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7490740},
isbn = {7490740},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {254},
number = {2},
pages = {163-174},
abstract = {A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore of great interest. However, some of the suboptimal RNA secondary structures computed with classic methods are unsaturated structures, i.e. some structures are included into others. Thus, the incorporation of constraints during the process of folding is not possible, while the incorporation of constraints before the process of folding often introduces a bias into the energy function. This paper describes a new procedure which allows for the incorporation of constraints before and during the process of RNA folding. SAPSSARN is an interactive program which offers a framework, both to specify a secondary structure through a set of folding constraints and to compute all the supoptimal saturated RNA secondary structures which satisfy all the folding constraints. At the start, it relies on the computation of the probabilities of pairing of each base with all others according to McCaskill's algorithm. The constraint satisfaction formulation of the problem deals dynamically with a chosen set of folding constraints and, finally, a search algorithm computes all the suboptimal saturated secondary structures which satisfy those folding constraints. Within such a framework, it is possible to test new ideas about RNA folding and secondary structures, including pseudoknots, can be computed. The program is illustrated with RNA sequences on which we obtained results in agreement with known structures by using a protocol which mimics the hierarchical folding of RNA molecules.},
note = {0022-2836
Journal Article},
keywords = {Algorithms Base Sequence Endoribonucleases/*chemistry Escherichia coli/chemistry Introns Models, Bacterial/*chemistry RNA, Catalytic/*chemistry Ribonuclease P *Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN},
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}
}
el Adlouni C, Tremblay J, Walsh P, Lagueux J, Bureau J, Laliberte D, Keith G, Nadeau D, Poirier G G
Comparative study of DNA adducts levels in white sucker fish (Catostomus commersoni) from the basin of the St. Lawrence River (Canada) Article de journal
Dans: Mol Cell Biochem, vol. 148, no. 2, p. 133-138, 1995, ISBN: 8594417, (0300-8177 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Comparative Study Cypriniformes/genetics/*metabolism DNA Adducts/*analysis *DNA Damage Fresh Water Industrial Waste Liver/chemistry Polycyclic Hydrocarbons/adverse effects Quebec Support, Chemical/*adverse effects, Non-U.S. Gov't Water Pollutants, Unité ARN
@article{,
title = {Comparative study of DNA adducts levels in white sucker fish (Catostomus commersoni) from the basin of the St. Lawrence River (Canada)},
author = {C el Adlouni and J Tremblay and P Walsh and J Lagueux and J Bureau and D Laliberte and G Keith and D Nadeau and G G Poirier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8594417},
isbn = {8594417},
year = {1995},
date = {1995-01-01},
journal = {Mol Cell Biochem},
volume = {148},
number = {2},
pages = {133-138},
abstract = {The levels of DNA adducts in the hepatic tissue of the white sucker fish species Catostomus commersoni were determined by 32P-postlabelling. The fish were caught at four sites: two sites near the city of Windsor (Quebec, Canada) on the St. Francois River, a downstream tributary of the St. Lawrence River, and two sites in the St. Lawrence River itself, near the city of Montreal (Quebec, Canada). The latter sites are known to be contaminated by many pollutants including polycyclic aromatic hydrocarbons. Total adduct levels in all fish ranged from 25.1-178.0 adducts per 10(9) nucleotides. White sucker from the selected sites of the St. Lawrence River had a significantly higher mean level of DNA adducts than those of the St. Francois River (129.4 vs 56.8, respectively). These results suggest that the effluents of many heavy industries (e.g. from a Soderberg aluminium plant) flowing in the St. Lawrence River are more likely to produce genotoxic damage to fish than those released in one of its tributary, and mainly associated to the activities of a small town and a nearby pulp and paper mill.},
