Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization. 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. 61-72, Adenine Press, 1996.
Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@inbook{,
title = {Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization.},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books?hl=fr&id=SOpqAAAAMAAJ&q=Marquet#search_anchor},
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 = {61-72},
publisher = {Adenine Press},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Rudinger J, Hillenbrandt R, Sprinzl M, Giege R
Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu Article de journal
Dans: EMBO J, vol. 15, no. 3, p. 650-657, 1996, ISBN: 8599948, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN
@article{,
title = {Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu},
author = {J Rudinger and R Hillenbrandt and M Sprinzl and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8599948},
isbn = {8599948},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {3},
pages = {650-657},
abstract = {During protein biosynthesis, all aminoacylated elongator tRNAs except selenocysteine-inserting tRNA Sec form ternary complexes with activated elongation factor. tRNA Sec is bound by its own translation factor, an elongation factor analogue, e.g. the SELB factor in prokaryotes. An apparent reason for this discrimination could be related to the unusual length of tRNA Sec amino acid-acceptor branch formed by 13 bp. However, it has been recently shown that an aspartylated minihelix of 13 bp derived from yeast tRNA Asp is an efficient substrate for Thermus thermophilus EF-Tu-GTP, suggesting that features other than the length of tRNA Sec prevent its recognition by EF-Tu-GTP. A stepwise mutational analysis of a minihelix derived from tRNA Sec in which sequence elements of tRNA Asp were introduced showed that the sequence of the amino acid- acceptor branch of Escherichia coli tRNA Sec contains a specific structural element that hinders its binding to T.thermophilus EF-Tu-GTP. This antideterminant is located in the 8th, 9th and 10th bp in the acceptor branch of tRNA Sec, corresponding to the last base pair in the amino acid acceptor stem and the two first pairs in the T-stem. The function of this C7.G66/G49.U65/C50.G64 box was tested by its transplantation into a minihelix derived from tRNA Asp, abolishing its recognition by EF-Tu-GTP. The specific role of this nucleotide combination is further supported by its absence in all known prokaryotic elongator tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid-Specific/*chemistry/genetics/*metabolism RNA, Antisense/chemistry/genetics/metabolism RNA, Asp/chemistry/genetics/metabolism Saccharomyces cerevisiae/genetics/metabolism Support, Base Sequence Escherichia coli/genetics/metabolism Evolution Guanosine Triphosphate/metabolism Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Non-U.S. Gov't Thermus thermophilus/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
de Barros J P Pais, Keith G, Adlouni C El, Glasser A L, Mack G, Dirheimer G, Desgres J
2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 8, p. 1489-1496, 1996, ISBN: 8628682, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver},
author = {J P Pais de Barros and G Keith and C El Adlouni and A L Glasser and G Mack and G Dirheimer and J Desgres},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8628682},
isbn = {8628682},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {8},
pages = {1489-1496},
abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.},
note = {0305-1048
Journal Article},
keywords = {Amino Acyl/*chemistry/isolation & purification Support, Animals Base Sequence Borohydrides/chemistry Cattle Cytidine/*analogs & derivatives/chemistry/isolation & purification Cytoplasm Hela Cells Human Liver/*chemistry Mass Fragmentography Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 11, p. 5572-5577, 1996, ISBN: 8643617, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support
@article{,
title = {A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 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=8643617},
isbn = {8643617},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {11},
pages = {5572-5577},
abstract = {RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.},
note = {0027-8424
Journal Article},
keywords = {Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of retroviral genomic RNAs: structural and functional implications Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 639-653, 1996, ISBN: 8955907, (0300-9084 Journal Article Review Review, Academic).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis
@article{,
title = {Dimerization of retroviral genomic RNAs: structural and functional implications},
author = {J C Paillart and R Marquet and E Skripkin and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955907},
isbn = {8955907},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {639-653},
abstract = {Retroviruses are a family of widespread small animal viruses at the origin of a diversity of diseases. They share common structural and functional properties such as reverse transcription of their RNA genome and integration of the proviral DNA into the host genome, and have the particularity of packaging a diploid genome. The genome of all retroviruses is composed of two homologous RNA molecules that are non-covalently linked near their 5' end in a region called the dimer linkage structure (DLS). There is now considerable evidence that a specific site (or sites) in the 5' leader region of all retroviruses, located either upstream or/and downstream of the major splice donor site, is involved in the dimer linkage. For MoMuLV and especially HIV-1, it was shown that dimerization is initiated at a stem-loop structure named the dimerization initiation site (DIS). The DIS of HIV-1 and related regions in other retroviruses corresponds to a highly conserved structure with a self-complementary loop sequence, that is involved in a typical loop-loop 'kissing' complex which can be further stabilized by long distance interactions or by conformational rearrangements. RNA interactions involved in the viral RNA dimer were postulated to regulate several key steps in retroviral cycle, such as: i) translation and encapsidation: the arrest of gag translation imposed by the highly structured DLS-encapsidation signal would leave the RNA genome available for the encapsidation machinery; and ii) recombination during reverse transcription: the presence of two RNA molecules in particles would be necessary for variability and viability of virus progeny and the ordered structure imposed by the DLS would be required for efficient reverse transcription.},
note = {0300-9084
Journal Article
Review
Review, Academic},
keywords = {Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis Article de journal
Dans: J Virol, vol. 70, no. 12, p. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome
@article{,
title = {A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis},
author = {J C Paillart and L Berthoux and M Ottmann and J L Darlix and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8970954},
isbn = {8970954},
year = {1996},
date = {1996-01-01},
journal = {J Virol},
volume = {70},
number = {12},
pages = {8348-8354},
abstract = {In retroviruses, the genomic RNA is in the form of a 60S-70S complex composed of two identical genome-length RNA molecules tightly associated through numerous interactions. A major interaction, called the dimer linkage structure, has been found near the RNA 5' end and is probably involved in the control of translation, packaging, and recombination during proviral DNA synthesis. Recently, a small sequence corresponding to a stem-loop structure located in the 5' leader of human immunodeficiency virus type 1 (HIV-1) RNA was found to be required for the initiation of HIV-1 RNA dimerization in vitro and named the dimerization initiation site (E. Skripkin, J.-C. Paillart, R. Marquet, B. Ehresmann, and C. Ehresmann, Proc. Natl. Acad. Sci. USA 91: 4945-4949, 1994). To investigate the possible role of this 5' stem-loop in HIV-1 virion formation and infectivity, four mutant viruses were generated and analyzed in vivo. Results show that deletion of the stem-loop structure reduces infectivity by a factor of 10(3) whereas loop substitutions cause a decrease of 10- to 100-fold. The level of genomic RNA packaging was found to be decreased fivefold in mutants virions containing the stem-loop deletion and only twofold in the loop-substituted virions. Surprisingly, the second DNA strand transfer during reverse transcription was found to be severely impaired upon stem-loop deletion. Taken together, these results indicate that the stem-loop structure called the dimerization initiation site is a cis element acting on both genomic RNA packaging and synthesis of proviral DNA.},
note = {0022-538x
Journal Article},
keywords = {Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome},
pubstate = {published},
tppubtype = {article}
}
Mazauric M H, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D
Dans: Eur J Biochem, vol. 241, no. 3, p. 814-826, 1996, ISBN: 8944770, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN
@article{,
title = {An example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus},
author = {M H Mazauric and J Reinbolt and B Lorber and C Ebel and G Keith and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8944770},
isbn = {8944770},
year = {1996},
date = {1996-01-01},
journal = {Eur J Biochem},
volume = {241},
number = {3},
pages = {814-826},
abstract = {Glycyl-tRNA synthetase (Gly-tRNA synthetase) from Thermus thermophilus was purified to homogeneity and with high yield using a five-step purification procedure in amounts sufficient to solve its crystallographic structure [Logan, D.T., Mazauric, M.-H., Kern, D. & Moras, D. (1995) EMBO J. 14, 4156-4167]. Molecular-mass determinations of the native and denatured protein indicate an oligomeric structure of the alpha 2 type consistent with that found for eukaryotic Gly-tRNA synthetases (yeast and Bombyx mori), but different from that of Gly-tRNA synthetases from mesophilic prokaryotes (Escherichia coli and Bacillus brevis) which are alpha 2 beta 2 tetramers. N-terminal sequencing of the polypeptide chain reveals significant identity, reaching 50% with those of the eukaryotic enzymes (B. mori, Homo sapiens, yeast and Caenorhabditis elegans) but no significant identity was found with both alpha and beta chains of the prokaryotic enzymes (E. coli, Haemophilus influenzae and Coxiella burnetii) albeit the enzyme is deprived of the N-terminal extension characterizing eukaryotic synthetases. Thus, the thermophilic Gly-tRNA synthetase combines strong structural homologies of eukaryotic Gly-tRNA synthetases with a feature of prokaryotic synthetases. Heat-stability measurements show that this synthetase keeps its ATP-PPi exchange and aminoacylation activities up to 70 degrees C. Glycyladenylate strongly protects the enzyme against thermal inactivation at higher temperatures. Unexpectedly, tRNA(Gly) does not induce protection. Cross-aminoacylations reveal that the thermophilic Gly-tRNA synthetase charges heterologous E. coli tRNA(gly(GCC)) and tRNA(Gly(GCC)) and yeast tRNA(Gly(GCC)) as efficiently as T. thermophilus tRNA(Gly). All these aminoacylation reactions are characterized by similar activation energies as deduced from Arrhenius plots. Therefore, contrary to the E. coli and H. sapiens Gly-tRNA synthetases, the prokaryotic thermophilic enzyme does not possess a strict species specificity. The results are discussed in the context of the three-dimensional structure of the synthetase and in the view of the particular evolution of the glycinylation systems.},
note = {0014-2956
Journal Article},
keywords = {Amino Acid Species Specificity Substrate Specificity Support, Amino Acid Sequence Comparative Study Enzyme Stability Eukaryotic Cells Glycine-tRNA Ligase/chemistry/*isolation & purification/metabolism Heat Kinetics Molecular Sequence Data Molecular Weight Prokaryotic Cells Protein Conformation RNA, Gly/metabolism Sequence Analysis Sequence Homology, Non-U.S. Gov't Thermodynamics Thermus thermophilus/*enzymology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization. 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. 61-72, Adenine Press, 1996.
Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@inbook{,
title = {Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization.},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books?hl=fr&id=SOpqAAAAMAAJ&q=Marquet#search_anchor},
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 = {61-72},
publisher = {Adenine Press},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Marquet R
L'initiation de la transcription inverse du HIV-1: spécificités structurales et fonctionelles. Article de journal
Dans: Regard sur la Biochimie, vol. 4, p. 62-69, 1996, ISSN: 0336-1640.
Liens | BibTeX | Étiquettes: MARQUET, Unité ARN, Virus HIV1 Transcription inverse Initiation transcription Article synthèse Virus immunodéficience humaine Lentivirinae Retroviridae Virus
@article{,
title = {L'initiation de la transcription inverse du HIV-1: spécificités structurales et fonctionelles.},
author = {R Marquet},
url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=2524109},
issn = {0336-1640},
year = {1996},
date = {1996-01-01},
journal = {Regard sur la Biochimie},
volume = {4},
pages = {62-69},
keywords = {MARQUET, Unité ARN, Virus HIV1 Transcription inverse Initiation transcription Article synthèse Virus immunodéficience humaine Lentivirinae Retroviridae Virus},
pubstate = {published},
tppubtype = {article}
}
Malmgren C, Engdahl H M, Romby P, Wagner E G
An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1 Article de journal
Dans: RNA, vol. 2, no. 10, p. 1022-1032, 1996, ISBN: 8849778, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1},
author = {C Malmgren and H M Engdahl and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8849778},
isbn = {8849778},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {10},
pages = {1022-1032},
abstract = {Antisense RNAs in prokaryotic systems often inhibit translation of mRNAs. In some cases, this involves sequestration of Shine-Dalgarno (SD) sequences and start codons. In other cases, antisense/target RNA duplexes do not overlap these signals, but form upstream. We have performed toeprinting analyses on repA mRNA of plasmid R1, both free and in duplex with the antisense RNA, CopA. An intermolecular RNA duplex 2 nt upstream of the tap SD prevents ribosome binding. An intrastrand stem-loop at this location yields the same inhibition. Thus, stable secondary structures immediately upstream of the tap SD sequence inhibit translation, as shown by toeprinting in vitro and repA-lacZ expression in vivo. Previous work showed that repA (initiator protein) expression requires tap (leader peptide) translation. Toeprinting data confirm that the tap ribosome binding site (RBS) is accessible, whereas the repA RBS, which is sequestered by a stable stem-loop, is weakly recognized by the ribosome. Truncated CopA RNA (CopI) is unable to pair completely with target RNA, but proceeds normally to a kissing intermediate. This mutant RNA species inhibits repA expression in vivo. By a kinetic toeprint inhibition protocol, we have shown that the structure of the kissing complex is sufficient to sterically prevent ribosome binding. These results are discussed in comparison with the effect of RNA structures elsewhere in the ribosome-binding region of an mRNA.},
note = {1355-8382
Journal Article},
keywords = {Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Louise-May S, Auffinger P, Westhof E
Calculations of nucleic acid conformations Article de journal
Dans: Curr Opin Struct Biol, vol. 6, no. 3, p. 289-298, 1996, ISBN: 8804831, (0959-440x Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: DNA/chemistry DNA, Molecular *Nucleic Acid Conformation Nucleic Acid Hybridization Nucleosides/chemistry Protein Binding RNA/chemistry Telomere/chemistry, Superhelical/chemistry *Genetic Techniques Models, Unité ARN
@article{,
title = {Calculations of nucleic acid conformations},
author = {S Louise-May and P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8804831},
isbn = {8804831},
year = {1996},
date = {1996-01-01},
journal = {Curr Opin Struct Biol},
volume = {6},
number = {3},
pages = {289-298},
abstract = {The present computational power and sophistication of theoretical approaches to nucleic acid structural investigation are sufficient for the realization of static and dynamic models that correlate accurately with current crystallographic, NMR and solution-probing structural data, and consequently are able to provide valuable insights and predictions for a variety of nucleic acid conformational families. In molecular dynamics simulations, the year 1995 was marked by the foray of fast Ewald methods, an accomplishment resulting from several years' work in the search for an adequate treatment of the electrostatic long-range forces so primordial in nucleic acid behavior. In very large systems, and particularly in the RNA-folding field, techniques originating from artificial intelligence research, like constraint satisfaction programming or genetic algorithms, have established their utility and potential.},
note = {0959-440x
Journal Article
Review
Review, Tutorial},
keywords = {DNA/chemistry DNA, Molecular *Nucleic Acid Conformation Nucleic Acid Hybridization Nucleosides/chemistry Protein Binding RNA/chemistry Telomere/chemistry, Superhelical/chemistry *Genetic Techniques Models, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lorber B, Jenner G, Giege R
Effect of high hydrostatic pressure on nucleation and growth of protein crystals Article de journal
Dans: J Crystal Growth, vol. 158, no. 1-2, p. 103-117, 1996, ISBN: 10.1016/0022-0248(95)00399-1.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Effect of high hydrostatic pressure on nucleation and growth of protein crystals},
author = {B Lorber and G Jenner and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/0022024895003991},
isbn = {10.1016/0022-0248(95)00399-1},
year = {1996},
date = {1996-01-01},
journal = {J Crystal Growth},
volume = {158},
number = {1-2},
pages = {103-117},
abstract = {The influence of hydrostatic pressure on the nucleation and growth of protein crystals was studied. A micromethod was developed to establish a solubility phase diagram of hen egg-white lysozyme as a function of pressure and protein concentration. The pressure dependence of the formation of canonical tetragonal crystals was investigated at different precipitating agent and protein concentrations (in the range 0.61.2M NaCl and 1035 mg/ml lysozyme). The apparent protein solubility significantly increases when pressure is raised from 0.1 MPa (atmospheric pressure) to 250 MPa. With an increase in pressure, the size and number of lysozyme crystals decline and a transition to urchin-like particles made of crystalline needles progressively occurs. The shape of tetragonal crystals becomes more elongated in a limited region of the phase diagram as indicated by the ratio of the lengths of the (110) and (101) faces. Single tetragonal crystals grown under high pressure diffract X-rays at high resolution. They belong to the same space group and have identical cell parameters as control crystals grown at atmospheric pressure. Changes in solubility and crystallizability are explained by pressure-induced minor reversible alterations in the protein structure.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lorber B, Giege R
Containerless protein crystallization in floating drops: application to crystal growth monitoring under reduced nucleation conditions Article de journal
Dans: J Crystal Growth, vol. 168, no. 1-4, p. 204-215, 1996, ISBN: 10.1016/0022-0248(96)00356-9.
