Wagner C, Ehresmann C, Ehresmann B, Brunel C
Mechanism of dimerization of bicoid mRNA: initiation and stabilization Article de journal
Dans: J Biol Chem, vol. 279, no. 6, p. 4560-4569, 2004, ISBN: 14607826, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: BRUNEL Animals Base Sequence Dimerization Drosophila Proteins/*genetics Drosophila melanogaster/embryology/*genetics/*metabolism Homeodomain Proteins/*genetics Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA Interference RNA Stability RNA, Messenger/chemistry/*genetics/*metabolism Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics Trans-Activators/*genetics, U.S. Gov't, Unité ARN
@article{,
title = {Mechanism of dimerization of bicoid mRNA: initiation and stabilization},
author = {C Wagner and C Ehresmann and B Ehresmann and C Brunel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14607826},
isbn = {14607826},
year = {2004},
date = {2004-01-01},
journal = {J Biol Chem},
volume = {279},
number = {6},
pages = {4560-4569},
abstract = {Dimerization of bcd mRNA was shown to be important for the formation of ribonucleoprotein particles and their localization in Drosophila embryo. The cis-element responsible for dimerization is localized in a stem-loop domain (domain III) containing two essential complementary 6-nucleotide sequences in a hairpin loop (LIIIb) and an interior loop (LIIIa). Such an RNA element can potentially generate single or double "hand-by-arm" interactions leading to open and closed complexes, respectively. The former retains the possibility of forming multimers, whereas the latter does not. We showed previously that dimerization proceeds through a two-step mechanism, which includes a transition from the reversible initiation complex into a very stable one. Here we have addressed the nature of the initial interactions and the mechanism of transition. We engineered a series of different RNA fragments with the capacity to form defined open dimers, multimers, or closed dimers. We compared their thermodynamic and kinetic behavior and mapped nucleotides involved in intermolecular interactions by enzymatic and chemical footprinting experiments and chemical modification interference. Our results indicate that the initiation step leads to a reversible open dimer, involving a more limited number of intermolecular base pairs than expected. The two loops play distinct roles in this process, and the structure of loop IIIb is more constrained than that of loop IIIa. Thus, loop IIIa appears to be the driving element of the recognition process. The initial open dimer is then converted into a stable closed dimer, possibly through a kinetically controlled mechanism.},
note = {0021-9258
Journal Article},
keywords = {BRUNEL Animals Base Sequence Dimerization Drosophila Proteins/*genetics Drosophila melanogaster/embryology/*genetics/*metabolism Homeodomain Proteins/*genetics Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA Interference RNA Stability RNA, Messenger/chemistry/*genetics/*metabolism Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics Trans-Activators/*genetics, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sohm B, Sissler M, Park H, King M P, Florentz C
Recognition of human mitochondrial tRNALeu(UUR) by its cognate leucyl-tRNA synthetase Article de journal
Dans: J Mol Biol, vol. 339, no. 1, p. 17-29, 2004, ISBN: 15123417, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Cultured, FLORENTZ, FLORENTZ *Acylation Base Sequence Comparative Study Human Kinetics Leucine/metabolism Leucine-tRNA Ligase/genetics/*metabolism Mitochondria/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation Osteosarcoma/metabolism RNA/*genetics/metabolism RNA, Genetic/*genetics Tumor Cells, Leu/genetics/*metabolism Solutions Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S. Transcription, SISSLER, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Recognition of human mitochondrial tRNALeu(UUR) by its cognate leucyl-tRNA synthetase},
author = {B Sohm and M Sissler and H Park and M P King and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15123417},
isbn = {15123417},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {339},
number = {1},
pages = {17-29},
abstract = {Accuracy of protein synthesis depends on specific recognition and aminoacylation of tRNAs by their cognate aminoacyl-tRNA synthetases. Rules governing these processes have been established for numerous prokaryotic and eukaryotic cytoplasmic systems, but only limited information is available for human mitochondrial systems. It has been shown that the in vitro transcribed human mitochondrial tRNA(Leu(UUR)) does not fold into the expected cloverleaf, but is however aminoacylated by the human mitochondrial leucyl-tRNA synthetase. Here, the role of the structure of the amino acid acceptor branch and the anticodon branch of tRNA(Leu(UUR)) in recognition by leucyl-tRNA synthetase was investigated. The kinetic parameters for aminoacylation of wild-type and mutant tRNA(Leu(UUR)) transcripts and of native tRNA(Leu(UUR)) were determined. Solution structure probing was performed in the presence or in the absence of leucyl-tRNA synthetase and correlated with the aminoacylation kinetics for each tRNA. Replacement of mismatches in either the anticodon-stem or D-stem that are present in the wild-type tRNA(Leu(UUR)) by G-C base-pairs is sufficient to induce (i) cloverleaf folding, (ii) improved aminoacylation efficiency, and (iii) interactions with the synthetase that are similar to those with the native tRNA(Leu(UUR)). Leucyl-tRNA synthetase contacts tRNA(Leu(UUR)) in the amino acid acceptor stem, the anticodon stem, and the D-loop, which is unprecedented for a leucine aminoacylation system.},