note = {0300-8177
Journal Article},
keywords = {Animals Comparative Study Cypriniformes/genetics/*metabolism DNA Adducts/*analysis *DNA Damage Fresh Water Industrial Waste Liver/chemistry Polycyclic Hydrocarbons/adverse effects Quebec Support, Chemical/*adverse effects, Non-U.S. Gov't Water Pollutants, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ehresmann C, Philippe C, Westhof E, Benard L, Portier C, Ehresmann B
A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15 Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 1131-1140, 1995, ISBN: 8722030, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Genetic Code Molecular Sequence Data Nucleic Acid Conformation *Peptide Chain Initiation Ribosomal Proteins/*genetics *Translation, Bacterial/*physiology *Genes, Base Sequence Escherichia coli/*genetics Gene Expression Regulation, Genetic, Unité ARN
@article{,
title = {A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15},
author = {C Ehresmann and C Philippe and E Westhof and L Benard and C Portier and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722030},
isbn = {8722030},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {1131-1140},
abstract = {Escherichia coli ribosomal protein S15 down regulates its own synthesis by binding to its mRNA in a region overlapping the ribosome binding site, called the translational operator. This binding stabilizes a pseudoknot structure that exists in equilibrium with two stem-loop structures. When synthesized in excess over 16S rRNA, S15 binds to its translational operator and traps the ribosome on its loading site in a transient state, preventing the formation of the active ternary (30S-mRNA-rRNA(f)Met) complex. This inhibition can be suppressed by 16S rRNA, which displaces S15 from the mRNA. An extensive mutational analysis showed that the pseudoknot is the structural element required for S15 recognition and in vivo translational control. Specific sequence determinants are located in limited regions of the structure formed by the pseudoknot. An unexpected result is that the pseudoknot can exist in a variety of topologically equivalent structures recognizable and shapable by S15. Based on footprinting experiments and computer graphic modelling, S15 shields the two stems of the pseudoknot, sitting in the major groove of the coaxial stack.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {Bacterial Genetic Code Molecular Sequence Data Nucleic Acid Conformation *Peptide Chain Initiation Ribosomal Proteins/*genetics *Translation, Bacterial/*physiology *Genes, Base Sequence Escherichia coli/*genetics Gene Expression Regulation, Genetic, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cura V, Kern D, Mitschler A, Moras D
Crystallization of threonyl-tRNA synthetase from Thermus thermophilus and preliminary crystallographic data Article de journal
Dans: FEBS Lett, vol. 374, no. 1, p. 110-112, 1995, ISBN: 7589494, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Cloning, Molecular Crystallization Crystallography, Non-U.S. Gov't Temperature Thermus thermophilus/*enzymology Threonine-tRNA Ligase/*chemistry/genetics, Unité ARN, X-Ray Escherichia coli Solubility Support
@article{,
title = {Crystallization of threonyl-tRNA synthetase from Thermus thermophilus and preliminary crystallographic data},
author = {V Cura and D Kern and A Mitschler and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7589494},
isbn = {7589494},
year = {1995},
date = {1995-01-01},
journal = {FEBS Lett},
volume = {374},
number = {1},
pages = {110-112},
abstract = {Threonyl-tRNA synthetase from Thermus thermophilus (ttTRS) has been overproduced in Escherichia coli, purified and crystallized in solutions containing ammonium sulfate and glycerol. The crystals grew in the orthorhombic space group C222(1) with unit cell dimensions a = 119.5 A},
note = {0014-5793
Journal Article},
keywords = {Cloning, Molecular Crystallization Crystallography, Non-U.S. Gov't Temperature Thermus thermophilus/*enzymology Threonine-tRNA Ligase/*chemistry/genetics, Unité ARN, X-Ray Escherichia coli Solubility Support},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Louise-May S, Westhof E
