Publications
1994
Westhof E, Altman S
Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 91, no. 11, p. 5133-5137, 1994, ISBN: 7515186, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*chemistry/metabolism RNA, Base Sequence Computer Graphics Computer Simulation Endoribonucleases/*chemistry/metabolism Escherichia coli/*enzymology Molecular Sequence Data *Nucleic Acid Conformation RNA, Catalytic/*chemistry/metabolism Ribonuclease P Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN
@article{,
title = {Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli},
author = {E Westhof and S Altman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7515186},
isbn = {7515186},
year = {1994},
date = {1994-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {91},
number = {11},
pages = {5133-5137},
abstract = {A three-dimensional model of M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was constructed with the aid of a computer. The modeling process took into account data from chemical and enzymatic protection experiments, phylogenetic analysis, studies of the activities of mutants, and the kinetics of reactions catalyzed by the binding of substrate to M1 RNA. The model provides a plausible picture of the binding to M1 RNA of the tRNA domain of a precursor tRNA substrate. The scissile bond and adjacent segments of the aminoacyl acceptor stem of a precursor tRNA substrate can fit into a cleft that leads to the phylogenetically conserved, central part of the structure.},
note = {0027-8424
Journal Article},
keywords = {Bacterial/*chemistry/metabolism RNA, Base Sequence Computer Graphics Computer Simulation Endoribonucleases/*chemistry/metabolism Escherichia coli/*enzymology Molecular Sequence Data *Nucleic Acid Conformation RNA, Catalytic/*chemistry/metabolism Ribonuclease P Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Vysotskaya V, Tischenko S, Garber M, Kern D, Mougel M, Ehresmann C, Ehresmann B
The ribosomal protein S8 from Thermus thermophilus VK1. Sequencing of the gene, overexpression of the protein in Escherichia coli and interaction with rRNA Article de journal
Dans: Eur J Biochem, vol. 223, no. 2, p. 437-445, 1994, ISBN: 7519982, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*metabolism Recombinant Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/isolation & purification/metabolism Sequence Alignment Support, Amino Acid Sequence Base Sequence Blotting, Bacterial Molecular Sequence Data Molecular Weight Nucleic Acid Hybridization Polymerase Chain Reaction Promoter Regions (Genetics) Protein Binding Protein Structure, Bacterial/chemistry/genetics/isolation & purification Escherichia coli/genetics/metabolism *Gene Expression *Genes, Bacterial/metabolism RNA, Genetic, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics Transcription, Ribosomal, Secondary RNA, Southern Cloning, Unité ARN
@article{,
title = {The ribosomal protein S8 from Thermus thermophilus VK1. Sequencing of the gene, overexpression of the protein in Escherichia coli and interaction with rRNA},
author = {V Vysotskaya and S Tischenko and M Garber and D Kern and M Mougel and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7519982},
isbn = {7519982},
year = {1994},
date = {1994-01-01},
journal = {Eur J Biochem},
volume = {223},
number = {2},
pages = {437-445},
abstract = {The gene of the ribosomal protein S8 from Thermus thermophilus VK1 has been isolated from a genomic library by hybridization of an oligonucleotide coding for the N-terminal amino acid sequence of the protein, amplified by PCR and sequenced. Nucleotide sequence reveals an open reading frame coding for a protein of 138 amino acid residues (M(r) 15,839). The codon usage shows that 94% of the codons possess G or C in the third position, and agrees with the preferential usage of codons of high G+C content in the bacteria of the genus Thermus. The amino acid sequence of the protein shows 48% identity with the protein from Escherichia coli. Ribosomal protein S8 from T. thermophilus has been expressed in E. coli under the control of the T7 promoter and purified to homogeneity by heat treatment of the extract followed by cation-exchange chromatography. Conditions were defined in which T. thermophilus protein S8 binds specifically an homologous 16S rRNA fragment containing the putative S8 binding site with an apparent association constant of 5 x 10(7) M-1. The overexpressed protein binds the rRNA with the same affinity as that extracted from T. thermophilus, indicating that the thermophilic protein is correctly folded in E. coli. The specificity of this binding is dependent on the ionic strength. The protein S8 from T. thermophilus recognizes the E. coli rRNA binding sites as efficiently as the S8 protein from E. coli. This result agrees with sequence comparisons of the S8 binding site on the small subunit rRNA from E. coli and from T. thermophilus, showing strong similarities in the regions involved in the interaction. It suggests that the structural features responsible for the recognition are conserved in the mesophilic and thermophilic eubacteria, despite structural peculiarities in the thermophilic partners conferring thermostability.},
note = {0014-2956
Journal Article},
keywords = {16S/*metabolism Recombinant Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/isolation & purification/metabolism Sequence Alignment Support, Amino Acid Sequence Base Sequence Blotting, Bacterial Molecular Sequence Data Molecular Weight Nucleic Acid Hybridization Polymerase Chain Reaction Promoter Regions (Genetics) Protein Binding Protein Structure, Bacterial/chemistry/genetics/isolation & purification Escherichia coli/genetics/metabolism *Gene Expression *Genes, Bacterial/metabolism RNA, Genetic, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics Transcription, Ribosomal, Secondary RNA, Southern Cloning, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
van Gelder C W, Thijssen J P, Klaassen E C, Sturchler C, Krol A, van Venrooij W J, Pruijn G J
Common structural features of the Ro RNP associated hY1 and hY5 RNAs Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 13, p. 2498-2506, 1994, ISBN: 8041611, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Autoantigens/*genetics/metabolism Base Sequence Cloning, Molecular Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA Probes RNA, Non-U.S. Gov't, Ribosomal/*chemistry/metabolism Ribonucleoproteins/*genetics/metabolism Sequence Alignment Support, Unité ARN
@article{,
title = {Common structural features of the Ro RNP associated hY1 and hY5 RNAs},
author = {C W van Gelder and J P Thijssen and E C Klaassen and C Sturchler and A Krol and W J van Venrooij and G J Pruijn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8041611},
isbn = {8041611},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {13},
pages = {2498-2506},
abstract = {The secondary structures of human hY1 and hY5 RNAs were determined using both chemical modification techniques and enzymatic structure probing. The results indicate that both for hY1 and for hY5 RNA the secondary structure largely corresponds to the structure predicted by sequence alignment and computerized energy-minimization. However, some important deviations were observed. In the case of hY1 RNA, two regions forming a predicted helix appeared to be single-stranded. Furthermore, the pyrimidine-rich region of hY1 RNA appeared to be very resistant to reagents under native conditions, although it was accessible to chemical reagents under semi-denaturing conditions. This may point to yet unidentified tertiary interactions for this region of hY1 RNA. In the case of hY5 RNA, two neighbouring internal loops in the predicted structure appeared to form one large internal loop.},
note = {0305-1048
Journal Article},
keywords = {Animals Autoantigens/*genetics/metabolism Base Sequence Cloning, Molecular Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA Probes RNA, Non-U.S. Gov't, Ribosomal/*chemistry/metabolism Ribonucleoproteins/*genetics/metabolism Sequence Alignment Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tuschl T, Gohlke C, Jovin T M, Westhof E, Eckstein F
A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements Article de journal
Dans: Science, vol. 266, no. 5186, p. 785-789, 1994, ISBN: 7973630, (0036-8075 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence Energy Transfer Fluoresceins Least-Squares Analysis *Models, Catalytic/*chemistry Rhodamines Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN
@article{,
title = {A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements},
author = {T Tuschl and C Gohlke and T M Jovin and E Westhof and F Eckstein},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7973630},
isbn = {7973630},
year = {1994},
date = {1994-01-01},
journal = {Science},
volume = {266},
number = {5186},
pages = {785-789},
abstract = {For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.},
note = {0036-8075
Journal Article},
keywords = {Base Composition Base Sequence Energy Transfer Fluoresceins Least-Squares Analysis *Models, Catalytic/*chemistry Rhodamines Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tanner N K, Schaff S, Thill G, Petit-Koskas E, Crain-Denoyelle A M, Westhof E
A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses Article de journal
Dans: Curr Biol, vol. 4, no. 6, p. 488-498, 1994, ISBN: 7922369, (0960-9822 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Catalytic/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Nucleic Acid Support, Site-Directed Nucleic Acid Conformation RNA, Unité ARN, Viral/chemistry/genetics/metabolism Sequence Homology, Viral/genetics Hepatitis Delta Virus/*enzymology/genetics Human Kinetics Models
@article{,
title = {A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses},
author = {N K Tanner and S Schaff and G Thill and E Petit-Koskas and A M Crain-Denoyelle and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7922369},
isbn = {7922369},
year = {1994},
date = {1994-01-01},
journal = {Curr Biol},
volume = {4},
number = {6},
pages = {488-498},
abstract = {BACKGROUND: Hepatitis delta virus (HDV), which has a single-stranded RNA genome about 1700 nucleotides long, is a satellite virus of hepatitis B, and is associated with a high incidence of fulminant hepatitis and death in infected humans. Like certain pathogenic subviral RNAs that infect plants, HDV RNA features a closed-circular conformation, a rolling-circle mechanism of replication and RNA-catalyzed self-cleaving reactions of both genomic and anti-genomic strands in vitro. The catalytic domains cannot be folded into either the hammerhead or hairpin secondary-structure motifs that have been found in other self-cleaving RNAs. RESULTS: A pseudoknot secondary-structure model has been suggested for the catalytic domain (ribozyme) of HDV RNA. We conducted extensive mutational analyses of regions of the HDV ribozyme predicted in this model to be single stranded, and found that several of them are important for catalytic activity. We used these data, sequence comparisons between different isolates and previously published structural analyses to produce a computer graphic model of the three-dimensional architecture of the HDV ribozyme. CONCLUSIONS: Our model supports the pseudoknotted structure and rationalizes several observations relating to the lengths of the various stems and the sequence requirements of the single-stranded regions. It also provides insight into the catalytic mechanism of the HDV ribozyme. We specifically propose that residues C75, U20 and C21 form the basis of the catalytic region and are close to the cleavable phosphate.},