Résumé | Liens | BibTeX | Étiquettes: * Protein crystallization * Heterogeneous nucleation * Growth kinetics * Instrumentation, Unité ARN
@article{,
title = {Containerless protein crystallization in floating drops: application to crystal growth monitoring under reduced nucleation conditions},
author = {B Lorber and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/0022024896003569},
isbn = {10.1016/0022-0248(96)00356-9},
year = {1996},
date = {1996-01-01},
journal = {J Crystal Growth},
volume = {168},
number = {1-4},
pages = {204-215},
abstract = {A micromethod was developed for the batch crystallization of proteins under conditions were the solution has no contact with the container walls. Drops of crystallization solutions (5 to 100 μl) are placed at the interface between two layers of inert and non-miscible silicone fluids contained in square glass or plastic cuvettes. The densities of the fluids are either lower or higher than those of the major precipitating agents of macromolecules, including aqueous solutions containing salts, polyethylene glycols or alcohols. Several proteins and a spherical plant virus were crystallized in the temperature range 4°C20°C using this set-up. A thermostated device was built for the dynamic control of the temperature of crystallization drops and the monitoring of crystal growth by video-microscopy. In all cases, the habit of the crystals grown in floating drops are identical to those of controls grown in sealed glass tubes without silicone fluid. The comparison of the number of crystals in drops kept under one layer of fluid and in floating drops of the same volume indicates that heterogeneous nucleation is minimized when protein crystallization is performed in floating drops. The advantages and limitations of this novel containerless crystallization method are discussed.},
keywords = {* Protein crystallization * Heterogeneous nucleation * Growth kinetics * Instrumentation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lehnert V, Jaeger L, Michel F, Westhof E
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme Article de journal
Dans: Chem Biol, vol. 3, no. 12, p. 993-1009, 1996, ISBN: 9000010, (1074-5521 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Composition Base Sequence Electrophoresis, Catalytic/*chemistry Sequence Alignment Support, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation RNA/chemistry/metabolism RNA Splicing/*genetics RNA, Non-U.S. Gov't Tetrahymena thermophila/*metabolism, Polyacrylamide Gel Ferrous Compounds/metabolism/pharmacology Introns/*genetics Models, Unité ARN
@article{,
title = {New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme},
author = {V Lehnert and L Jaeger and F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9000010},
isbn = {9000010},
year = {1996},
date = {1996-01-01},
journal = {Chem Biol},
volume = {3},
number = {12},
pages = {993-1009},
abstract = {BACKGROUND: Group I introns self-splice via two consecutive trans-esterification reactions in the presence of guanosine cofactor and magnesium ions. Comparative sequence analysis has established that a catalytic core of about 120 nucleotides is conserved in all known group I introns. This core is generally not sufficient for activity, however, and most self-splicing group I introns require non-conserved peripheral elements to stabilize the complete three-dimensional (3D) structure. The physico-chemical properties of group I introns make them excellent systems for unraveling the structural basis of the RNA-RNA interactions responsible for promoting the self-assembly of complex RNAs. RESULTS: We present phylogenetic and experimental evidence for the existence of three additional tertiary base pairings between hairpin loops within peripheral components of subgroup IC1 and ID introns. Each of these new long range interactions, called P13, P14 and P16, involves a terminal loop located in domain 2. Although domains 2 of IC and ID introns share very strong sequence similarity, their terminal loops interact with domains 5 and 9 (subgroup IC1) and domain 6 (subgroup ID). Based on these tertiary contacts, comparative sequence analysis, and published experimental results such as Fe(II)-EDTA protection patterns, we propose 3D models for two entire group I introns, the subgroup IC1 intron in the large ribosomal precursor RNA of Tetrahymena thermophila and the SdCob.1 subgroup ID intron found in the cytochrome b gene of Saccharomyces douglasii. CONCLUSIONS: Three-dimensional models of group I introns belonging to four different subgroups are now available. They all emphasize the modular and hierarchical organization of the architecture of group I introns and the widespread use of base-pairings between terminal hairpin loops for stabilizing the folded and active structures of large and complex RNA molecules.},
note = {1074-5521
Journal Article},
keywords = {Animals Base Composition Base Sequence Electrophoresis, Catalytic/*chemistry Sequence Alignment Support, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation RNA/chemistry/metabolism RNA Splicing/*genetics RNA, Non-U.S. Gov't Tetrahymena thermophila/*metabolism, Polyacrylamide Gel Ferrous Compounds/metabolism/pharmacology Introns/*genetics Models, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Ehresmann C, Grice S F Le, Ehresmann B, Marquet R
Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription Article de journal
Dans: EMBO J, vol. 15, no. 24, p. 7178-7187, 1996, ISBN: 9003793, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN
@article{,
title = {Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription},
author = {J M Lanchy and C Ehresmann and S F Le Grice and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9003793},
isbn = {9003793},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {24},
pages = {7178-7187},
abstract = {We recently showed that primer tRNA3Lys, human immunodeficiency virus type 1 (HIV-1) RNA and HIV-1 reverse transcriptase (RT) form a specific complex of initiation of reverse transcription that can be functionally distinguished from the elongation complex, which can be obtained by substituting an 18mer oligodeoxyribonucleotide (ODN) for the natural primer (Isel et al., 1996). Here, we compared the binding properties and the single and multiple turnover kinetics of HIV-1 RT in the initiation and elongation complexes. Even though the equilibrium dissociation constants of HIV-1 RT are not very different for the two complexes, RT dissociates approximately 200-fold faster from the initiation complex. Furthermore, nucleotide incorporation by the pre-formed primer-template-RT complexes is reduced by a approximately 50-fold factor during initiation of reverse transcription, compared with elongation. As a consequence, processivity of HIV-1 RT in the initiation complex is close to unity, while it increases by four orders of magnitude during elongation, as expected for a replication enzyme. This processivity change is reminiscent of the transition from initiation to elongation of transcription. Furthermore, our results indicate that the post-transcriptional modifications of tRNA3Lys play a role similar to that of the sigma factor in transcription by the Escherichia coli RNA polymerase: they favour the formation of the specific initiation complex but do not affect the polymerization rate of the bound enzyme.},
note = {0261-4189
Journal Article},
keywords = {DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Jaeger L, Westhof E, Michel F
Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron Article de journal
Dans: Biochimie, vol. 78, no. 6, p. 466-473, 1996, ISBN: 8915536, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alternative Splicing/*genetics Base Sequence Cytochrome b Group/genetics Electrophoresis, Genetic/genetics, Genetic/genetics Transcription, Molecular Molecular Sequence Data Mutation/genetics *Nucleic Acid Conformation RNA Precursors/metabolism RNA Splicing/genetics Saccharomyces/*metabolism Suppression, Polyacrylamide Gel Introns/genetics Mitochondria/metabolism Models, Unité ARN
@article{,
title = {Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron},
author = {L Jaeger and E Westhof and F Michel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8915536},
isbn = {8915536},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {6},
pages = {466-473},
abstract = {Like most mitochondrial group I introns with a free-standing open reading frame (ORF) located downstream of their catalytic core, the Sd.cob, 1 intron in the gene coding for the cytochrome b of Saccharomyces douglasii mitochondria possesses a putative proximal 3' splice site. However, incubation of Sd.cob, 1 preRNA transcripts under optimal in vitro splicing conditions essentially results in splicing at the authentic, distal 3' splice junction. The mechanism by which the proximal splicing event is suppressed in vitro involves formation of a tertiary interaction which is only found in the Sd.cob, 1 intron. Core nucleotides located in loop L5 block proximal splicing by forming Watson-Crick base pairs with the nucleotide sequence of the proximal 3' splice site. This tertiary base pairing, also important for the folding of the intron into an active conformation, may be regarded as equivalent to the L9/P5, GNRA-loop/helix interaction found in more than one-third of known group I introns.},
note = {0300-9084
Journal Article},