Multiple Molecular Dynamics Simulations of the Anticodon Loop of tRNAAsp in Aqueous Solution with Counterions Article de journal
Dans: J Am Chem Soc, vol. 117, no. 25, p. 6720-6726, 1995.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Multiple Molecular Dynamics Simulations of the Anticodon Loop of tRNAAsp in Aqueous Solution with Counterions},
author = {P Auffinger and S Louise-May and E Westhof},
url = {http://pubs.acs.org/doi/abs/10.1021/ja00130a011},
doi = {10.1021/ja00130a011},
year = {1995},
date = {1995-01-01},
journal = {J Am Chem Soc},
volume = {117},
number = {25},
pages = {6720-6726},
abstract = {In a systematic search for a stable protocol with which to extend our dynamical investigations, a nanosecond
of molecular dynamics simulations of the solvated anticodon loop of tRNAASp consisting of ten unique trajectories
was obtained by slight modifications to the starting conditions. These changes produced divergent trajectories which
varied widely in structural and dynamical characteristics. However, the properties of these trajectories could not be
directly correlated to the slight modifications introduced in the system, and thus, questions were raised regarding the
probity of the standard protocol we utilized. Instead of a detailed analysis of the results, the multiple molecular
dynamics (MD) approach was used as a diagnostic for estimating the reliability of the set of trajectories generated
and the extent of relevant biochemical information which can be extracted from it. We address here issues concerning
critical evaluation of molecular dynamics methodology and detection of protocol instabilities. We infer that an
ensemble of initial uncorrelated trajectories should be generated in order to investigate the constancy of structural
and dynamical properties of the system under study.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Beveridge D L
A simple test for evaluating the truncation effects in simulations of systems involving charged groups Article de journal
Dans: Chem Phys Lett, vol. 234, no. 4-6, p. 413-415, 1995.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {A simple test for evaluating the truncation effects in simulations of systems involving charged groups},
author = {P Auffinger and D L Beveridge},
url = {http://www.sciencedirect.com/science/article/pii/000926149500065C},
doi = {10.1016/0009-2614(95)00065-C},
year = {1995},
date = {1995-01-01},
journal = {Chem Phys Lett},
volume = {234},
number = {4-6},
pages = {413-415},
abstract = {We report the results from a molecular dynamics (MD) simulation on a 1.0 M aqueous NaCl solution using the classical SPC water model and a treatment of long-range electrostatic forces involving a 916 Å twin-range cut-off. This study was undertaken to explore the importance of truncation effects in simulations involving charged species which employ cut-offs at longer range than typically used in MD. Artefacts were discerned in the ion-ion radial distribution functions at ≈ 16 Å, indicating that increasing the length scale of the truncation scheme does not necessarily lead to reliable trajectories. Our results indicate that ムcharge group-charge groupメ radial distribution functions are a sensitive test for the detection of artefacts due to truncation and it is suggested that they should be used as a routine screening device in the analysis of MD systems involving charged groups.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P
Dans: Eur J Biochem, vol. 231, no. 3, p. 726-735, 1995, ISBN: 7544283, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN
@article{,
title = {A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex},
author = {M Zenkova and C Ehresmann and J Caillet and M Springer and G Karpova and B Ehresmann and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7544283},
isbn = {7544283},
year = {1995},
date = {1995-01-01},
journal = {Eur J Biochem},
volume = {231},
number = {3},
pages = {726-735},
abstract = {We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.},
note = {0014-2956
Journal Article},
keywords = {Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Patel D
Nucleic acids: Diversity, folding, and stability of nucleic acid structures. Article de journal
Dans: Curr Opin Struct Biol, vol. 5, no. 3, p. 279281, 1995.
Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Nucleic acids: Diversity, folding, and stability of nucleic acid structures.},
author = {E Westhof and D Patel},
url = {http://www.sciencedirect.com/science/article/pii/0959440X95800883},
doi = {10.1016/0959-440X(95)80088-3},
year = {1995},
date = {1995-01-01},
journal = {Curr Opin Struct Biol},
volume = {5},
number = {3},
pages = {279281},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E
On the role of single-stranded adenines in RNA-RNA recognition. Chapitre d'ouvrage
Dans: Pullman, A; Jortner, J; Pullman, B (Ed.): Modelling of Biomolecular Structures and Mechanisms (Jerusalem Symposia), p. 305-313, Kluwer Academic Publishers, 1995.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {On the role of single-stranded adenines in RNA-RNA recognition.},
author = {E Westhof},
editor = {A Pullman and J Jortner and B Pullman},
url = {http://www.springer.com/life+sciences/biochemistry+%26+biophysics/book/978-0-7923-3102-5},
year = {1995},
date = {1995-01-01},
booktitle = {Modelling of Biomolecular Structures and Mechanisms (Jerusalem Symposia)},
pages = {305-313},
publisher = {Kluwer Academic Publishers},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Wang E D, Gu W L, Wang Y L, Eriani G, Gangloff J
Lys306 of E. coli arginyl-tRNA synthetase is necessary for the activity of this enzyme. Article de journal
Dans: Acta Bioch Bioph Sin, vol. 27, p. 123-128, 1995.
Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{,
title = {Lys306 of E. coli arginyl-tRNA synthetase is necessary for the activity of this enzyme.},
author = {E D Wang and W L Gu and Y L Wang and G Eriani and J Gangloff},
url = {none},
year = {1995},
date = {1995-01-01},
journal = {Acta Bioch Bioph Sin},
volume = {27},
pages = {123-128},
keywords = {ERIANI, Unité ARN},
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}
}
Sturchler-Pierrat C, Carbon P, Krol A
Selenium, selenoproteines: une autre lecture du code genétique. Article de journal
Dans: Med Sci (Paris), vol. 11, no. 8, p. 1081-1088, 1995.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Selenium, selenoproteines: une autre lecture du code genétique.},
author = {C Sturchler-Pierrat and P Carbon and A Krol},
url = {http://vinci.bibli.be/opac/index.php?lvl=bulletin_display&id=638},
year = {1995},
date = {1995-01-01},
journal = {Med Sci (Paris)},
volume = {11},
number = {8},
pages = {1081-1088},
abstract = {Le sélénium est un élément présent à l'état de trace, trace dont l'importance physiologique n'a été appréciée à sa juste valeur que dans un passé récent. Sa forme biologique consiste essentiellement en l'acide aminé sélénocystéine, composé n'existant pas naturellement à l'état libre dans la cellule. Une machinerie complexe mais originale, mettant en oeuvre plusieurs produits géniques, insère cet acide aminé de manière cotraductionnelle. Parmi les sélénoenzymes identifiées à l'heure actuelle chez les mammifères, les glutathion peroxydases constituent une des lignes de défense contre les agressions par les radicaux libres oxygénés; la tétra-iodothyronine-5'-désiodinase, pour sa part, active l'hormone thyroïdienne. Ces deux exemples mettent clairement en exergue l'importance cruciale du sélénium, aussi bien dans la prévention des dommages causés aux macromolécules biologiques qu'au cours du développement.},
keywords = {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}
}
Marquet R, Isel C, Ehresmann C, Ehresmann B
tRNAs as primer of reverse transcriptases Article de journal
Dans: Biochimie, vol. 77, no. 1-2, p. 113-124, 1995, ISBN: 7541250, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Binding Sites DNA Nucleotidylexotransferase/genetics/metabolism Hepadnaviridae/genetics Introns Plant Viruses/genetics Plasmids RNA/chemistry/*metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer/chemistry/*metabolism RNA, Unité ARN, Viral/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Retroelements/genetics Retroviridae/genetics Support
@article{,
title = {tRNAs as primer of reverse transcriptases},
author = {R Marquet and C Isel and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7541250},