note = {0960-9822
Journal Article},
keywords = {Base Sequence DNA, Catalytic/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Nucleic Acid Support, Site-Directed Nucleic Acid Conformation RNA, Unité ARN, Viral/chemistry/genetics/metabolism Sequence Homology, Viral/genetics Hepatitis Delta Virus/*enzymology/genetics Human Kinetics Models},
pubstate = {published},
tppubtype = {article}
}
Szweykowska-Kulinska Z, Senger B, Keith G, Fasiolo F, Grosjean H
Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile) Article de journal
Dans: EMBO J, vol. 13, no. 19, p. 4636-4644, 1994, ISBN: 7925304, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*metabolism Base Sequence Introns/*physiology Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/*biosynthesis RNA Processing, Fungal/*metabolism RNA, Ile/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't, Post-Transcriptional/physiology RNA, Transfer, Unité ARN
@article{,
title = {Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile)},
author = {Z Szweykowska-Kulinska and B Senger and G Keith and F Fasiolo and H Grosjean},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7925304},
isbn = {7925304},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {19},
pages = {4636-4644},
abstract = {We have isolated and sequenced the minor species of tRNA(Ile) from Saccharomyces cerevisiae. This tRNA contains two unusual pseudouridines (psi s) in the first and third positions of the anticodon. As shown earlier by others, this tRNA derives from two genes having an identical 60 nt intron. We used in vitro procedures to study the structural requirements for the conversion of the anticodon uridines to psi 34 and psi 36. We show here that psi 34/psi 36 modifications require the presence of the pre-tRNA(Ile) intron but are not dependent upon the particular base at any single position of the anticodon. The conversion of U34 to psi 34 occurs independently from psi 36 synthesis and vice versa. However, psi 34 is not formed when the middle and the third anticodon bases of pre-tRNA(Ile) are both substituted to yield ochre anticodon UUA. This ochre pre-tRNA(Ile) mutant has the central anticodon uridine modified to psi 35 as is the case for S.cerevisiae SUP6 tyrosine-inserting ochre suppressor tRNA. In contrast, neither the first nor the third anticodon pseudouridine is formed, when the ochre (UUA) anticodon in the pre-tRNA(Tyr) is substituted with the isoleucine UAU anticodon. A synthetic mini-substrate consisting of the anticodon stem and loop and the wild-type intron of pre-tRNA(Ile) is sufficient to fully modify the anticodon U34 and U36 into psi s. This is the first example of the tRNA intron sequence, rather than the whole tRNA or pre-tRNA domain, being the main determinant of nucleoside modification.},
note = {0261-4189
Journal Article},
keywords = {Anticodon/*metabolism Base Sequence Introns/*physiology Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/*biosynthesis RNA Processing, Fungal/*metabolism RNA, Ile/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't, Post-Transcriptional/physiology RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sturchler C, Lescure A, Keith G, Carbon P, Krol A
Base modification pattern at the wobble position of Xenopus selenocysteine tRNA(Sec) Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 8, p. 1354-1358, 1994, ISBN: 8031393, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/chemistry/*genetics/metabolism Selenocysteine/*metabolism Support, Animals *Anticodon Base Composition Base Sequence Microinjections Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, LESCURE, Non-U.S. Gov't Uridine Xenopus laevis, Transfer, Unité ARN
@article{,
title = {Base modification pattern at the wobble position of Xenopus selenocysteine tRNA(Sec)},
author = {C Sturchler and A Lescure and G Keith and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8031393},
isbn = {8031393},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {8},
pages = {1354-1358},
abstract = {We examined the base modification pattern of Xenopus tRNA(Sec) using microinjection into Xenopus oocytes, with particular focus on the wobble base U34 at the first position of the anticodon. We found that U34 becomes modified to mcm5U34 (5-methylcarboxymethyluridine) in the oocyte cytoplasm in a rather complex manner. When the tRNA(Sec) gene is injected into Xenopus oocyte nuclei, psi 55 and m1A58 are readily obtained, but not mcm5U34. This will appear only upon cytoplasmic injection of the gene product arising from the first nuclear injection. In contrast, tRNA(Sec) produced by in vitro transcription with T7 RNA polymerase readily acquires i6A37, psi 55, m1A58, and mcm5U34. The latter is obtained after direct nuclear or cytoplasmic injections. It has been reported by others that mcm5Um, a 2'-O-methylated derivative of mcm5U34, also exists in rat and bovine tRNA(Sec). With both the gene product and the in vitro transcript, and using the sensitive RNase T2 assay, we were unable to detect under our conditions the presence of a dinucleotide carrying mcm5Um and that would be therefore refractory to hydrolysis. We showed that the unusual mcm5U acquisition pathway does not result from impairment of nucleocytoplasmic transport. Rather, these data can be interpreted to mean that the modification is performed by a tRNA(Sec) specific enzyme, limiting in the oocyte cytoplasm.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/chemistry/*genetics/metabolism Selenocysteine/*metabolism Support, Animals *Anticodon Base Composition Base Sequence Microinjections Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, LESCURE, Non-U.S. Gov't Uridine Xenopus laevis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Skripkin E, Paillart J C, Marquet R, Ehresmann B, Ehresmann C
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 91, no. 11, p. 4945-4949, 1994, ISBN: 8197162, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences
@article{,
title = {Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro},
author = {E Skripkin and J C Paillart 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=8197162},
isbn = {8197162},
year = {1994},
date = {1994-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {91},
number = {11},
pages = {4945-4949},
abstract = {The diploid genome of all retroviruses is made of two homologous copies of RNA intimately associated near their 5' end, in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for crucial functions of the retroviral life cycle (reverse transcription, translation, encapsidation). Previous in vitro studies mapped the dimer linkage structure of human immunodeficiency virus type 1 (HIV-1) in a region downstream of the splice donor site, containing conserved purine tracts that were postulated to mediate dimerization, through purine quartets. However, we recently showed that dimerization of HIV-1 RNA also involves sequences upstream of the splice donor site. Here, we used chemical modification interference to identify nucleotides that are required in unmodified form for dimerization of a RNA fragment containing nucleotides 1-707 of HIV-1 RNA. These nucleotides map exclusively in a restricted area upstream of the splice donor site and downstream of the primer binding site. They are centered around a palindromic sequence (GUGCAC279) located in a hairpin loop. Our results support a model in which dimer formation is initiated by the annealing of the palindromic sequences, possibly by a loop-loop interaction between the two monomers. Further experiments show that the deletion of the stem-loop or base substitutions in the loop abolish dimerization, despite the presence of the previously postulated dimer linkage structure. On the other hand, deletions of the purine tracts downstream of the splice donor site do not prevent dimerization. Therefore, we conclude that the palindromic region represents the dimerization initiation site of genomic RNA.},
note = {0027-8424
Journal Article},
keywords = {Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Florentz C, Giege R
Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 23, p. 5031-5037, 1994, ISBN: 7800496, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics Base Sequence Genes, Asp/genetics RNA, FLORENTZ, His/*chemistry/*genetics RNA, Non-U.S. Gov't Tymovirus/genetics Yeasts/enzymology, Synthetic/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Transfer, Unité ARN, Viral/metabolism Support
@article{,
title = {Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context},
author = {J Rudinger and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7800496},
isbn = {7800496},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {23},
pages = {5031-5037},
abstract = {Residue G-1 and discriminator base C73 are the major histidine identity elements in prokaryotes. Here we evaluate the importance of these two nucleotides in yeast histidine aminoacylation identity. Deletion of G-1 in yeast tRNA(His) transcript leads to a drastic loss of histidylation specificity (about 500-fold). Mutation of discriminator base A73, common to all yeast tRNA(His) species, into G73 has a more moderate but still significant effect with a 22-fold decrease in histidylation specificity. Changes at position 36 in the anticodon loop has negligible effect on histidylation. The role of residues -1 and 73 for specific aminoacylation by yeast HisRS was further investigated by studying the histidylation capacities of seven minihelices derived from the Turnip Yellow Mosaic Virus tRNA-like structure. Changes in the nature of nucleotides -1 and 73 modulate this activity but do not suppress it. The optimal mini-substrate for HisRS presents a G.A mismatch at the position equivalent to residues G-1.A73 in yeast tRNA(His), confirms the importance of this structural feature in yeast histidine identity. The fact that the minisubstrates contain a pseudoknot in which position -1 is mimicked by an internal nucleotide from the pseudoknot highlights further the necessity of a stacking interaction of this position over the amino acid accepting branch of the tRNA during the aminoacylation process. Individual transplantation of G-1 or A73 into yeast tRNA(Asp) transcript improves the histidylation efficiency of the engineered tRNA(Asp). However, a tRNA(Asp) transcript presenting simultaneously both residues G-1 and A73 becomes a less good substrate for HisRS, suggesting the importance of the structural context and/or the presence of antideterminants for an optimal expression of these two identity elements.},
note = {0305-1048
Journal Article},
keywords = {Anticodon/genetics Base Sequence Genes, Asp/genetics RNA, FLORENTZ, His/*chemistry/*genetics RNA, Non-U.S. Gov't Tymovirus/genetics Yeasts/enzymology, Synthetic/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Transfer, Unité ARN, Viral/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Putz J, Florentz C, Benseler F, Giege R
A single methyl group prevents the mischarging of a tRNA Article de journal
Dans: Nat Struct Biol, vol. 1, no. 9, p. 580-582, 1994, ISBN: 7634096, (1072-8368 Letter).