keywords = {Alternative Splicing/*genetics Base Sequence Cytochrome b Group/genetics Electrophoresis, Genetic/genetics, Genetic/genetics Transcription, Molecular Molecular Sequence Data Mutation/genetics *Nucleic Acid Conformation RNA Precursors/metabolism RNA Splicing/genetics Saccharomyces/*metabolism Suppression, Polyacrylamide Gel Introns/genetics Mitochondria/metabolism Models, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Ehresmann B, Marquet R
Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 11-19, 1996, ISBN: 8786994, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding},
author = {C Isel and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8786994},
isbn = {8786994},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {11-19},
abstract = {RNAs play a crucial and central role in a large variety of biological functions obviously linked to the wide variety of structures that they can adopt. Understanding the function of RNAs thus requires the knowledge of their two- and three-dimensional structures. We describe in detail the way to access the secondary structure of RNAs, by combining sequence comparison, secondary structure prediction by computer and, mainly, experimental data obtained by probing with chemicals and ribonucleases. These approaches were used to investigate secondary structure of the region containing the primer binding site of HIV-1 genomic RNA either free or involved in the binary complex with the replication primer tRNA(3Lys).},
note = {0031-6865
Journal Article},
keywords = {Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
Hubert N, Walczak R, Carbon P, Krol A
A protein binds the selenocysteine insertion element in the 3'-UTR of mammalian selenoprotein mRNAs Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 464-469, 1996, ISBN: 8602359, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Protein Binding Proteins/*genetics/metabolism RNA, Genetic, Messenger/genetics/*metabolism Rats Selenocysteine/genetics/*metabolism Support, Non-U.S. Gov't Translation, Unité ARN
@article{,
title = {A protein binds the selenocysteine insertion element in the 3'-UTR of mammalian selenoprotein mRNAs},
author = {N Hubert and R Walczak and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602359},
isbn = {8602359},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {464-469},
abstract = {Several gene products are involved in co-translational insertion of selenocysteine by the tRNA(Sec). In addition, a stem-loop structure in the mRNAs coding for selenoproteins is essential to mediate the selection of the proper selenocysteine UGA codon. Interestingly, in eukaryotic selenoprotein mRNAs, this stem-loop structure, the selenocysteine insertion sequence (SECIS) element, resides in the 3'-untranslated region, far downstream of the UGA codon. In view of unravelling the underlying complex mechanism, we have attempted to detect RNA-binding proteins with specificity for the SECIS element. Using mobility shift assays, we could show that a protein, present in different types of mammalian cell extracts, possesses the capacity of binding the SECIS element of the selenoprotein glutathione peroxidase (GPx) mRNA. We have termed this protein SBP, for Secis Binding Protein. Competition experiments attested that the binding is highly specific and UV cross-linking indicated that the protein has an apparent molecular weight in the range of 60-65 kDa. Finally, some data suggest that the SECIS elements in the mRNAs of GPx and another selenoprotein, type I iodothyronine 5' deiodinase, recognize the same SBP protein. This constitutes the first report of the existence of a 3' UTR binding protein possibly involved in the eukaryotic selenocysteine insertion mechanism.},
note = {0305-1048
Journal Article},
keywords = {Animals Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Protein Binding Proteins/*genetics/metabolism RNA, Genetic, Messenger/genetics/*metabolism Rats Selenocysteine/genetics/*metabolism Support, Non-U.S. Gov't Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Grosjean H, Edqvist J, Straby K B, Giege R
Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture Article de journal
Dans: J Mol Biol, vol. 255, no. 1, p. 67-85, 1996, ISBN: 8568876, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Isomerases/metabolism Microinjections Molecular Sequence Data Mutation *Nucleic Acid Conformation Oocytes Pentosyltransferases/metabolism RNA Processing, Asp/*chemistry/metabolism Ribonucleosides/biosynthesis/*metabolism Support, Non-U.S. Gov't Xenopus laevis tRNA Methyltransferases/*metabolism, Post-Transcriptional/*physiology RNA, Transfer, Unité ARN
@article{,
title = {Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture},
author = {H Grosjean and J Edqvist and K B Straby and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8568876},
isbn = {8568876},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {255},
number = {1},
pages = {67-85},
abstract = {Information is still quite limited concerning the structural requirements in tRNA molecules for their post-transcriptional maturation by base and ribose modification enzymes. To address this question, we have chosen as the model system yeast tRNAAsp that has a known three-dimensional structure and the in vivo modifying machinery of the Xenopus laevis oocyte able to act on microinjected tRNA precursors. We have systematically compared the modification pattern of wild-type tRNAAsp with that of a series of structural mutants (21 altogether) altered at single or multiple positions in the D-, T-and the anticodon branch, as well as in the variable region. The experimental system allowed us to analyze the effects of structural perturbations in tRNA on the enzymatic formation of modified nucleosides at 12 locations scattered over the tRNA cloverleaf. We found that the formation of m1G37 and psi 40 in the anticodon loop and stem and psi 13 in the D-stem, were extremely sensitive to 3D perturbations. In contrast, the formation of T54, psi 55 and m1A58 in the T-loop, m5C49 in the T-stem and m2G6 in the amino acid accepting stem were essentially insensitive to change in the overall tRNA architecture; these modified nucleosides were also formed in appropriate minimalist (stems and loops) tRNA domains. The formation of m2G26 at the junction between the anticodon and the D-stem, of Q34 and manQ34 in the anticodon loop were sensitive only to drastic structural perturbation of the tRNA. Altogether, these results reflect the existence of different modes of tRNA recognition by the many different modifying enzymes. A classification of this family of maturation enzymes into two major groups, according to their sensitivities to structural perturbations in tRNA, is proposed.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Isomerases/metabolism Microinjections Molecular Sequence Data Mutation *Nucleic Acid Conformation Oocytes Pentosyltransferases/metabolism RNA Processing, Asp/*chemistry/metabolism Ribonucleosides/biosynthesis/*metabolism Support, Non-U.S. Gov't Xenopus laevis tRNA Methyltransferases/*metabolism, Post-Transcriptional/*physiology RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gotte M, Marquet R, Isel C, Anderson V E, Keith G, Gross H J, Ehresmann C, Ehresmann B, Heumann H
Probing the higher order structure of RNA with peroxonitrous acid Article de journal
Dans: FEBS Lett, vol. 390, no. 2, p. 226-228, 1996, ISBN: 8706865, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Probing the higher order structure of RNA with peroxonitrous acid},
author = {M Gotte and R Marquet and C Isel and V E Anderson and G Keith and H J Gross and C Ehresmann and B Ehresmann and H Heumann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8706865},
isbn = {8706865},
year = {1996},
date = {1996-01-01},
journal = {FEBS Lett},
volume = {390},
number = {2},
pages = {226-228},
abstract = {Potassium peroxonitrite (ONOOK) and [Fe(EDTA)]2- were used to analyze the influence of chemically entirely different hydroxyl radical sources on tRNA cleavage profiles. [Fe(EDTA)]2- gives rise to hydroxyl radicals via a Fenton-like reaction during the oxidation of chelated Fe2+, while ONOOK generates hydroxyl radicals via its conjugate acid (ONOOH) when adding a stable alkaline solution of ONOOK in samples buffered at neutral pH. [Fe(EDTA)]2- is known to induce oxidative strand scission at sugar moieties thought to be solvent accessible, while those residues located in the 'inside' of structured RNAs are protected. Although ONOOH is neutral and significantly smaller than the metal complex, both reagents generate the same protection pattern on tRNAs, suggesting that access of the commonly formed hydroxyl radical, rather than access of its source, is the determining factor when probing the higher order structure of RNA. Strong difference in reactivity is only seen at the modified 2-thiouridine S34 of tRNA(Lys3) which shows hyperreactivity towards ONOOK treatment. This particular reaction may require interaction between the peroxonitrite anion and the thiocarbonyl group of the base, since hyperreactivity is not observed when probing the dethiolated tRNA(Lys3).},
note = {0014-5793
Journal Article},
keywords = {Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R, Florentz C, Kern D, Gangloff J, Eriani G, Moras D
Aspartate identity of transfer RNAs Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 605-623, 1996, ISBN: 8955904, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN
@article{,
title = {Aspartate identity of transfer RNAs},
author = {R Giege and C Florentz and D Kern and J Gangloff and G Eriani and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955904},