isbn = {7541250},
year = {1995},
date = {1995-01-01},
journal = {Biochimie},
volume = {77},
number = {1-2},
pages = {113-124},
abstract = {Genetic elements coding for proteins that present amino acid identity with the conserved motifs of retroviral reverse transcriptases constitute the retroid family. With the exception of reverse transcriptases encoded by mitochondrial plasmids of Neurospora, all reverse transcriptases have an absolute requirement for a primer to initiate DNA synthesis. In retroviruses, plant pararetroviruses, and retrotransposons (transposons containing long terminal repeats), DNA synthesis is primed by specific tRNAs. All these retroelements contain a primer binding site presenting a Watson-Crick complementarity with the primer tRNA. The tRNAs most widely used as primers are tRNA(Trp), tRNA(Pro), tRNA(1,2Lys), tRNA(3Lys), tRNA(iMet). Other tRNAs such as tRNA(Gln), tRNA(Leu), tRNA(Ser), tRNA(Asn) and tRNA(Arg) are also occasionally used as primers. In the retroviruses and plant pararetroviruses, the primer binding site is complementary to the 3' end of the primer tRNA. In the case of retrotransposons, the primer binding site is either complementary to the 3' end or to an internal region of the primer tRNA. Additional interactions taking place between the primer tRNA and the retro-RNA outside of the primer binding site have been evidenced in the case of Rous sarcoma virus, human immunodeficiency virus type I, and yeast retrotransposon Ty1. A selective encapsidation of the primer tRNA, probably promoted by interactions with reverse transcriptase, occurs during the formation of virus or virus-like particles. Annealing of the primer tRNA to the primer binding site appears to be mediated by reverse transcriptase and/or the nucleocapsid protein. Modified nucleosides of the primer tRNA have been shown to be important for replication of the primer binding site, encapsidation of the primer (in the case of Rous sarcoma virus), and interaction with the genomic RNA (in the case of human immunodeficiency virus type I).},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Binding Sites DNA Nucleotidylexotransferase/genetics/metabolism Hepadnaviridae/genetics Introns Plant Viruses/genetics Plasmids RNA/chemistry/*metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer/chemistry/*metabolism RNA, Unité ARN, Viral/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Retroelements/genetics Retroviridae/genetics Support},
pubstate = {published},
tppubtype = {article}
}
Keith G, Dirheimer G
Postlabeling: a sensitive method for studying DNA adducts and their role in carcinogenesis Article de journal
Dans: Curr Opin Biotechnol, vol. 6, no. 1, p. 3-11, 1995, ISBN: 7894079, (0958-1669 Journal Article Review Review, Academic).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Cell Division *Cell Transformation, Genetic Molecular Sequence Data Mutagenesis Neoplasms/*genetics/pathology Phosphorus Radioisotopes Precancerous Conditions/genetics/pathology Radioisotope Dilution Technique Sensitivity and Specificity Support, Human Human Models, Neoplastic DNA Adducts/*analysis *Genome, Non-U.S. Gov't Xenobiotics, Unité ARN
@article{,
title = {Postlabeling: a sensitive method for studying DNA adducts and their role in carcinogenesis},
author = {G Keith and G Dirheimer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7894079},
isbn = {7894079},
year = {1995},
date = {1995-01-01},
journal = {Curr Opin Biotechnol},
volume = {6},
number = {1},
pages = {3-11},
abstract = {The covalent binding of xenobiotics to DNA is an important trigger of the multistage process that leads to carcinogenesis. 32P-postlabeling represents a highly sensitive method for biomonitoring exposure to genotoxic agents and for cancer risk assessment; it is capable of detecting less than one DNA adduct per human genome. Recent improvements to the technique have shown that the resistance of adducted DNA to enzyme digestion may lead to an overestimation of the number of different adducts present in a sample.},
note = {0958-1669
Journal Article
Review
Review, Academic},