Liens | BibTeX | Étiquettes: Arginine/*genetics Arginine-tRNA Ligase/metabolism Base Sequence Methylation Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*genetics/metabolism, FLORENTZ, Transfer, Unité ARN
@article{,
title = {A single methyl group prevents the mischarging of a tRNA},
author = {J Putz and C Florentz and F Benseler and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7634096},
isbn = {7634096},
year = {1994},
date = {1994-01-01},
journal = {Nat Struct Biol},
volume = {1},
number = {9},
pages = {580-582},
note = {1072-8368
Letter},
keywords = {Arginine/*genetics Arginine-tRNA Ligase/metabolism Base Sequence Methylation Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*genetics/metabolism, FLORENTZ, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Philippe C, Benard L, Eyermann F, Cachia C, Kirillov S V, Portier C, Ehresmann B, Ehresmann C
Structural elements of rps0 mRNA involved in the modulation of translational initiation and regulation of E. coli ribosomal protein S15 Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 13, p. 2538-2546, 1994, ISBN: 8041615, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cloning, Genetic, Messenger/*chemistry/metabolism RNA, Molecular Escherichia coli/*genetics Kinetics Lac Operon Molecular Sequence Data Mutation Nucleic Acid Conformation Operon Protein Binding RNA, Non-U.S. Gov't *Translation, Ribosomal/metabolism Ribosomal Proteins/*genetics Support, Unité ARN
@article{,
title = {Structural elements of rps0 mRNA involved in the modulation of translational initiation and regulation of E. coli ribosomal protein S15},
author = {C Philippe and L Benard and F Eyermann and C Cachia and S V Kirillov and C Portier and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8041615},
isbn = {8041615},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {13},
pages = {2538-2546},
abstract = {Previous experiments showed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops and to trap the ribosome on its mRNA loading site in a transitory state. In this study, we investigated the effect of mutations in the translational operator on: the binding of protein S15, the formation of the 30S/mRNA/tRNA(fMet) ternary initiation complex, the ability of S15 to inhibit the formation of this ternary complex. The results were compared to in vivo expression and repression rates. The results show that (1) the pseudoknot is required for S15 recognition and translational control; (2) mRNA and 16S rRNA efficiently compete for S15 binding and 16S rRNA suppresses the ability of S15 to inhibit the formation of the active ternary complex; (3) the ribosome binds more efficiently to the pseudoknot than to the stem-loop; (4) sequences located between nucleotides 12 to 47 of the S15 coding phase enhances the efficiency of ribosome binding in vitro; this is correlated with enhanced in vivo expression and regulation rates.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cloning, Genetic, Messenger/*chemistry/metabolism RNA, Molecular Escherichia coli/*genetics Kinetics Lac Operon Molecular Sequence Data Mutation Nucleic Acid Conformation Operon Protein Binding RNA, Non-U.S. Gov't *Translation, Ribosomal/metabolism Ribosomal Proteins/*genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann B, Ehresmann C
Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA Article de journal
Dans: J Biol Chem, vol. 269, no. 44, p. 27486-27493, 1994, ISBN: 7961663, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support
@article{,
title = {Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA},
author = {J C Paillart and R Marquet and E Skripkin and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7961663},
isbn = {7961663},
year = {1994},
date = {1994-01-01},
journal = {J Biol Chem},
volume = {269},
number = {44},
pages = {27486-27493},
abstract = {The genome of all retroviruses consists in two homologous RNA molecules associated near their 5' end in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for several functions of the retroviral cycle such as encapsidation, reverse transcription, and translation. In human immunodeficiency virus type 1 (HIV-1), a region downstream of the splice donor site was initially postulated to mediate dimerization. However, we recently showed that the dimerization initiation site is located upstream of the splice donor site and suggested that dimerization may initiate through a loop-loop interaction. Here, we show that single base mutations in the palindromic loop of the dimerization initiation site completely abolish dimerization, while introduction of compensatory mutations restores the process. Furthermore, two single nucleotide mutants that are unable to form homodimers efficiently codimerize, while the wild type RNA and the compensatory mutant, which both form homodimers, are unable to codimerize. These results unambiguously prove the interaction between the palindromic loops of each monomer. By contrast, none of the deletions that we introduced downstream of the splice donor site abolishes dimerization. However, deletions of two purine tracts located in the vicinity of the initiation codon of the gag gene significantly decrease the thermal stability of the HIV-1 RNA dimer.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Nureki O, Niimi T, Muramatsu T, Kanno H, Kohno T, Florentz C, Giege R, Yokoyama S
Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli Article de journal
Dans: J Mol Biol, vol. 236, no. 3, p. 710-724, 1994, ISBN: 8114089, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/chemistry Base Composition Base Sequence Binding Sites Computer Graphics Escherichia coli/genetics/*metabolism Genes, Bacterial Genes, FLORENTZ, Ile/*chemistry/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Non-U.S. Gov't, Structural, Synthetic Isoleucine-tRNA Ligase/*metabolism Models, Transfer, Unité ARN
@article{,
title = {Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli},
author = {O Nureki and T Niimi and T Muramatsu and H Kanno and T Kohno and C Florentz and R Giege and S Yokoyama},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8114089},
isbn = {8114089},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {236},
number = {3},
pages = {710-724},
abstract = {Molecular recognition of Escherichia coli tRNA(Ile) by the cognate isoleucyl-tRNA synthetase (IleRS) was studied by analyses of chemical footprinting with N-nitroso-N-ethylurea and aminoacylation kinetics of variant tRNA(Ile) transcripts prepared with bacteriophage T7 RNA polymerase. IleRS binds to the acceptor, dihydrouridine (D), and anticodon stems as well as to the anticodon loop. The "complete set" of determinants for the tRNA(Ile) identity consists of most of the nucleotides in the anticodon loop (G34, A35, U36, t6A37 and A38), the discriminator nucleotide (A73), and the base-pairs in the middle of the anticodon, D and acceptor stems (C29.G41, U12.A23 and C4.G69, respectively). As for the tertiary base-pairs, two are indispensable for the isoleucylation activity, whereas the others are dispensable. Correspondingly, some of the phosphate groups of these dispensable tertiary base-pair residues were shown to be exposed to N-nitroso-N-ethylurea when tRNA(Ile) was bound with IleRS. Furthermore, deletion of the T psi C-arm only slightly impaired the tRNA(Ile) activity. Thus, it is proposed that the recognition by IleRS of all the widely distributed identity determinants is coupled with a global conformational change that involves the loosening of a particular set of tertiary base-pairs of tRNA(Ile).},
note = {0022-2836
Journal Article},
keywords = {Anticodon/chemistry Base Composition Base Sequence Binding Sites Computer Graphics Escherichia coli/genetics/*metabolism Genes, Bacterial Genes, FLORENTZ, Ile/*chemistry/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Non-U.S. Gov't, Structural, Synthetic Isoleucine-tRNA Ligase/*metabolism Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H, Dahlberg A E
Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis Article de journal
Dans: J Mol Biol, vol. 243, no. 3, p. 402-412, 1994, ISBN: 7966269, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics Ribosomes/*metabolism Support, Base Sequence Codon, Genetic beta-Galactosidase/genetics, Non-U.S. Gov't Support, P.H.S. *Translation, Ribosomal, Terminator Escherichia coli/*genetics/growth & development Molecular Sequence Data *Mutation *Nucleic Acid Conformation RNA, U.S. Gov't, Unité ARN
@article{,
title = {Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis},
author = {H Moine and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7966269},
isbn = {7966269},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {243},
number = {3},
pages = {402-412},
abstract = {Helix 34 of E. coli 16 S rRNA (1046 to 1067 and 1189 to 1211) has been proposed to participate directly in the termination of translation at UGA stop codons. We have constructed mutations in this helix in plasmid-encoded rDNA to explore the specific functional roles of the sequence UCAUCA (1199 to 1204) and a secondary structure also involving positions 1054 and 1057-1058. The rRNA mutations were analyzed for their effects on in vivo translational accuracy (stop codon readthrough and frameshifting) as well as growth rate, ribosome synthesis and incorporation into polysomes. Mutations at positions 1054, 1057, 1058, 1199 and 1200 had significant effects on translational accuracy, causing non-specific readthrough of all three stop codons as well as enhanced +1 and -1 frameshifting. Mutations at 1202 and 1203, however, had no effect. The incorporation of deleterious mutant subunits into 70 S ribosomes and polysomes was severely reduced and was associated with a slower growth rate and increased synthesis of host-encoded ribosomes. These data support the proposal that helix 34 is an essential component of the decoding center of the 30 S ribosomal subunit and is not restricted in function to UGA-codon specific termination.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics Ribosomes/*metabolism Support, Base Sequence Codon, Genetic beta-Galactosidase/genetics, Non-U.S. Gov't Support, P.H.S. *Translation, Ribosomal, Terminator Escherichia coli/*genetics/growth & development Molecular Sequence Data *Mutation *Nucleic Acid Conformation RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Michel F, Westhof E
Slippery substrates Article de journal
Dans: Nat Struct Biol, vol. 1, no. 1, p. 5-7, 1994, ISBN: 7656007, (1072-8368 News).