isbn = {8955904},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {605-623},
abstract = {Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R
Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 22, p. 12078-12081, 1996, ISBN: 8901535, (0027-8424 Comment Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: Amino Acyl/*physiology RNA, Base Sequence Evolution, Genetic Molecular Sequence Data Peptide Elongation Factors/metabolism Plant Viruses/*genetics RNA, Genetic Virus Replication, Molecular Models, Transfer, Unité ARN, Viral/biosynthesis Translation
@article{,
title = {Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries},
author = {R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8901535},
isbn = {8901535},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {22},
pages = {12078-12081},
note = {0027-8424
Comment
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acyl/*physiology RNA, Base Sequence Evolution, Genetic Molecular Sequence Data Peptide Elongation Factors/metabolism Plant Viruses/*genetics RNA, Genetic Virus Replication, Molecular Models, Transfer, Unité ARN, Viral/biosynthesis Translation},
pubstate = {published},
tppubtype = {article}
}
Friant S, Heyman T, Wilhelm M L, Wilhelm F X
Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 441-449, 1996, ISBN: 8602356, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA/genetics/*metabolism RNA, Met/genetics/*metabolism Retroelements/*genetics Saccharomyces cerevisiae Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon},
author = {S Friant and T Heyman and M L Wilhelm and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602356},
isbn = {8602356},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {441-449},
abstract = {Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA/genetics/*metabolism RNA, Met/genetics/*metabolism Retroelements/*genetics Saccharomyces cerevisiae Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, Giege R, Westhof E
A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA Article de journal
Dans: RNA, vol. 2, no. 3, p. 201-212, 1996, ISBN: 8608444, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support
@article{,
title = {A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608444},
isbn = {8608444},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {3},
pages = {201-212},
abstract = {A three-dimensional model of the histidylable 3'-terminal tRNA-like domain of tobacco mosaic virus RNA is proposed on the basis of a comparative structural analysis, chemical and enzymatic probing, combined with graphical modeling of three RNA constructs of increasing size (38, 108, and 182 nt) derived from the 3'-terminal viral RNA sequence. The comparison between the probing patterns of the three RNAs allowed the determination of the relative orientation of these structural domains in the full-length viral tRNA-like structure. Modeling data indicate that only one of the two possible isomers of the three-way junction located at a central position of the tRNA-like domain is in agreement with structural data. Interestingly, this isomer gives rise to a molecule bearing a structural mimicry with the L-shape of canonical tRNAs. A pseudoknotted acceptor branch containing a T-like loop is located perpendicularly to an anticodon-like branch. Moreover, a single-stranded RNA stretch belonging to the pseudoknotted central core mimics a D-like loop and it is proposed that it interacts via two conserved guanosines with nucleotides of the T-like loop as found in canonical tRNAs. This model is valid for the 3' noncoding regions of tobamoviral RNAs as well as for the tRNA-like domain of the satellite tobacco mosaic virus RNA. All three molecules are substrates for yeast HisRS; however, whereas the complete viral genome is required for optimal histidylation capacities, both charging levels and affinity constants are decreased for the three RNA transcripts, suggesting that additional contacts located outside the tRNA-like domain are needed for an optimal aminoacylation process.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Caprara M G, Lehnert V, Lambowitz A M, Westhof E
A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core Article de journal
Dans: Cell, vol. 87, no. 6, p. 1135-1145, 1996, ISBN: 8978617, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN
@article{,
title = {A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core},
author = {M G Caprara and V Lehnert and A M Lambowitz and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8978617},
isbn = {8978617},
year = {1996},
date = {1996-01-01},
journal = {Cell},
volume = {87},
number = {6},
pages = {1135-1145},
abstract = {The Neurospora crassa mitochondrial (mt) tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns, in addition to aminoacylating tRNA(Tyr). Here, we compared the CYT-18 binding sites in the N. crassa mt LSU and ND1 introns with that in N. crassa mt tRNA(Tyr) by constructing three-dimensional models based on chemical modification and RNA footprinting data. Remarkably, superimposition of the CYT-18 binding sites in the model structures revealed an extended three-dimensional overlap between the tRNA and the group I intron catalytic core. Our results provide insight into how an RNA-splicing factor can evolve from a cellular RNA-binding protein. Further, the structural similarities between group I introns and tRNAs are consistent with an evolutionary relationship and suggest a general mechanism for the evolution of complex catalytic RNAs.},
note = {0092-8674
Journal Article},
keywords = {Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Boeglin M, Dock-Brégeon A C, Eriani G, Gangloff J, Ruff M, Poterszman A, Thierry J C, Moras D
Crystallization of Escherichia coli aspartyl-tRNA synthetase in its free state and in a complex with yeast tRNA(Asp). Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 52, no. Pt 1, p. 211-214, 1996, ISBN: 15299749.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{,
title = {Crystallization of Escherichia coli aspartyl-tRNA synthetase in its free state and in a complex with yeast tRNA(Asp).},
author = {M Boeglin and A C Dock-Brégeon and G Eriani and J Gangloff and M Ruff and A Poterszman and J C Thierry and D Moras},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15299749},
isbn = {15299749},
year = {1996},
date = {1996-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {52},
number = {Pt 1},
pages = {211-214},
abstract = {Overexpressed dimeric E. coli aspartyl-tRNA synthetase (AspRS) has been crystallized in its free state and complexed with yeast tRNA(Asp). Triclinic crystals of the enzyme alone (a = 104.4},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Benard L, Philippe C, Ehresmann B, Ehresmann C, Portier C
Pseudoknot and translational control in the expression of the S15 ribosomal protein Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 568-576, 1996, ISBN: 8955900, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data Nucleic Acid Conformation Ribosomal Proteins/*biosynthesis/chemistry/genetics/metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't *Translation, Unité ARN
@article{,
title = {Pseudoknot and translational control in the expression of the S15 ribosomal protein},
author = {L Benard and C Philippe and B Ehresmann and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955900},
isbn = {8955900},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {568-576},
abstract = {Translational autocontrol of the expression of the ribosomal protein S15 proceeds through the transitory formation of a pseudoknot. A synopsis of the known data is used to propose a molecular model of the mechanism involved and for the role of the pseudoknot. This latter structure is able to recruit 30S ribosomal subunits to initiate translation, but also to bind S15 and to stop translation by trapping the ribosome on its loading site. Information on the S15 protein recognition of the messenger RNA site was deduced from mutational analyses and chemical probing. A comparison of this messenger site with the S15 ribosomal binding site was conducted by analysing hydroxyl radical footprintings of these two sites. The existence of two subsites in 16S RNA suggests that the ribosomal protein S15 might present either two different binding sites or at least one common subsite. Clues for the presence of a common site between the messenger and 16S RNA are given which cannot rule out that recognition specificity is linked to a few other determinants. Whether these determinants are different or not remains an open question.},
note = {0300-9084
Journal Article},
keywords = {Base Sequence Molecular Sequence Data Nucleic Acid Conformation Ribosomal Proteins/*biosynthesis/chemistry/genetics/metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't *Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Becker H D, Giege R, Kern D
Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus Article de journal
Dans: Biochemistry, vol. 35, no. 23, p. 7447-7458, 1996, ISBN: 8652522, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN
@article{,
title = {Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus},
author = {H D Becker and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8652522},
isbn = {8652522},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {23},
pages = {7447-7458},