keywords = {Animals Base Sequence Cell Division *Cell Transformation, Genetic Molecular Sequence Data Mutagenesis Neoplasms/*genetics/pathology Phosphorus Radioisotopes Precancerous Conditions/genetics/pathology Radioisotope Dilution Technique Sensitivity and Specificity Support, Human Human Models, Neoplastic DNA Adducts/*analysis *Genome, Non-U.S. Gov't Xenobiotics, 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}
}
Dirheimer G, Keith G, Dumas P, Westhof E
Primary, secondary and tertiary structures of tRNAs. Chapitre d'ouvrage
Dans: Soll, D; RajBhandary, U L (Ed.): tRNA: Structure, Biosynthesis and Function, p. 93-126, American Society for Microbiology, Washington DC, 1995.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {Primary, secondary and tertiary structures of tRNAs.},
author = {G Dirheimer and G Keith and P Dumas and E Westhof},
editor = {D Soll and U L RajBhandary},
url = {http://books.google.fr/books?hl=fr&lr=&id=jx6mGLkB-E0C&oi=fnd&pg=PA93&dq=Primary,+secondary+and+tertiary+structures+of+tRNAs.&ots=7GJsXp6gAB&sig=F_uhTMBSTQE7VvPN6XpmbNO_V00#v=onepage&q=Primary%2C%20secondary%20and%20tertiary%20structures%20of%20tRNAs.&f=false},
year = {1995},
date = {1995-01-01},
booktitle = {tRNA: Structure, Biosynthesis and Function},
pages = {93-126},
publisher = {American Society for Microbiology, Washington DC},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Dirheimer G, Baranowski W, Keith G
Variations in tRNA modifications, particularly of their queuine content in higher eukaryotes. Its relation to malignancy grading Article de journal
Dans: Biochimie, vol. 77, no. 1-2, p. 99-103, 1995, ISBN: 7599283, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Animals Cell Transformation, Neoplastic/genetics Female Guanine/*analogs & derivatives/analysis Human Neoplasms/*genetics/pathology Ovarian Neoplasms/*genetics/pathology Purines/analysis Pyrimidines/analysis RNA Processing, Non-U.S. Gov't, Post-Transcriptional RNA, Transfer/*chemistry/metabolism Support, Unité ARN
@article{,
title = {Variations in tRNA modifications, particularly of their queuine content in higher eukaryotes. Its relation to malignancy grading},
author = {G Dirheimer and W Baranowski and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7599283},
isbn = {7599283},
year = {1995},
date = {1995-01-01},
journal = {Biochimie},
volume = {77},
number = {1-2},
pages = {99-103},
abstract = {Literature references dealing with the variations in the modification level of nucleosides in total eukaryotic tRNAs as a function of different physiological status and after drug administration as well as in sequenced cytoplasmic tRNAs between normal and tumor cells and in SV40-transformed cells are reviewed. In addition, special attention is given to guanine replacement of queuine in the first position of the anticodon of tRNAs. A correlation between the level of this undermodification in cancer tissues and the malignancy grading could be found in human ovarian tumors, confirming the results reported in several laboratories for lymphomas and lung cancer tissues. Indeed tRNAs from primary and metastatic human ovarian malignant tumors are Q deficient as compared to tRNAs from normal tissues or benign tumors: thus queuine deficiency increases with malignancy and grading of differentiation.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Animals Cell Transformation, Neoplastic/genetics Female Guanine/*analogs & derivatives/analysis Human Neoplasms/*genetics/pathology Ovarian Neoplasms/*genetics/pathology Purines/analysis Pyrimidines/analysis RNA Processing, Non-U.S. Gov't, Post-Transcriptional RNA, Transfer/*chemistry/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Romby P, Sacerdot C, de Smit M, Graffe M, Dondon J, van Duin J, Ehresmann B, Ehresmann C, Springer M
Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli Article de journal