Liens | BibTeX | Étiquettes: Animals Binding Sites Models, Catalytic/*chemistry/genetics/metabolism Substrate Specificity Tetrahymena/enzymology/genetics, Molecular Nucleic Acid Conformation RNA, Unité ARN
@article{,
title = {Slippery substrates},
author = {F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7656007},
isbn = {7656007},
year = {1994},
date = {1994-01-01},
journal = {Nat Struct Biol},
volume = {1},
number = {1},
pages = {5-7},
note = {1072-8368
News},
keywords = {Animals Binding Sites Models, Catalytic/*chemistry/genetics/metabolism Substrate Specificity Tetrahymena/enzymology/genetics, Molecular Nucleic Acid Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Massire C, Gaspin C, Westhof E
DRAWNA: a program for drawing schematic views of nucleic acids Article de journal
Dans: J Mol Graph, vol. 12, no. 3, p. 201-206, 196, 1994, ISBN: 7529557, (0263-7855 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Computer Graphics DNA/*chemistry *Models, Molecular Models, Theoretical *Nucleic Acid Conformation RNA/*chemistry *Software, Unité ARN
@article{,
title = {DRAWNA: a program for drawing schematic views of nucleic acids},
author = {C Massire and C Gaspin and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7529557},
isbn = {7529557},
year = {1994},
date = {1994-01-01},
journal = {J Mol Graph},
volume = {12},
number = {3},
pages = {201-206, 196},
abstract = {A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X11/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.},
note = {0263-7855
Journal Article},
keywords = {Computer Graphics DNA/*chemistry *Models, Molecular Models, Theoretical *Nucleic Acid Conformation RNA/*chemistry *Software, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 2, p. 145-151, 1994, ISBN: 8121797, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support
@article{,
title = {Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site},
author = {R Marquet and J C Paillart 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=8121797},
isbn = {8121797},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {2},
pages = {145-151},
abstract = {The retroviral genome consists of two homologous RNA molecules associated close to their 5' ends. We studied the spontaneous dimerization of four HIV-1 RNA fragments (RNAs 1-707, 1-615, 311-612, and 311-415) containing the previously defined dimerization domain, and a RNA fragment (RNA 1-311) corresponding to the upstream sequences. Significant dimerization of all RNAs is observed on agarose gels when magnesium is included in the electrophoresis buffer. In contrast to dimerization of RNAs 311-612 and 311-415, dimerization of RNAs 1-707, 1-615 and 1-311 strongly depends on the size of the monovalent cation present in the incubation buffer. Also, dimerization of RNAs 1-707, 1-615, and 1-311 is 10 times faster than that of RNAs 311-612 and 311-415. The dimers formed by the latter RNAs are substantially more stable than that of RNA 1-615, while RNA 1-311 dimer is 5-7 degrees C less stable than RNA 1-615 dimer. These results indicate that dimerization of HIV-1 genomic RNA involves elements located upstream of the splice donor site (position 305), i.e. outside of the previously defined dimerization domain.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Logan D T, Cura V, Touzel J P, Kern D, Moras D
Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data Article de journal
Dans: J Mol Biol, vol. 241, no. 5, p. 732-735, 1994, ISBN: 8071996, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Crystallization Crystallography, Unité ARN, X-Ray Glycine-tRNA Ligase/*chemistry Molecular Structure Thermus thermophilus/*enzymology
@article{,
title = {Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data},
author = {D T Logan and V Cura and J P Touzel and D Kern and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8071996},
isbn = {8071996},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {241},
number = {5},
pages = {732-735},
abstract = {The glycyl-tRNA synthetase from Thermus thermophilus is a dimer of molecular mass 115 kDa, which has been crystallised using the vapour diffusion method from 5 to 7% polyethylene glycol 6000, 0.8 to 1.4 M NaCl at protein concentrations of 2 to 8 mg/ml. Nucleation is carried out at 4 degrees C and crystals are subsequently transferred to 15 degrees C to maximise growth. Crystals are truncated rhombohedra measuring on average 0.4 mm x 0.4 mm x 0.2 mm, which appear within a few days and reach full size in one to two months. GlyRS crystallises in two closely related space groups, P2(1)2(1)2(1) and C2,2,2(1), both with the same cell a = 125 A},
note = {0022-2836
Journal Article},
keywords = {Crystallization Crystallography, Unité ARN, X-Ray Glycine-tRNA Ligase/*chemistry Molecular Structure Thermus thermophilus/*enzymology},
pubstate = {published},
tppubtype = {article}
}
Lescure A, Lutz Y, Eberhard D, Jacq X, Krol A, Grummt I, Davidson I, Chambon P, Tora L
The N-terminal domain of the human TATA-binding protein plays a role in transcription from TATA-containing RNA polymerase II and III promoters Article de journal
Dans: EMBO J, vol. 13, no. 5, p. 1166-1175, 1994, ISBN: 7510635, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antibodies, Genetic, LESCURE, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factor TFIIA Transcription Factor TFIIB Transcription Factor TFIID Transcription Factors/biosynthesis/isolation & purification/*metabolism *Transcription, Unité ARN
@article{,
title = {The N-terminal domain of the human TATA-binding protein plays a role in transcription from TATA-containing RNA polymerase II and III promoters},
author = {A Lescure and Y Lutz and D Eberhard and X Jacq and A Krol and I Grummt and I Davidson and P Chambon and L Tora},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7510635},
isbn = {7510635},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {5},
pages = {1166-1175},
abstract = {In eukaryotes, the TATA box binding protein (TBP) is an integral component of the transcription initiation complexes of all three classes of nuclear RNA polymerases. In this study we have investigated the role of the N-terminal region of human TBP in transcription initiation from RNA polymerase (Pol) I, II and III promoters by using three monoclonal antibodies (mAbs). Each antibody recognizes a distinct epitope in the N-terminal domain of human TBP. We demonstrate that these antibodies differentially affect transcription from distinct classes of promoters. One antibody, mAb1C2, and a synthetic peptide comprising its epitope selectively inhibited in vitro transcription from TATA-containing, but not from TATA-less promoters, irrespective of whether they were transcribed by Pol II or Pol III. Transcription by Pol I, on the other hand, was not affected. Two other antibodies and their respective epitope peptides did not affect transcription from any of the promoters tested. Order of addition experiments indicate that mAb1C2 did not prevent binding of TBP to the TATA box or the formation of the TBP-TFIIA-TFIIB complex but rather inhibited a subsequent step of preinitiation complex formation. These data suggest that a defined region within the N-terminal domain of human TBP may be involved in specific protein-protein interactions required for the assembly of functional preinitiation complexes on TATA-containing, but not on TATA-less promoters.},
note = {0261-4189
Journal Article},
keywords = {Antibodies, Genetic, LESCURE, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factor TFIIA Transcription Factor TFIIB Transcription Factor TFIID Transcription Factors/biosynthesis/isolation & purification/*metabolism *Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Jaeger L, Michel F, Westhof E
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions Article de journal
Dans: J Mol Biol, vol. 236, no. 5, p. 1271-1276, 1994, ISBN: 7510342, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T4 Base Sequence Hydrogen Bonding Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN, Viral/chemistry Support
@article{,
title = {Involvement of a GNRA tetraloop in long-range RNA tertiary interactions},
author = {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=7510342},
isbn = {7510342},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {236},
number = {5},
pages = {1271-1276},
abstract = {Terminal loops with a GNRA consensus sequence are widespread in RNA. It has been suggested that these loops act as "anchors" during tertiary folding, by interacting in a sequence-specific way with helices at distant locations along the molecule. We now show that a GUGA loop changes state upon disruption of the tertiary architecture of a self-splicing group I intron. Successful replacement of the postulated loop-helix contact by classical base-pairing points to binding of the loop into the shallow (minor) groove of the helix, as also indicated by partial restoration of ribozyme stability upon a specific double nucleotide substitution.},
note = {0022-2836
Journal Article},
keywords = {Bacteriophage T4 Base Sequence Hydrogen Bonding Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN, Viral/chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Giege R, Lorber B, Théobald-Dietrich A
Crystallogenesis of biological macromolecules: facts and perspectives Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 50, no. Pt 4, p. 339-350, 1994, ISBN: 15299382, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Crystallogenesis of biological macromolecules: facts and perspectives},
author = {R Giege and B Lorber and A Théobald-Dietrich},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15299382},
isbn = {15299382},
year = {1994},
date = {1994-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {50},
number = {Pt 4},
pages = {339-350},
abstract = {This paper gives an overview of the science of crystals of biological macromolecules. The historical background of the field is outlined and the main achievements and open problems are discussed from both biological and physical-chemical viewpoints. Selected results, including data from the authors, illustrate this overview. The perspectives of crystallogenesis for structural biology, but also more general trends, are presented.},
note = {0907-4449
Journal Article},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gaspin C, Westhof E
The determination of the secondary structures of RNA as a constraint satisfaction problem. Chapitre d'ouvrage
Dans: Schulze-Kremer, S (Ed.): Advances in Molecular Bioinformatics (Frontiers in Artificial Intelligence and Applications), p. 103-122, IOS Press, 1994.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {The determination of the secondary structures of RNA as a constraint satisfaction problem.},
author = {C Gaspin and E Westhof},
editor = {S Schulze-Kremer},
url = {http://books.google.fr/books?hl=de&id=VmFSNNm7k6cC&q=Westhof#v=snippet&q=Westhof&f=false},
year = {1994},
date = {1994-01-01},
booktitle = {Advances in Molecular Bioinformatics (Frontiers in Artificial Intelligence and Applications)},
pages = {103-122},
publisher = {IOS Press},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Frugier M, Soll D, Giege R, Florentz C
Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases Article de journal
Dans: Biochemistry, vol. 33, no. 33, p. 9912-9921, 1994, ISBN: 8060999, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases},
author = {M Frugier and D Soll and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8060999},
isbn = {8060999},
year = {1994},
date = {1994-01-01},
journal = {Biochemistry},
volume = {33},
number = {33},
pages = {9912-9921},
abstract = {High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.},
note = {0006-2960
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Florentz C, Hosseini M W, Lehn J M, Giege R
Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 14, p. 2784-2790, 1994, ISBN: 8052534, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support
@article{,
title = {Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase},
author = {M Frugier and C Florentz and M W Hosseini and J M Lehn and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8052534},
isbn = {8052534},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {14},
pages = {2784-2790},
abstract = {The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.},
note = {0305-1048
Journal Article},
keywords = {Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Florentz C, Giege R
Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide Article de journal
Dans: EMBO J, vol. 13, no. 9, p. 2218-2226, 1994, ISBN: 8187774, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8187774},
isbn = {8187774},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {9},
pages = {2218-2226},
abstract = {We show here that small RNA helices which recapitulate part or all of the acceptor stem of yeast aspartate tRNA are efficiently aminoacylated by cognate class II aspartyl-tRNA synthetase. Aminoacylation is strongly dependent on the presence of the single-stranded G73 'discriminator' identity nucleotide and is essentially insensitive to the sequence of the helical region. Substrates which contain as few as 3 bp fused to G73CCAOH are aspartylated. Their charging is insensitive to the sequence of the loop closing the short helical domains. Aminoacylation of the aspartate mini-helix is not stimulated by a hairpin helix mimicking the anticodon domain and containing the three major anticodon identity nucleotides. A thermodynamic analysis demonstrates that enzyme interactions with G73 in the resected RNA substrates and in the whole tRNA are the same. Thus, if the resected RNA molecules resemble in some way the earliest substrates for aminoacylation with aspartate, then the contemporary tRNA(Asp) has quantitatively retained the influence of the major signal for aminoacylation in these substrates.},
note = {0261-4189
Journal Article},
keywords = {Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, McPherson A, Giege R
A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 15, p. 2882-2886, 1994, ISBN: 8065897, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support
@article{,
title = {A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA},
author = {B Felden and C Florentz and A McPherson and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8065897},
isbn = {8065897},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {15},
pages = {2882-2886},
abstract = {A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.},
note = {0305-1048
Journal Article},
keywords = {Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, Giege R, Westhof E
Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs Article de journal
Dans: J Mol Biol, vol. 235, no. 2, p. 508-531, 1994, ISBN: 8289279, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8289279},
isbn = {8289279},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {235},
number = {2},
pages = {508-531},
abstract = {The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
Dumas P, Bergdoll M, Cagnon C, Masson J M
Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering Article de journal
Dans: EMBO J, vol. 13, no. 11, p. 2483-2492, 1994, ISBN: 7516875, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Acetyltransferases Amino Acid Sequence Bacterial Proteins/*chemistry/genetics/isolation & purification/metabolism Base Sequence Binding Sites Bleomycin/*metabolism/pharmacology Crystallization Crystallography, Bacterial/*genetics Models, Microbial/genetics Genes, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Secondary Recombinant Fusion Proteins/isolation & purification Structure-Activity Relationship Support, Site-Directed Protein Conformation Protein Structure, Structural, Unité ARN, X-Ray Drug Resistance
@article{,
title = {Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering},
author = {P Dumas and M Bergdoll and C Cagnon and J M Masson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7516875},
isbn = {7516875},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {11},
pages = {2483-2492},
abstract = {The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.},
note = {0261-4189
Journal Article},
keywords = {*Acetyltransferases Amino Acid Sequence Bacterial Proteins/*chemistry/genetics/isolation & purification/metabolism Base Sequence Binding Sites Bleomycin/*metabolism/pharmacology Crystallization Crystallography, Bacterial/*genetics Models, Microbial/genetics Genes, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Secondary Recombinant Fusion Proteins/isolation & purification Structure-Activity Relationship Support, Site-Directed Protein Conformation Protein Structure, Structural, Unité ARN, X-Ray Drug Resistance},
pubstate = {published},
tppubtype = {article}
}
Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry J C, Moras D
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction Article de journal
Dans: EMBO J, vol. 13, no. 2, p. 327-337, 1994, ISBN: 8313877, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Adenosine Triphosphate/metabolism Amino Acid Sequence Animals Aspartate-tRNA Ligase/chemistry/genetics/*metabolism Binding Sites Computer Graphics Human Molecular Sequence Data Mutagenesis, Amino Acid Structure-Activity Relationship Support, ERIANI, Non-U.S. Gov't, Site-Directed Saccharomyces cerevisiae/*enzymology Sequence Homology, Unité ARN
@article{,
title = {The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction},
author = {J Cavarelli and G Eriani and B Rees and M Ruff and M Boeglin and A Mitschler and F Martin and J Gangloff and J C Thierry and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8313877},
isbn = {8313877},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {2},
pages = {327-337},
abstract = {The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group and by amino acids conserved in the aspartyl synthetase family. The amino acids in contact with the substrates have been probed by site-directed mutagenesis for their functional implication.},
note = {0261-4189
Journal Article},
keywords = {Acylation Adenosine Triphosphate/metabolism Amino Acid Sequence Animals Aspartate-tRNA Ligase/chemistry/genetics/*metabolism Binding Sites Computer Graphics Human Molecular Sequence Data Mutagenesis, Amino Acid Structure-Activity Relationship Support, ERIANI, Non-U.S. Gov't, Site-Directed Saccharomyces cerevisiae/*enzymology Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Buttcher V, Senger B, Schumacher S, Reinbolt J, Fasiolo F
Dans: Biochem Biophys Res Commun, vol. 200, no. 1, p. 370-377, 1994, ISBN: 8166708, (0006-291x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/metabolism Anticodon/*genetics Base Composition Base Sequence Chromosomes, Artificial, Bacterial Guanine Inversion (Genetics) Lysine-tRNA Ligase/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Plasmids RNA, Genetic Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation & purification Uracil, Gln/chemistry/genetics RNA, Ile/chemistry/*genetics RNA, Lys/chemistry/*genetics Saccharomyces cerevisiae/*genetics *Suppression, Structural, Transfer, Unité ARN, Yeast Escherichia coli/*genetics Genes
@article{,
title = {Modulation of the suppression efficiency and amino acid identity of an artificial yeast amber isoleucine transfer RNA in Escherichia coli by a G-U pair in the anticodon stem},
author = {V Buttcher and B Senger and S Schumacher and J Reinbolt and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8166708},
isbn = {8166708},
year = {1994},
date = {1994-01-01},
journal = {Biochem Biophys Res Commun},
volume = {200},
number = {1},
pages = {370-377},
abstract = {The artificial amber suppressor corresponding to the major isoleucine tRNA from yeast (pVBt5), when expressed in E. coli, is a poor suppressor of the amber mutation lacIam181-Z. By analysing mutant forms, we could show that this was due to the presence of a U30-G40 wobble pair in the anticodon stem of the yeast tRNA and not to the level of the heterologously expressed tRNA. Efficient suppressors were obtained by restoring a normal U30-A40 or G30-C40 Watson-Crick pair. In vivo the mutant forms are exclusively charged by the bacterial lysyl-tRNA synthetase (LysRS), whereas the original yeast amber tRNA is charged at a low level by E. coli glutaminyl-tRNA synthetase (GlnRS) and LysRS. The inversion of the U30-G40 pair also induces a loss of the Gln identity. We conclude from these experiments that the U30-G40 base pair constitutes a negative determinant for LysRS interaction which operates either at the level of complex formation or at the catalytic step. As no direct contacts are seen between GlnRS and positions 30-40 of the complexed homologous tRNA, the U30-G40 pair of pVBt5 is believed to influence aminoacylation by GlnRS indirectly, probably at the level of the anticodon loop conformation by favouring an optimal apposition of the anticodon nucleotides with the protein.},
note = {0006-291x
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/metabolism Anticodon/*genetics Base Composition Base Sequence Chromosomes, Artificial, Bacterial Guanine Inversion (Genetics) Lysine-tRNA Ligase/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Plasmids RNA, Genetic Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation & purification Uracil, Gln/chemistry/genetics RNA, Ile/chemistry/*genetics RNA, Lys/chemistry/*genetics Saccharomyces cerevisiae/*genetics *Suppression, Structural, Transfer, Unité ARN, Yeast Escherichia coli/*genetics Genes},
pubstate = {published},
tppubtype = {article}
}
Blomberg P, Engdahl H M, Malmgren C, Romby P, Wagner E G
Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap-independent RepA synthesis Article de journal
Dans: Mol Microbiol, vol. 12, no. 1, p. 49-60, 1994, ISBN: 7520116, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN
@article{,
title = {Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap-independent RepA synthesis},
author = {P Blomberg and H M Engdahl and C Malmgren 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=7520116},
isbn = {7520116},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {12},
number = {1},
pages = {49-60},
abstract = {The replication frequency of plasmid R1 is controlled by an antisense RNA, CopA, that inhibits the synthesis of the replication initiator protein, RepA, at the post-transcriptional level. This inhibition is indirect and affects translation of a leader peptide reading frame (tap). Translation of tap is required for repA translation (Blomberg et al., 1992). Here we asked whether an RNA stem-loop sequestering the repA ribosome-binding site blocks tap translation-independent repA expression. Destabilization of this structure resulted in tap-independent RepA synthesis, concomitant with a loss of CopA-mediated inhibition; thus, CopA acts at the level of tap translation. Structure probing of RepA mRNAs confirmed that the introduced mutations induced a local destabilization in the repA ribosome-binding site stem-loop. An increased spacing between the repA Shine-Dalgarno region and the start codon permitted even higher repA expression. In Incl alpha/IncB plasmids, an RNA pseudoknot acts as an activator for rep translation. We suggest that the regulatory pathway in plasmid R1 does not involve an activator RNA pseudoknot.},
note = {0950-382x
Journal Article},
keywords = {Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Benard L, Philippe C, Dondon L, Grunberg-Manago M, Ehresmann B, Ehresmann C, Portier C
Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli Article de journal
Dans: Mol Microbiol, vol. 14, no. 1, p. 31-40, 1994, ISBN: 7830558, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN
@article{,