abstract = {The aspartate identity of tRNA for AspRS from Thermus thermophilus has been investigated by kinetic analysis of the aspartylation reaction of different tRNA molecules and their variants as well as of tRNAPhe variants with transplanted aspartate identity elements. It is shown that G10, G34, U35, C36, C38, and G73 determine recognition and aspartylation of yeast and T.thermophilus tRNA(Asp) by the thermophilic AspRS. This set of nucleotides specifies also tRNA aspartylation in the homologous yeast and Escherichia coli systems. Structural considerations indicate that the major aspartate identity elements interact with amino acids conserved in all AspRSs. It follows that the structural features of tRNA and synthetase specifying aspartylation are mainly conserved in various structural contexts and in organisms adapted to different life conditions. Mutations of tRNA identity elements provoke drastic losses of charging in the heterologous system involving yeast tRNA(Asp) and T. thermophilus AspRS. In the homologous systems, the mutational effects are less pronounced. However, effects in E. coli and T. thermophilus exceed those in yeast which are particularly moderate, indicating variations in the individual contributions of identity elements for aspartylation in prokaryotes and eukaryotes. Analysis of multiple tRNA mutants reveals cooperativity between the cluster of determinants of the anticodon loop and the additional determinants G10 and G73 for efficient aspartylation in the thermophilic system, suggesting that conformational changes trigger formation of the functional tRNA/synthetase complex.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Westhof E
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations Article de journal
Dans: Biophys J, vol. 71, no. 2, p. 940-954, 1996, ISBN: 8842234, (0006-3495 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8842234},
isbn = {8842234},
year = {1996},
date = {1996-01-01},
journal = {Biophys J},
volume = {71},
number = {2},
pages = {940-954},
abstract = {Multiple molecular dynamics trajectories of the solvated and neutralized 17-residue tRNA(Asp) anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16-A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base pairs, the noncanonical G30-U40 "wobble" base pair, and the psi 32-C38 pseudo-base pair is presented as well as that of two C--H. O hydrogen bonds found to contribute to the array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biological function. The set of multiple molecular dynamics trajectories obtained does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.},
note = {0006-3495
Journal Article},
keywords = {Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Louise-May S, Westhof E
Molecular Dynamics Simulations of the Anticodon Hairpin of tRNAAsp: Structuring Effects of C−H···O Hydrogen Bonds and of Long-Range Hydration Forces Article de journal
Dans: J Am Chem Soc, vol. 118, no. 5, p. 11811189, 1996.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Molecular Dynamics Simulations of the Anticodon Hairpin of tRNAAsp: Structuring Effects of C−H···O Hydrogen Bonds and of Long-Range Hydration Forces},
author = {P Auffinger and S Louise-May and E Westhof},
url = {http://pubs.acs.org/doi/abs/10.1021/ja952494j?prevSearch=Auffinger&searchHistoryKey=},
doi = {10.1021/ja952494j},
year = {1996},
date = {1996-01-01},
journal = {J Am Chem Soc},
volume = {118},
number = {5},
pages = {11811189},
abstract = {The inclusion of long-range solvent interactions out to 16 Å in a molecular dynamics study of the anticodon loop of tRNAAsp led to an overall structural stabilization of the RNA hairpin tertiary interactions in a set of six independent fully solvated and neutralized 100 ps MD trajectories as compared to a shorter-ranged solvent interaction electrostatic model (8 Å). The increased structural stabilization allowed for the emergence of non-classical C−H···O hydrogen bonds in the MD trajectories. The presence of the C−H···O hydrogen bonds in the crystal structure was subsequently verified and dynamically characterized and their contribution to the preservation of the tertiary native conformation was assessed. The MD trajectories generated using a truncation distance of 16 Å for the electrostatic solute−solvent and solvent−solvent interactions, with no cutoffs applied to the electrostatic solute−solute interactions, compared to an earlier set of eight independent 100 ps MD trajectories using a smaller truncation distance of 8 Å (Auffinger, P.; Louise-May, S.; Westhof, E. J. Am. Chem. Soc. 1995, 117, 6720−6726), revealed an increase in consistency of structural characteristics between individual MD trajectories of a given set and on average a decrease in root-mean-square deviation values from the starting crystal structure. Dihedral transitions in the sugar−phosphate backbone decreased and tertiary interactions specific to the loop topology were better preserved and showed reduced dynamical fluctuation. These results emphasize the important influence of long-ranged solvation forces on the stabilization of the tertiary structure of highly charged nucleic acid systems and signify that long-ranged theoretical models may be necessary for a truly accurate description of biomacromolecular solution structure and dynamics.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Louise-May S, Westhof E
Hydration of C-H groups in tRNA Article de journal
Dans: Faraday Discuss, no. 103, p. 151-173, 1996, ISBN: 9136637, (1359-6640 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Carbon/chemistry Hydrogen/chemistry Models, Non-U.S. Gov't Water/chemistry, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer/*chemistry Support, Unité ARN
@article{,
title = {Hydration of C-H groups in tRNA},
author = {P Auffinger and S Louise-May and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9136637},
isbn = {9136637},
year = {1996},
date = {1996-01-01},
journal = {Faraday Discuss},
number = {103},
pages = {151-173},
abstract = {Molecular dynamic (MD) simulations of the anticodon hairpin of tRNA(Asp) and of the full tRNA, both in a solvent bath with neutralizing NH4+ counter-ions, have been produced with the particle mesh ewald (PME) method and the multiple molecular dynamics (MMD) strategy. The latter consists of generating uncorrelated trajectories starting from the same initial configuration but with a slightly perturbed initial velocity distribution. The 3 ns (six uncorrelated 500 ps MD trajectories) MMD set of the 17 nucleotide anticodon fragment and the single 500 ps trajectory of the 75 nucleotide tRNA were analyzed with the aim of characterizing long lived C-H.Ow interactions for the two main nucleic acid base and ribose C-H bond types. Some C-H sites present very long residence lifetimes for water molecules, especially those around the ribose H(3') and the pyrimidine H(5) atoms. The C(3')-H(3').Ow contacts occur concurrently with the strong hydration of the anionic phosphate oxygen atoms and especially with the water bridges linking successive phosphate groups along the polynucleotide chain. Therefore, these contacts are of opportunistic character and result from the geometries of the covalent structure and adjacent interactions. On the other hand, the pyrimidine H(5) atoms display a hydrophilic character with interaction geometries indicating that water contacts in which they are involved should be considered as bona fide hydrogen bonds.},
note = {1359-6640
Journal Article},
keywords = {Base Sequence Carbon/chemistry Hydrogen/chemistry Models, Non-U.S. Gov't Water/chemistry, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer/*chemistry Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Stetor S R, Li X, Rausch J W, Howard K J, Ehresmann B, North T W, Wohrl B M, Goody R S, Wainberg M A, Grice S F
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 19, p. 10063-10068, 1996, ISBN: 8816751, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support
@article{,
title = {Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases},
author = {E J Arts and S R Stetor and X Li and J W Rausch and K J Howard and B Ehresmann and T W North and B M Wohrl and R S Goody and M A Wainberg and S F Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8816751},
isbn = {8816751},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {19},
pages = {10063-10068},
abstract = {Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Ghosh M, Jacques P S, Ehresmann B, Grice S F Le
Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication Article de journal
Dans: J Biol Chem, vol. 271, no. 15, p. 9054-9061, 1996, ISBN: 8621554, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication},
author = {E J Arts and M Ghosh and P S Jacques and B Ehresmann and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621554},
isbn = {8621554},
year = {1996},
date = {1996-01-01},
journal = {J Biol Chem},
volume = {271},
number = {15},
pages = {9054-9061},
abstract = {The mechanism for the initiation of reverse transcription in human immunodeficiency virus type 1 (HIV-1) was studied utilizing a unique reverse transcriptase (RT) mutant altered in its noncatalytic p51 subunit. This mutant (p66/p51Delta13) retains full DNA- and RNA-dependent DNA polymerase activity but has reduced affinity for tRNA3Lys, the cognate HIV primer. When the ability to support(-)-strand DNA synthesis on a viral RNA template was evaluated, this mutant initiated from an 18-nucleotide (nt) oligoribo- or oligodeoxyribonucleotide primer complementary to the primer binding site (pbs). However, it failed to do so from natural and synthetic versions of tRNA3Lys. tRNA-primed(-)-strand synthesis could, however, be rescued by substituting the 76-nt tRNA3Lys with 81- and 107-nt tRNA-DNA chimeras, i.e. tRNA3Lys extended by 5 and 31 deoxyribonucleotides complementary to the viral genome upstream of the pbs. These findings imply that through interactions involving its p51 subunit, RT may be required to disrupt additional tRNA-viral RNA duplexes outside the pbs to proceed into productive(-)-strand DNA synthesis. Alternatively, specific interactions between tRNA3Lys and HIV-1 RT may be necessary for efficient initiation of(-)-strand DNA synthesis.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Senger B, Rengers J U, Sprinzl M, Walter P, Nussbaum G, Fasiolo F