Dans: J Mol Biol, vol. 253, no. 2, p. 277-290, 1995, ISBN: 7563089, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial *Gene Expression Regulation, Base Composition Base Sequence Binding Sites Comparative Study Enzyme Repression Escherichia coli/genetics/*metabolism Gene Expression Regulation, Enzymologic Homeostasis Kinetics Mathematics Models, Genetic *Translation, Genetic beta-Galactosidase/biosynthesis, Messenger/biosynthesis/*chemistry/*metabolism Recombinant Proteins/biosynthesis Ribosomes/*metabolism Support, Non-U.S. Gov't Temperature Threonine-tRNA Ligase/*biosynthesis Transcription, ROMBY, Site-Directed *Nucleic Acid Conformation RNA, Theoretical Molecular Sequence Data Mutagenesis, Unité ARN
@article{,
title = {Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli},
author = {C Brunel and P Romby and C Sacerdot and M de Smit and M Graffe and J Dondon and J van Duin and B Ehresmann and C Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7563089},
isbn = {7563089},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {277-290},
abstract = {The expression of the gene encoding Escherichia coli threonyl-tRNA synthetase is negatively autoregulated at the translational level. The negative feedback is due to the binding of the synthetase to an operator site on its own mRNA located upstream of the initiation codon. The present work describes the characterisation of operator mutants that have the rare property of enhancing repression. These mutations cause (1) a low basal level of expression, (2) a temperature-dependent expression, and (3) an increased capacity of the synthetase to repress its own expression at low temperature. Surprisingly, this enhancement of repression is not explained by an increase of affinity of the mutant operators for the enzyme but by the formation, at low temperature, of a few supplementary base-pairs between the ribosomal binding site and a normally single-stranded domain of the operator. Although this additional base-pairing only slightly inhibits ribosome binding in the absence of repressor, simple thermodynamic considerations indicate that this is sufficient to increase repression. This increase is explained by the competition between the ribosome and repressor for overlapping regions of the mRNA. When the ribosomal binding site is base-paired, the ribosome cannot bind while the repressor can, giving the repressor the advantage in the competition. Thus, the existence of an open versus base-paired equilibrium in a ribosomal binding site of a translational operator amplifies the magnitude of control. This molecular amplification device might be an essential component of translational control considering the low free repressor/ribosome ratio of the low affinity of translational repressors for their target operators.},
note = {0022-2836
Journal Article},
keywords = {Bacterial *Gene Expression Regulation, Base Composition Base Sequence Binding Sites Comparative Study Enzyme Repression Escherichia coli/genetics/*metabolism Gene Expression Regulation, Enzymologic Homeostasis Kinetics Mathematics Models, Genetic *Translation, Genetic beta-Galactosidase/biosynthesis, Messenger/biosynthesis/*chemistry/*metabolism Recombinant Proteins/biosynthesis Ribosomes/*metabolism Support, Non-U.S. Gov't Temperature Threonine-tRNA Ligase/*biosynthesis Transcription, ROMBY, Site-Directed *Nucleic Acid Conformation RNA, Theoretical Molecular Sequence Data Mutagenesis, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Rubin-Carrez C, Fritsch V
The Use of Molecular Dynamics Simulations for Modelling Nucleic Acids Chapitre d'ouvrage
Dans: Goodfellow, J M (Ed.): Computer Modelling in Molecular Biology, p. 103-131, Wiley-VCH, 1995.
Liens | BibTeX | Étiquettes: * molecular dynamics simulations * nucleic acids * potential energy function * treatment of solvent * counterions, Unité ARN
@inbook{,
title = {The Use of Molecular Dynamics Simulations for Modelling Nucleic Acids},
author = {E Westhof and C Rubin-Carrez and V Fritsch},
editor = {J M Goodfellow},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527615339.ch5/summary},
doi = {10.1002/9783527615339.ch5},
year = {1995},
date = {1995-01-01},
booktitle = {Computer Modelling in Molecular Biology},
pages = {103-131},
publisher = {Wiley-VCH},
keywords = {* molecular dynamics simulations * nucleic acids * potential energy function * treatment of solvent * counterions, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}