title = {Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli},
author = {L Benard and C Philippe and L Dondon and M Grunberg-Manago 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=7830558},
isbn = {7830558},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {14},
number = {1},
pages = {31-40},
abstract = {Expression of rpsO, the gene encoding the small ribosomal protein S15, is autoregulated at the translational level by S15, which binds to its mRNA in a region overlapping the ribosome-binding site. By measuring the effect of mutations on the expression of a translational rpsO-lacZ fusion and the S15 binding affinity for the translational operator, the formation of a pseudoknot in the operator site in vivo is fully demonstrated and appears to be a prerequisite for S15 binding. The mutational analysis suggests also that specific determinants for S15 binding are located in very limited regions of the structure formed by the pseudoknot. It is deduced that a specific pseudoknot conformation is a key element for autoregulation.},
note = {0950-382x
Journal Article},
keywords = {Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baron C, Sturchler C, Wu X Q, Gross H J, Krol A, Bock A
Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 12, p. 2228-2233, 1994, ISBN: 8036149, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/chemistry/*genetics Selenocysteine/chemistry Serine-tRNA Ligase/metabolism Support, Animals Bacterial Proteins/metabolism Base Sequence Cloning, Molecular Escherichia coli/*genetics Genetic Complementation Test Human Nucleic Acid Conformation Peptide Elongation Factors/metabolism Proteins/*biosynthesis/genetics RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN
@article{,
title = {Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli},
author = {C Baron and C Sturchler and X Q Wu and H J Gross and A Krol and A Bock},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8036149},
isbn = {8036149},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {12},
pages = {2228-2233},
abstract = {Although the tRNA species directing selenocysteine insertion in prokaryotes differ greatly in their primary structure from that of their eukaryotic homologues they share very similar three-dimensional structures. To analyse whether this conservation of the overall shape of the molecules reflects a conservation of their functional interactions it was tested whether the selenocysteine inserting tRNA species from Homo sapiens supports selenoprotein synthesis in E. coli. It was found that the expression of the human tRNA(Sec) gene in E.coli can complement a lesion in the tRNA(Sec) gene of this organism. Transcripts of the Homo sapiens and Xenopus laevis tRNA(Sec) genes synthesised in vitro were amino-acylated by the E.coli seryl-tRNA ligase although at a very low rate and the resulting seryl-tRNA(Sec) was bound to and converted into selenocysteyl-tRNA(Sec) by the selenocysteine synthase of this organism. Selenocysteyl-tRNA(Sec) from both eukaryotes was able to form a complex with translation factor SELB from E.coli. Although the mechanism of selenocysteine incorporation into seleno-proteins appears to be rather different in E.coli and in vertebrates, we observe here a surprising conservation of functions over an enormous evolutionary distance.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/chemistry/*genetics Selenocysteine/chemistry Serine-tRNA Ligase/metabolism Support, Animals Bacterial Proteins/metabolism Base Sequence Cloning, Molecular Escherichia coli/*genetics Genetic Complementation Test Human Nucleic Acid Conformation Peptide Elongation Factors/metabolism Proteins/*biosynthesis/genetics RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baranowski W, Dirheimer G, Jakowicki J A, Keith G
Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women Article de journal
Dans: Cancer Res, vol. 54, no. 16, p. 4468-4471, 1994, ISBN: 8044797, (0008-5472 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adolescent Adult Female Guanine/*analogs & derivatives/analysis Human Middle Aged Ovarian Neoplasms/*chemistry/pathology RNA, Neoplasm/*chemistry RNA, Non-U.S. Gov't, Transfer/*chemistry Support, Unité ARN
@article{,
title = {Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women},
author = {W Baranowski and G Dirheimer and J A Jakowicki and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8044797},
isbn = {8044797},
year = {1994},
date = {1994-01-01},
journal = {Cancer Res},
volume = {54},
number = {16},
pages = {4468-4471},
abstract = {The tRNAs from rapidly growing tissues, particularly from neoplasia, often exhibit queuine deficiency. In order to check whether different kinds of ovarian tumors display queuine deficiencies we have analyzed tRNA samples from 16 ovarian malignancies. The tRNAs from histologically normal myometrium (4 samples) and myoma (6 samples) were taken as healthy tissue and benign tumor references. Queuine deficiency was determined by an exchange assay using [8-3H]guanine and tRNA:guanine transglycosylase from Escherichia coli. The mean values of queuine deficiencies in tRNAs were: 10.95 +/- 2.21 (SD) pmol/A260 in gonadal and germ cell tumors (5 cases); 23.75 +/- 7.89 pmol/A260 in primary epithelial tumors (9 cases); and 34.58 +/- 7.18 pmol/A260 in metastatic tumors (2 cases). These values displayed statistically significant differences (P = 0.0003, Kruskal-Wallis test). The queuine deficiencies in tRNAs significantly increased when moving from well-differentiated through moderately differentiated to poorly differentiated tumors, with the highest values found in poorly differentiated metastatic tumors (P = 0.0002, Kruskal-Wallis test). Queuine deficiency determination in tRNAs is proposed as a factor for clinical outcome prognosis of ovarian malignancies.},
note = {0008-5472
Journal Article},
keywords = {Adolescent Adult Female Guanine/*analogs & derivatives/analysis Human Middle Aged Ovarian Neoplasms/*chemistry/pathology RNA, Neoplasm/*chemistry RNA, Non-U.S. Gov't, Transfer/*chemistry Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Allmang C, Mougel M, Westhof E, Ehresmann B, Ehresmann C
Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8 Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 18, p. 3708-3714, 1994, ISBN: 7937081, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN
@article{,
title = {Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8},
author = {C Allmang and M Mougel and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7937081},
isbn = {7937081},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {18},
pages = {3708-3714},
abstract = {Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.},
note = {0305-1048
Journal Article},
keywords = {16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M L, Reinbolt J, Gangloff J, Dirheimer G, Wilhelm F X
Transfer RNA binding protein in the nucleus of Saccharomyces cerevisiae Article de journal
Dans: FEBS Lett, vol. 349, no. 2, p. 260-264, 1994, ISBN: 8050578, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Cell Nucleus/*metabolism Chromatography, Fungal/*isolation & purification RNA, High Pressure Liquid DNA/metabolism DNA-Binding Proteins/genetics/*metabolism Fungal Proteins/genetics/*metabolism Molecular Sequence Data RNA, Transfer/*isolation & purification Saccharomyces cerevisiae/*metabolism *Saccharomyces cerevisiae Proteins, Unité ARN
@article{,
title = {Transfer RNA binding protein in the nucleus of Saccharomyces cerevisiae},
author = {M L Wilhelm and J Reinbolt and J Gangloff and G Dirheimer and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8050578},
isbn = {8050578},
year = {1994},
date = {1994-01-01},
journal = {FEBS Lett},
volume = {349},
number = {2},
pages = {260-264},
abstract = {A yeast nuclear protein that binds to tRNA was identified using a RNA mobility shift assay. Northwestern blotting and N-terminal sequencing experiments indicate that this tRNA-binding protein is identical to zuotin which has previously been shown to bind to Z-DNA [(1992) EMBO J. 11, 3787-3796]. Labeled tRNA and poly(dG-m5dC) stabilized in the Z-DNA form identify the same protein on a Northwestern blot. In a gel retardation assay poly(dG-m5dC) in the Z-form strongly diminishes the binding of tRNA to zuotin. These studies establish that zuotin is able to bind to both tRNA and Z-DNA. Zuotin may be transiently associated with tRNA in the nucleus of yeast cells and play a role in its processing or transport to the cytoplasm.},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Sequence Cell Nucleus/*metabolism Chromatography, Fungal/*isolation & purification RNA, High Pressure Liquid DNA/metabolism DNA-Binding Proteins/genetics/*metabolism Fungal Proteins/genetics/*metabolism Molecular Sequence Data RNA, Transfer/*isolation & purification Saccharomyces cerevisiae/*metabolism *Saccharomyces cerevisiae Proteins, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Wilhelm F X, Keith G, Agoutin B, Heyman T
Dans: Nucleic Acids Res, vol. 22, no. 22, p. 4560-4565, 1994, ISBN: 7527135, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN
@article{,
title = {Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles},
author = {M Wilhelm and F X Wilhelm and G Keith and B Agoutin and T Heyman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7527135},
isbn = {7527135},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {22},
pages = {4560-4565},
abstract = {Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Santos M A, el-Adlouni C, Cox A D, Luz J M, Keith G, Tuite M F
Transfer RNA profiling: a new method for the identification of pathogenic Candida species Article de journal
Dans: Yeast, vol. 10, no. 5, p. 625-636, 1994, ISBN: 7941747, (0749-503x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Candida/classification/*genetics/pathogenicity Electrophoresis, Fungal RNA, Non-U.S. Gov't, Polyacrylamide Gel Genetic Markers RNA, Transfer/*analysis Support, Unité ARN
@article{,
title = {Transfer RNA profiling: a new method for the identification of pathogenic Candida species},
author = {M A Santos and C el-Adlouni and A D Cox and J M Luz and G Keith and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7941747},
isbn = {7941747},
year = {1994},
date = {1994-01-01},
journal = {Yeast},
volume = {10},
number = {5},
pages = {625-636},
abstract = {A new molecular taxonomic method applicable to the identification of medically important Candida species and other yeast species has been developed. It is based on the electrophoretic pattern of total tRNA samples (a 'tRNA profile') isolated from Candida species and generated using high-resolution semi-denaturing urea-polyacrylamide gel electrophoresis and methylene blue staining. Species-specific tRNA profiles for the species C. albicans, C. tropicalis, C. parapsilosis, C. guilliermondii, C. glabrata and Pichia guilliermondii were obtained. Detailed studies with the major human pathogen of the Candida genus, C. albicans, demonstrated that the tRNA profile for a given species was both reproducible and strain-independent; seven different C. albicans strains generated identical tRNA profiles. Minor strain-specific heterogeneities in the tRNA profiles of C. guilliermondii and C. parapsilosis were detected, but in neither case did they significantly alter the species-specific diagnostic tRNA profile. The potential of this method in clarifying taxonomic anomalies was demonstrated by the finding that Type I and Type II strains of C. stellatoidea generate very different tRNA profiles, with that of a Type II strain being identical to the C. albicans tRNA profile. This method offers a number of advantages over current electrophoretic karyotype methods for species identification, both within the Candida genus and with yeast species in general.},
note = {0749-503x
Journal Article},