Conservation in evolution for a small monomeric phenylalanyl-tRNA synthetase of the tRNA(Phe) recognition nucleotides and initial aminoacylation site Article de journal
Dans: Biochemistry, vol. 35, no. 1, p. 117-123, 1996, ISBN: 8555164, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Non-U.S. Gov't Variation (Genetics), Nucleic Acid Substrate Specificity Support, Phe/*chemistry/*metabolism Saccharomyces cerevisiae/enzymology/genetics Sequence Homology, Transfer, Unité ARN
@article{,
title = {Conservation in evolution for a small monomeric phenylalanyl-tRNA synthetase of the tRNA(Phe) recognition nucleotides and initial aminoacylation site},
author = {R Aphasizhev and B Senger and J U Rengers and M Sprinzl and P Walter and G Nussbaum and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8555164},
isbn = {8555164},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {1},
pages = {117-123},
abstract = {We previously showed that yeast mitochondrial phenylalanyl-tRNA synthetase (MSF protein) is evolutionarily distant to the cytoplasmic counterpart based on a high degree of divergence in protein sequence, molecular mass, and quaternary structure. Using yeast cytoplasmic tRNA(Phe) which is efficiently aminoacylated by MSF protein, we report here the tRNA(Phe) primary site of aminoacylation and the identity determinants for MSF protein. As for the cytoplasmic phenylalanyl-tRNA synthetase (Sampson, J. R., Di Renzo, A. B., Behlen, L. S., & Uhlenbeck, O. C. (1989) Science 243, 1363-1366), MSF protein recognizes nucleotides from the anticodon and the acceptor end including base A73 and, as shown here, adjacent G1-C72 base pair or at least C72 base. This indicates that the way of tRNA(Phe) binding for the two phenylalanine enzymes is conserved in evolution. However, tRNA(Phe) tertiary structure seems more critical for the interaction with the cytoplasmic enzyme than with MSF protein, and unlike cytoplasmic phenylalanyl-tRNA synthetase, the small size of the monomeric MSF protein probably does not allow contacts with residue 20 at the top corner of the L molecule. We also show that MSF protein preferentially aminoacylates the terminal 2'-OH group of tRNA(Phe) but with a catalytic efficiency for tRNA(Phe)-CC-3'-deoxyadenosine reduced 100-fold from that of native tRNA(Phe), suggesting a role of the terminal 3'-OH in catalysis. The loss is only 1.5-fold when tRNA(Phe)-CC-3'-deoxyadenosine is aminoacylated by yeast cytoplasmic PheRS (Sprinzl, M., & Cramer, F. (1973) Nature 245, 3-5), indicating mechanistic differences between the two PheRS's active sites for the amino acid transfer step.},
note = {0006-2960
Journal Article},
keywords = {Non-U.S. Gov't Variation (Genetics), Nucleic Acid Substrate Specificity Support, Phe/*chemistry/*metabolism Saccharomyces cerevisiae/enzymology/genetics Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Reinbolt J, Wakao H, Laalami S, Grunberg-Manago M, Romby P, Ehresmann B, Ehresmann C
Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking Article de journal
Dans: Biochemistry, vol. 35, no. 9, p. 2978-2984, 1996, ISBN: 8608135, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN
@article{,
title = {Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking},
author = {G Yusupova and J Reinbolt and H Wakao and S Laalami and M Grunberg-Manago and P Romby and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608135},
isbn = {8608135},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {9},
pages = {2978-2984},
abstract = {trans-Diamminedichloroplatinum(II) was used to induce reversible cross-links between Escherichia coli initiation factor 2 (IF-2) and fMet-tRNA(f)(Met). Two distinct cross-links between IF-2 and the initiator tRNA were produced. Analysis of the cross-linking regions on both RNA and protein moieties reveals that the T arm of the tRNA is in the proximity of a region of the C-terminal domain of IF-2 (residues Asn611-Arg645). This cross-link is well-correlated with the fact that the C-domain of IF-2 contains the fMet-tRNA binding site and that the cross-linked RNA fragment precisely maps in a region which is protected by IF-2 from chemical modification and enzymatic digestion. Rather unexpectedly, a second cross-link was characterized which involves the anticodon arm of fMet-tRNA(f)(Met) and the N-terminal part of IF-2 (residues Trp215-Arg237).},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy Article de journal
Dans: Science, vol. 272, no. 5266, p. 1343-1347, 1996, ISBN: 8650546, (0036-8075 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Arginine/chemistry/*metabolism Base Composition Base Sequence Citrulline/chemistry/*metabolism Crystallography, Molecular Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA/*chemistry/genetics/*metabolism, Unité ARN, X-Ray Hydrogen Bonding Ligands Magnetic Resonance Spectroscopy Models
@article{,
title = {Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy},
author = {Y Yang and M Kochoyan and P Burgstaller and E Westhof and M Famulok},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8650546},
isbn = {8650546},
year = {1996},
date = {1996-01-01},
journal = {Science},
volume = {272},
number = {5266},
pages = {1343-1347},
abstract = {In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.},
note = {0036-8075
Journal Article},
keywords = {Arginine/chemistry/*metabolism Base Composition Base Sequence Citrulline/chemistry/*metabolism Crystallography, Molecular Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA/*chemistry/genetics/*metabolism, Unité ARN, X-Ray Hydrogen Bonding Ligands Magnetic Resonance Spectroscopy Models},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Michel F
The structural domains of group I introns. Chapitre d'ouvrage
Dans: Green, R; Schroeder, R (Ed.): Ribosomal Rna and Group I Introns (Molecular Biology Intelligence Unit), p. 1-14, R G Landes Co, 1996.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {The structural domains of group I introns.},
author = {E Westhof and F Michel},
editor = {R Green and R Schroeder},
url = {https://catalyst.library.jhu.edu/catalog/bib_1891715},
year = {1996},
date = {1996-01-01},
booktitle = {Ribosomal Rna and Group I Introns (Molecular Biology Intelligence Unit)},
pages = {1-14},
publisher = {R G Landes Co},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Westhof E, Masquida B, Jaeger L
RNA tectonics: towards RNA design Article de journal
Dans: Fold Des, vol. 1, no. 4, p. R78-88, 1996, ISBN: 9079386, (1359-0278 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Drug Design Evolution, Catalytic/chemistry/genetics RNA, Molecular Models, Molecular Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Protozoan/chemistry/genetics Tetrahymena thermophila/chemistry/genetics, Unité ARN
@article{,
title = {RNA tectonics: towards RNA design},
author = {E Westhof and B Masquida and L Jaeger},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9079386},
isbn = {9079386},
year = {1996},
date = {1996-01-01},
journal = {Fold Des},
volume = {1},
number = {4},
pages = {R78-88},
abstract = {Our understanding of the structural, folding and catalytic properties of RNA molecules has increased enormously in recent years. The discovery of catalytic RNA molecules by Sidney Altman and Tom Cech, the development of in vitro selection procedures, and the recent crystallizations of hammerhead ribozymes and of a large domain of an autocatalytic group 1 intron are some of the milestones that have contributed to the explosion of the RNA field. The availability of a three-dimensional model for the catalytic core of group 1 introns contributed also a heuristic drive toward the development of new techniques and approaches for unravelling RNA architecture, folding and stability. Here, we emphasize the mosaic structure of RNA and review some of the recent literature pertinent to this working framework. In the long run, RNA tectonics aims at constructing combinatorial libraries, using RNA mosaic units for creating molecules with dedicated shapes and properties.},
note = {1359-0278
Journal Article
Review
Review, Tutorial},
keywords = {Animals Base Sequence Drug Design Evolution, Catalytic/chemistry/genetics RNA, Molecular Models, Molecular Molecular Sequence Data Molecular Structure Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Protozoan/chemistry/genetics Tetrahymena thermophila/chemistry/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Streicher B, Westhof E, Schroeder R
The environment of two metal ions surrounding the splice site of a group I intron Article de journal
Dans: EMBO J, vol. 15, no. 10, p. 2556-2564, 1996, ISBN: 8665863, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T4/genetics Base Sequence Calcium/physiology Catalysis *Cations, Catalytic/chemistry/*metabolism Strontium/physiology Support, Divalent Comparative Study Hydrogen-Ion Concentration Hydrolysis Introns/*genetics Lead/physiology Magnesium/physiology Manganese/physiology Models, Molecular Molecular Sequence Data RNA Precursors/genetics/*metabolism RNA Splicing/*physiology RNA, Non-U.S. Gov't Thymidylate Synthase/genetics, Unité ARN