keywords = {Candida/classification/*genetics/pathogenicity Electrophoresis, Fungal RNA, Non-U.S. Gov't, Polyacrylamide Gel Genetic Markers RNA, Transfer/*analysis Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Meissner W, Wanandi I, Carbon P, Krol A, Seifart K H
Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 4, p. 553-559, 1994, ISBN: 8127703, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics Support, Animals Base Sequence DNA-Binding Proteins/*physiology Human Molecular Sequence Data Oligonucleotide Probes RNA, Genetic Xenopus laevis, Non-U.S. Gov't TATA Box Transcription Factors/*genetics Transcription, Transfer, Unité ARN
@article{,
title = {Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro},
author = {W Meissner and I Wanandi and P Carbon and A Krol and K H Seifart},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8127703},
isbn = {8127703},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {4},
pages = {553-559},
abstract = {It has previously been reported that transcription in vivo of the tRNA(Sec) gene requires three promoter elements, a PSE and a TATA-box upstream of the coding region which are functionally interchangeable with the U6 snRNA gene counterparts and an internal B-block, resembling that of classical tRNA genes (1). We have established an in vitro transcription system from HeLa cells in which three factors, which are either essential for or stimulate transcription were identified. Apart from the TATA-binding protein TBP, the PSE-binding protein PBP was found to be essentially required for expression of the gene. Depletion of PBP from cell extracts by PSE-oligonucleotides abolished tRNA(Sec) transcription, which could be reconstituted by readdition of partially purified PBP. Addition of increasing amounts of recombinant human TBP to an S100 extract stimulated transcription of the tRNA(Sec), the mouse U6 snRNA and the human Y3 genes, an effect which was not observed in the case of a TATA-less tRNA gene. Purified human TFIIA strongly stimulated tRNA(Sec) transcription in a fashion depending on the concentration of TBP. Surprisingly, partially purified TFIIIC was shown to be dispensable for transcription in vitro and unable to bind the B-block of this gene in vitro, although its sequence matches the consensus for this element. Collectively, these data suggest that the mechanism by which transcription complexes are formed on the tRNA(Sec) gene is dramatically different from that observed for classical tRNA genes and much more resembles that observed for externally controlled pol III genes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*genetics Support, Animals Base Sequence DNA-Binding Proteins/*physiology Human Molecular Sequence Data Oligonucleotide Probes RNA, Genetic Xenopus laevis, Non-U.S. Gov't TATA Box Transcription Factors/*genetics Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Heyman T, Agoutin B, Fix C, Dirheimer G, Keith G
Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU Article de journal
Dans: FEBS Lett, vol. 347, no. 2-3, p. 143-146, 1994, ISBN: 8033992, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU},
author = {T Heyman and B Agoutin and C Fix and G Dirheimer and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8033992},
isbn = {8033992},
year = {1994},
date = {1994-01-01},
journal = {FEBS Lett},
volume = {347},
number = {2-3},
pages = {143-146},
abstract = {The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.},
note = {0014-5793
Journal Article},
keywords = {Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1993
Zhang G Y, Beltchev B, Fournier A, Zhang Y H, Malassine A, Bisbal C, Ehresmann B, Ehresmann C, Darlix J L, Thang M N
High levels of 2',5'-oligoadenylate synthetase and 2',5'-oligoadenylate-dependent endonuclease in human trophoblast Article de journal
Dans: AIDS Res Hum Retroviruses, vol. 9, no. 2, p. 189-196, 1993, ISBN: 8457385, (0889-2229 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 2', 5'-Oligoadenylate Synthetase/*metabolism Endoribonucleases/*metabolism Enzyme Activation/drug effects Female HIV Infections/transmission HIV-1/*physiology Human In Vitro Maternal-Fetal Exchange Pregnancy RNA, Non-U.S. Gov't Trophoblasts/*enzymology/*microbiology Virus Replication, Unité ARN, Viral/pharmacology Support
@article{,
title = {High levels of 2',5'-oligoadenylate synthetase and 2',5'-oligoadenylate-dependent endonuclease in human trophoblast},
author = {G Y Zhang and B Beltchev and A Fournier and Y H Zhang and A Malassine and C Bisbal and B Ehresmann and C Ehresmann and J L Darlix and M N Thang},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8457385},
isbn = {8457385},
year = {1993},
date = {1993-01-01},
journal = {AIDS Res Hum Retroviruses},
volume = {9},
number = {2},
pages = {189-196},
abstract = {Human placenta contains a high level of 2',5'-oligoadenylate (2-5A) synthetase activity of the 100-kD form of the enzyme. About 20% of the placental 2-5A synthetase activity was found to be cytosolic, whereas the remaining 80% was released by 0.5 M KCl in the presence of detergent. Most of the enzyme activity was localized in trophoblast cells, which also contain a high level of 2-5A-dependent RNase L activity. The purified trophoblast 100-kD 2-5A synthetase was shown to be activated by human immunodeficiency virus type 1 (HIV-1) 5' RNA 1-311 and 1-707, which both contain the TAR and primer binding site (PBS) structured regions. These two HIV-1 RNAs activated human trophoblast 2-5A synthetase at the same level as poly(I).poly (C), a standard highly efficient activator of the enzyme, and at the same optimal concentration. On the contrary, HIV-1 RNA 311-618, a poorly structured region missing TAR and PBS, was shown to be a poor activator of the enzyme. The specific cellular location of the 2-5A synthetase and its efficient activation by HIV 5' RNA favors the idea that the trophoblast 2-5A system negatively controls HIV replication in trophoblasts.},
note = {0889-2229
Journal Article},
keywords = {2', 5'-Oligoadenylate Synthetase/*metabolism Endoribonucleases/*metabolism Enzyme Activation/drug effects Female HIV Infections/transmission HIV-1/*physiology Human In Vitro Maternal-Fetal Exchange Pregnancy RNA, Non-U.S. Gov't Trophoblasts/*enzymology/*microbiology Virus Replication, Unité ARN, Viral/pharmacology Support},
pubstate = {published},
tppubtype = {article}
}
Xue H, Shen W, Giege R, Wong J T
Identity elements of tRNA(Trp). Identification and evolutionary conservation Article de journal
Dans: J Biol Chem, vol. 268, no. 13, p. 9316-9322, 1993, ISBN: 8486627, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN
@article{,
title = {Identity elements of tRNA(Trp). Identification and evolutionary conservation},
author = {H Xue and W Shen and R Giege and J T Wong},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8486627},
isbn = {8486627},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {13},
pages = {9316-9322},
abstract = {In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.},
note = {0021-9258
Journal Article},
keywords = {Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wohrl B M, Ehresmann B, Keith G, Grice S F Le
Nuclease footprinting of human immunodeficiency virus reverse transcriptase/tRNA(Lys-3) complexes Article de journal
Dans: J Biol Chem, vol. 268, no. 18, p. 13617-13624, 1993, ISBN: 7685766, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence HIV-1/*enzymology HIV-1 Reverse Transcriptase Hydrolysis Molecular Sequence Data Nucleic Acid Conformation RNA, Double-Stranded/metabolism RNA, Lys/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism Recombinant Proteins/metabolism Ribonuclease, Non-U.S. Gov't Support, P.H.S., Pancreatic/metabolism Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Nuclease footprinting of human immunodeficiency virus reverse transcriptase/tRNA(Lys-3) complexes},
author = {B M Wohrl and B Ehresmann and G Keith and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685766},
isbn = {7685766},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {18},
pages = {13617-13624},
abstract = {Nuclease footprinting has been used to probe features of binary complexes of type 1 human immunodeficiency virus reverse transcriptase (HIV-1 RT) with both natural and synthetic preparations of its cognate replication primer, tRNA(Lys-3). In addition to heterodimeric RT (p66/p51), ribonucleoprotein complexes containing either the p66 or p51 subunit were analyzed. Footprinting experiments employed both structure- and sequence-specific nucleases. Our results indicate a similar mode of interaction for the three RT preparations tested, suggesting contact with each loop of the tRNA primer (D, anticodon, and T psi C), as well as minor perturbation of the anticodon stem. Although there is little evidence for extensive disruption of the 3'-acceptor stem. RNase A footprinting data with natural and synthetic tRNA suggests that potential base pairing between the T psi C and D loops is disrupted in the presence of RT.},
note = {0021-9258
Journal Article},
keywords = {Anticodon Base Sequence HIV-1/*enzymology HIV-1 Reverse Transcriptase Hydrolysis Molecular Sequence Data Nucleic Acid Conformation RNA, Double-Stranded/metabolism RNA, Lys/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism Recombinant Proteins/metabolism Ribonuclease, Non-U.S. Gov't Support, P.H.S., Pancreatic/metabolism Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sturchler C, Westhof E, Carbon P, Krol A
Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec) Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 5, p. 1073-1079, 1993, ISBN: 8464694, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN
@article{,
title = {Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec)},
author = {C Sturchler and E Westhof and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464694},
isbn = {8464694},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {5},
pages = {1073-1079},
abstract = {Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Skripkin E, Yusupova G, Yusupov M, Kessler P, Ehresmann C, Ehresmann B
Synthesis and ribosome binding properties of model mRNAs modified with undecagold cluster Article de journal
Dans: Bioconjug Chem, vol. 4, no. 6, p. 549-553, 1993, ISBN: 8305524, (1043-1802 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study Escherichia coli/metabolism Gold/metabolism Models, Genetic/drug effects/genetics, Messenger/*chemical synthesis/chemistry/*metabolism RNA, Met/metabolism Ribosomes/*metabolism Support, Molecular Molecular Sequence Data Organometallic Compounds/*chemical synthesis/chemistry/*metabolism RNA, Non-U.S. Gov't Translation, Transfer, Unité ARN
@article{,
title = {Synthesis and ribosome binding properties of model mRNAs modified with undecagold cluster},
author = {E Skripkin and G Yusupova and M Yusupov and P Kessler and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8305524},
isbn = {8305524},
year = {1993},
date = {1993-01-01},
journal = {Bioconjug Chem},
volume = {4},
number = {6},
pages = {549-553},
abstract = {The synthesis and purification of short model messenger RNAs modified with undecagold cluster are described. A monoamino undecagold cluster was introduced on the oxidized 3' cis-glycol group of the mRNA followed by reduction of the formed Schiff's base. The stability of the modified mRNA under the conditions used for in vitro messenger RNA translation is studied. The possibility of the formation of a specific translational initiation complex with bacterial ribosomes and modified mRNAs is shown. The results of these experiments indicate that the attachment of an undecagold cluster to a mRNA is a useful tool for electron microscopic and crystallographic studies.},
note = {1043-1802
Journal Article},
keywords = {Base Sequence Comparative Study Escherichia coli/metabolism Gold/metabolism Models, Genetic/drug effects/genetics, Messenger/*chemical synthesis/chemistry/*metabolism RNA, Met/metabolism Ribosomes/*metabolism Support, Molecular Molecular Sequence Data Organometallic Compounds/*chemical synthesis/chemistry/*metabolism RNA, Non-U.S. Gov't Translation, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schimmel P, Giege R, Moras D, Yokoyama S
An operational RNA code for amino acids and possible relationship to genetic code Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 19, p. 8763-8768, 1993, ISBN: 7692438, (0027-8424 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/metabolism Base Sequence Conserved Sequence Escherichia coli/enzymology/genetics *Genetic Code Nucleic Acid Conformation Oligoribonucleotides RNA/*genetics RNA, Non-U.S. Gov't Support, P.H.S., Transfer/*genetics/metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {An operational RNA code for amino acids and possible relationship to genetic code},
author = {P Schimmel and R Giege and D Moras and S Yokoyama},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7692438},
isbn = {7692438},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {19},
pages = {8763-8768},
abstract = {RNA helical oligonucleotides that recapitulate the acceptor stems of transfer RNAs, and that are devoid of the anticodon trinucleotides of the genetic code, are aminoacylated by aminoacyl tRNA synthetases. The specificity of aminoacylation is sequence dependent, and both specificity and efficiency are generally determined by only a few nucleotides proximal to the amino acid attachment site. This sequence/structure-dependent aminoacylation of RNA oligonucleotides constitutes an operational RNA code for amino acids. To a rough approximation, members of the two different classes of tRNA synthetases are, like tRNAs, organized into two major domains. The class-defining conserved domain containing the active site incorporates determinants for recognition of RNA mini-helix substrates. This domain may reflect the primordial synthetase, which was needed for expression of the operational RNA code. The second synthetase domain, which generally is less or not conserved, provides for interactions with the second domain of tRNA, which incorporates the anticodon. The emergence of the genetic from the operational RNA code could occur when the second domain of synthetases was added with the anticodon-containing domain of tRNAs.},
note = {0027-8424
Journal Article
Review
Review, Tutorial},
keywords = {*Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/metabolism Base Sequence Conserved Sequence Escherichia coli/enzymology/genetics *Genetic Code Nucleic Acid Conformation Oligoribonucleotides RNA/*genetics RNA, Non-U.S. Gov't Support, P.H.S., Transfer/*genetics/metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Santos M A, Keith G, Tuite M F
Non-standard translational events in Candida albicans mediated by an unusual seryl-tRNA with a 5'-CAG-3' (leucine) anticodon Article de journal
Dans: EMBO J, vol. 12, no. 2, p. 607-616, 1993, ISBN: 8440250, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Base Sequence Candida albicans/*genetics Cloning, Fungal Genes, Fungal Leucine/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/isolation & purification RNA, Genetic, Molecular DNA, Non-U.S. Gov't *Translation, Ser/chemistry/*genetics/isolation & purification Support, Transfer, Unité ARN
@article{,
title = {Non-standard translational events in Candida albicans mediated by an unusual seryl-tRNA with a 5'-CAG-3' (leucine) anticodon},
author = {M A Santos and G Keith and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8440250},
isbn = {8440250},
year = {1993},
date = {1993-01-01},
journal = {EMBO J},
volume = {12},
number = {2},
pages = {607-616},
abstract = {From in vitro translation studies we have previously demonstrated the existence of an apparent efficient UAG (amber) suppressor tRNA in the dimorphic fungus Candida albicans (Santos et al., 1990). Using an in vitro assay for termination codon readthrough the tRNA responsible was purified to homogeneity from C.albicans cells. The determined sequence of the purified tRNA predicts a 5'-CAG-3' anticodon that should decode the leucine codon CUG and not the UAG termination codon as originally hypothesized. However, the tRNA(CAG) sequence shows greater nucleotide homology with seryl-tRNAs from the closely related yeast Saccharomyces cerevisiae than with leucyl-tRNAs from the same species. In vitro tRNA-charging studies demonstrated that the purified tRNA(CAG) is charged with Ser. The gene encoding the tRNA was cloned from C.albicans by a PCR-based strategy and DNA sequence analysis confirmed both the structure of the tRNA(CAG) and the absence of any introns in the tRNA gene. The copy number of the tRNA(CAG) gene (1-2 genes per haploid genome) is in agreement with the relatively low abundance (< 0.5% total tRNA) of this tRNA. In vitro translation studies revealed that the purified tRNA(CAG) could induce apparent translational bypass of all three termination codons. However, peptide mapping of in vitro translation products demonstrated that the tRNA(CAG) induces translational misreading in the amino-terminal region of two RNA templates employed, namely the rabbit alpha- and beta-globin mRNAs. These results suggest that the C.albicans tRNA(CAG) is not an 'omnipotent' suppressor tRNA but rather may mediate a novel non-standard translational event in vitro during the translation of the CUG codon. The possible nature of this non-standard translation event is discussed in the context of both the unusual structural features of the tRNA(CAG) and its in vitro behaviour.},
note = {0261-4189
Journal Article},
keywords = {*Anticodon Base Sequence Candida albicans/*genetics Cloning, Fungal Genes, Fungal Leucine/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/isolation & purification RNA, Genetic, Molecular DNA, Non-U.S. Gov't *Translation, Ser/chemistry/*genetics/isolation & purification Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Roth A, Eriani G, Dirheimer G, Gangloff J
Kinetic properties of pure overproduced Bacillus subtilis phenylalanyl-tRNA synthetase do not favour its in vivo inhibition by ochratoxin A Article de journal
Dans: FEBS Lett, vol. 326, no. 1-3, p. 87-91, 1993, ISBN: 8325392, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacillus subtilis/drug effects/*enzymology Binding, Bacterial, Competitive Escherichia coli/enzymology/genetics Kinetics Macromolecular Systems Ochratoxins/*pharmacology Phenylalanine/metabolism Phenylalanine-tRNA Ligase/antagonists & inhibitors/*metabolism Support, ERIANI, Non-U.S. Gov't Transformation, Unité ARN
@article{,
title = {Kinetic properties of pure overproduced Bacillus subtilis phenylalanyl-tRNA synthetase do not favour its in vivo inhibition by ochratoxin A},
author = {A Roth and G Eriani and G Dirheimer and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8325392},
isbn = {8325392},
year = {1993},
date = {1993-01-01},
journal = {FEBS Lett},
volume = {326},
number = {1-3},
pages = {87-91},
abstract = {Ochratoxine A (OTA) inhibits growth of Bacillus subtilis at pHs below 7. Since OTA is a phenylalanine analogue, this effect could be due to inhibition of phenylalanine-tRNA synthetase (PheRS) by competition of this mycotoxin with the amino acid. Homogeneous PheRS was purified from Bacillus subtilis and from E. coli transformed with the PheRS gene. The latter produced about 40 times more PheRS than B. subtilis. The Km and Ki values of PheRS, respectively, for phenylalanine and OTA were measured and their concentrations within the cell determined. It appears that the concentration of OTA in the cell, in spite of a 25-fold accumulation, remained too low to significantly compete with phenylalanine. This does not suggest PheRS to be the target of OTA in cell growth and protein synthesis inhibition in Bacillus subtilis. It was also shown that the 2-3-fold increase of PheRS in OTA-treated cells is not due to phenylalanine-controlled attenuation regulation.},
note = {0014-5793
Journal Article},
keywords = {Bacillus subtilis/drug effects/*enzymology Binding, Bacterial, Competitive Escherichia coli/enzymology/genetics Kinetics Macromolecular Systems Ochratoxins/*pharmacology Phenylalanine/metabolism Phenylalanine-tRNA Ligase/antagonists & inhibitors/*metabolism Support, ERIANI, Non-U.S. Gov't Transformation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Reinbolt J, Eliseikina I, Sedelnilkova S, Garber M, Ehresmann C, Ehresmann B
The complete amino acid sequence of ribosomal protein S8 from Thermus thermophilus Article de journal
Dans: J Protein Chem, vol. 12, no. 1, p. 79-83, 1993, ISBN: 8427638, (0277-8033 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Serine Endopeptidases/chemistry Thermus/chemistry Thermus thermophilus/*chemistry, Amino Acid Sequence Hydrolysis Metalloendopeptidases/chemistry Molecular Sequence Data Ribosomal Proteins/*chemistry Sequence Homology, Unité ARN
@article{,
title = {The complete amino acid sequence of ribosomal protein S8 from Thermus thermophilus},
author = {J Reinbolt and I Eliseikina and S Sedelnilkova and M Garber and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8427638},
isbn = {8427638},
year = {1993},
date = {1993-01-01},
journal = {J Protein Chem},
volume = {12},
number = {1},
pages = {79-83},
abstract = {Protein S8 from Thermus thermophilus consists of 138 amino acids of M(r) 15,840. Its primary structure was established using peptide sequences from two different digests. Protein S8 from T. thermophilus shares a high percentage of identity with protein S8 from Thermus aquaticus. There are some consensus sequences between proteins S8 from eubacteria, archebacteria, chloroplasts, and cyanelles.},
note = {0277-8033
Journal Article},
keywords = {Amino Acid Serine Endopeptidases/chemistry Thermus/chemistry Thermus thermophilus/*chemistry, Amino Acid Sequence Hydrolysis Metalloendopeptidases/chemistry Molecular Sequence Data Ribosomal Proteins/*chemistry Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Putz J, Puglisi J D, Florentz C, Giege R
Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA Article de journal
Dans: EMBO J, vol. 12, no. 7, p. 2949-2957, 1993, ISBN: 8335008, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA},
author = {J Putz and J D Puglisi and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8335008},
isbn = {8335008},
year = {1993},
date = {1993-01-01},
journal = {EMBO J},
volume = {12},
number = {7},
pages = {2949-2957},
abstract = {We have investigated the functional relationship between nucleotides in yeast tRNAAsp that are important for aspartylation by yeast aspartyl-tRNA synthetase. Transcripts of tRNAAsp with two or more mutations at identity positions G73, G34, U35, C36 and base pair G10-U25 have been prepared and the steady-state kinetics of their aspartylation were measured. Multiple mutations affect the catalytic activities of the synthetase mainly at the level of the catalytic constant, kcat. Kinetic data were expressed as free energy variation at transition state of these multiple mutants and comparison of experimental values with those calculated from results on single mutants defined three types of relationships between the identity nucleotides of this tRNA. Nucleotides located far apart in the three-dimensional structure of the tRNA act cooperatively whereas nucleotides of the anticodon triplet act either additively or anti-cooperatively. These results are related to the specific interactions of functional groups on identity nucleotides with amino acids in the protein as revealed by the crystal structure of the tRNAAsp/aspartyl-tRNA synthetase complex. These relationships between identity nucleotides may play an important role in the biological function of tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}