@article{,
title = {The environment of two metal ions surrounding the splice site of a group I intron},
author = {B Streicher and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8665863},
isbn = {8665863},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {10},
pages = {2556-2564},
abstract = {Several divalent metal ions (Ca2+, Sr2+ and Pb2+) do not promote splicing, but instead induce cleavage at a single site in the conserved group I intron core in the absence of the guanosine cofactor at elevated pH, generating products with 5'-OH and 3'-phosphate ends. The reaction is competed by Mg2+, which does not cleave at this position, but hydrolyses the splice sites producing 3'-OH and 5'-phosphate ends. Mn2+ promotes both core cleavage and splice site hydrolysis under identical conditions, suggesting that two different metal atoms are involved, each responsible for one type of cleavage, and with different chemical and geometric requirements. Based on the core cleavage position and on the previously proposed coordination sites for Mg2+, we propose a structural location for two metal ions surrounding the splice site in the Michel-Westhof three-dimensional model of the group I intron core. The proposed location was strengthened by a first mutational analysis which supported the suggested interaction between one of the metal ions and the bulged residue in P7.},
note = {0261-4189
Journal Article},
keywords = {Bacteriophage T4/genetics Base Sequence Calcium/physiology Catalysis *Cations, Catalytic/chemistry/*metabolism Strontium/physiology Support, Divalent Comparative Study Hydrogen-Ion Concentration Hydrolysis Introns/*genetics Lead/physiology Magnesium/physiology Manganese/physiology Models, Molecular Molecular Sequence Data RNA Precursors/genetics/*metabolism RNA Splicing/*physiology RNA, Non-U.S. Gov't Thymidylate Synthase/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt E C
The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases Article de journal
Dans: EMBO J, vol. 15, no. 19, p. 5437-5448, 1996, ISBN: 8895587, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Amino Acid Sequence Cytoplasm/chemistry Genes, Amino Acid Support, Fungal/genetics Glutamate-tRNA Ligase/*metabolism Kinetics Membrane Proteins/metabolism Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Mutation Nuclear Envelope/metabolism RNA, Non-U.S. Gov't Yeasts/enzymology/*genetics/growth & development, Transfer/*metabolism RNA-Binding Proteins/analysis/genetics/*metabolism Recombinant Fusion Proteins/metabolism *Saccharomyces cerevisiae Proteins Sequence Homology, Unité ARN
@article{,
title = {The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases},
author = {G Simos and A Segref and F Fasiolo and K Hellmuth and A Shevchenko and M Mann and E C Hurt},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8895587},
isbn = {8895587},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {19},
pages = {5437-5448},
abstract = {Arc1p was found in a screen for components that interact genetically with Los1p, a nuclear pore-associated yeast protein involved in tRNA biogenesis. Arc1p is associated with two proteins which were identified as methionyl-tRNA and glutamyl-tRNA synthetase (MetRS and GluRS) by a new mass spectrometry method. ARC1 gene disruption leads to slow growth and reduced MetRS activity, and synthetically lethal arc1- mutants are complemented by the genes for MetRS and GluRS. Recombinant Arc1p binds in vitro to purified monomeric yeast MetRS, but not to an N-terminal truncated form, and strongly increases its apparent affinity for tRNAMet. Furthermore, Arc1p, which is allelic to the quadruplex nucleic acid binding protein G4p1, exhibits specific binding to tRNA as determined by gel retardation and UV-cross-linking. Arc1p is, therefore, a yeast protein with dual specificity: it associates with tRNA and aminoacyl-tRNA synthetases. This functional interaction may be required for efficient aminoacylation in vivo.},
note = {0261-4189
Journal Article},
keywords = {Acylation Amino Acid Sequence Cytoplasm/chemistry Genes, Amino Acid Support, Fungal/genetics Glutamate-tRNA Ligase/*metabolism Kinetics Membrane Proteins/metabolism Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Mutation Nuclear Envelope/metabolism RNA, Non-U.S. Gov't Yeasts/enzymology/*genetics/growth & development, Transfer/*metabolism RNA-Binding Proteins/analysis/genetics/*metabolism Recombinant Fusion Proteins/metabolism *Saccharomyces cerevisiae Proteins Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Serganov A A, Masquida B, Westhof E, Cachia C, Portier C, Garber M, Ehresmann B, Ehresmann C
The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure Article de journal
Dans: RNA, vol. 2, no. 11, p. 1124-1138, 1996, ISBN: 8903343, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics/*metabolism Ribosomal Proteins/*metabolism Species Specificity Support, Bacterial/chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites/genetics Comparative Study Computer Simulation Conserved Sequence Escherichia coli/genetics/*metabolism Magnesium/metabolism Models, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/genetics/*metabolism, Ribosomal, Unité ARN
@article{,
title = {The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure},
author = {A A Serganov and B Masquida and E Westhof and C Cachia and C Portier and M Garber and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8903343},
isbn = {8903343},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {11},
pages = {1124-1138},
abstract = {Binding of Escherichia coli and Thermus thermophilus ribosomal proteins S15 to a 16S ribosomal RNA fragment from T. thermophilus (nt 559-753) has been investigated in detail by extensive deletion analysis, filter-binding assays, gel mobility shift, structure probing, footprinting with chemical, enzymatic, and hydroxyl radical probes. Both S15 proteins recognize two distinct sites. The first one maps in the bottom of helix 638-655/717-734 (H22) and in the three-way junction between helix 560-570/737-747 (H20), helix 571-600/606-634 (H21), and H22. The second is located in a conserved purine-rich region in the center of H22. The first site provides a higher contribution to the free energy of binding than the second one, and both are required for efficient binding. A short RNA fragment of 56 nt containing these elements binds S15 with high affinity. The structure of the rRNA is constrained by the three-way junction and requires both magnesium and S15 to be stabilized. A 3D model, derived by computer modeling with the use of experimental data, suggests that the bound form adopts a Y-shaped conformation, with a quasi-coaxial stacking of H22 on H20, and H21 forming an acute angle with H22. In this model, S15 binds to the shallow groove of the RNA on the exterior side of the Y-shaped structure, making contact with the two sites, which are separated by one helix turn.},
note = {1355-8382
Journal Article},
keywords = {16S/chemistry/genetics/*metabolism Ribosomal Proteins/*metabolism Species Specificity Support, Bacterial/chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites/genetics Comparative Study Computer Simulation Conserved Sequence Escherichia coli/genetics/*metabolism Magnesium/metabolism Models, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/genetics/*metabolism, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Fasiolo F
Yeast tRNA(Met) recognition by methionyl-tRNA synthetase requires determinants from the primary, secondary and tertiary structure: a review Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 597-604, 1996, ISBN: 8955903, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Anticodon Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Met/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {Yeast tRNA(Met) recognition by methionyl-tRNA synthetase requires determinants from the primary, secondary and tertiary structure: a review},
author = {B Senger and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955903},
isbn = {8955903},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {597-604},
abstract = {The primordial role of the CAU anticodon in methionine identity of the tRNA has been established by others nearly a decade ago in Escherichia coli and yeast tRNA(Met). We show here that the CAU triplet alone is unable to confer methionine acceptance to a tRNA. This requires the contribution of the discriminatory base A73 and the non-anticodon bases of the anticodon loop. To better understand the functional communication between the anticodon and the active site, we analysed the binding and aminoacylation of tRNA(Met) based anticodon and acceptor-stem minihelices and of tRNA(Met) chimeras where the central core region of yeast tRNA(Met) is replaced by that of unusual mitochondrial forms lacking either a D-stem or a T-stem. These studies suggest that the high selectivity of the anticodon bases in tRNA(Met) implies the L-conformation of the tRNA and the presence of a D-stem. The importance of a L-structure for recognition of tRNA(Met) was also deduced from mutations of tertiary interactions known to play a general role in tRNA(Met) folding.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acid Sequence Anticodon Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Met/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}