note = {0022-2836
Journal Article},
keywords = {Cultured, FLORENTZ, FLORENTZ *Acylation Base Sequence Comparative Study Human Kinetics Leucine/metabolism Leucine-tRNA Ligase/genetics/*metabolism Mitochondria/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation Osteosarcoma/metabolism RNA/*genetics/metabolism RNA, Genetic/*genetics Tumor Cells, Leu/genetics/*metabolism Solutions Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S. Transcription, SISSLER, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rangan P, Masquida B, Westhof E, Woodson S A
Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA Article de journal
Dans: J Mol Biol, vol. 339, no. 1, p. 41-51, 2004, ISBN: 15123419, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15123419},
isbn = {15123419},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {339},
number = {1},
pages = {41-51},
abstract = {Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA(ile) from the bacterium Azoarcus was probed by ribonuclease T(1) and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3'-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg(2+) and the concentration of urea, and RNase T(1) experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5' and 3' ends of unspliced pre-tRNA.},
note = {0022-2836
Journal Article},
keywords = {Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Mathy N, Pellegrini O, Serganov A, Patel D J, Ehresmann C, Portier C
Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation Article de journal
Dans: Mol Microbiol, vol. 52, no. 3, p. 661-675, 2004, ISBN: 15101974, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN
@article{,
title = {Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation},
author = {N Mathy and O Pellegrini and A Serganov and D J Patel and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15101974},
isbn = {15101974},
year = {2004},
date = {2004-01-01},
journal = {Mol Microbiol},
volume = {52},
number = {3},
pages = {661-675},
abstract = {The ribosomal protein S15 binds to 16S rRNA, during ribosome assembly, and to its own mRNA (rpsO mRNA), affecting autocontrol of its expression. In both cases, the RNA binding site is bipartite with a common subsite consisting of a G*U/G-C motif. The second subsite is located in a three-way junction in 16S rRNA and in the distal part of a stem forming a pseudoknot in Escherichia coli rpsO mRNA. To determine the extent of mimicry between these two RNA targets, we determined which amino acids interact with rpsO mRNA. A plasmid carrying rpsO (the S15 gene) was mutagenized and introduced into a strain lacking S15 and harbouring an rpsO-lacZ translational fusion. Analysis of deregulated mutants shows that each subsite of rpsO mRNA is recognized by a set of amino acids known to interact with 16S rRNA. In addition to the G*U/G-C motif, which is recognized by the same amino acids in both targets, the other subsite interacts with amino acids also involved in contacts with helix H22 of 16S rRNA, in the region adjacent to the three-way junction. However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited.},
note = {0950-382x
Journal Article},
keywords = {16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Oestreich I, Florentz C, Morl M
A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3'-end processing and CCA addition Article de journal
Dans: J Mol Biol, vol. 337, no. 3, p. 535-544, 2004, ISBN: 15019775, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: FLORENTZ, FLORENTZ Human Kinetics Mitochondrial Diseases/*genetics Nucleic Acid Conformation *Point Mutation RNA/*genetics/physiology *RNA 3' End Processing RNA Nucleotidyltransferases/metabolism RNA, Leu/*genetics/physiology Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3'-end processing and CCA addition},
author = {L Levinger and I Oestreich and C Florentz and M Morl},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15019775},
isbn = {15019775},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {337},
number = {3},
pages = {535-544},
abstract = {Point mutations in mitochondrial tRNAs can cause severe multisystemic disorders such as mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and myoclonus epilepsy with ragged-red fibers (MERRF). Some of these mutations impair one or more steps of tRNA maturation and protein biosynthesis including 5'-end-processing, post-transcriptional base modification, structural stability, aminoacylation, and formation of tRNA-ribosomal complexes. tRNALeu(UUR), an etiologic hot spot for such diseases, harbors 20 of more than 90 disease-associated mutations described to date. Here, the pathogenesis-associated base substitutions A3243G, T3250C, T3271C, A3302G and C3303T within this tRNA were tested for their effects on endonucleolytic 3'-end processing and CCA addition at the tRNA 3'-terminus. Whereas mutations A3243G, A3302G and C3303T reduced the efficiency of 3'-end cleavage, only the C3303T substitution was a less efficient substrate for CCA addition. These results support the view that pathogenesis may be elicited through cumulative effects of tRNA mutations: a mutation can impede several pre-tRNA processing steps, with each such reduction contributing to the overall impairment of tRNA function.},
note = {0022-2836
Journal Article},
keywords = {FLORENTZ, FLORENTZ Human Kinetics Mitochondrial Diseases/*genetics Nucleic Acid Conformation *Point Mutation RNA/*genetics/physiology *RNA 3' End Processing RNA Nucleotidyltransferases/metabolism RNA, Leu/*genetics/physiology Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Mörl M, Florentz C
Mitochondrial tRNA 3' end metabolism and human disease Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 18, p. 5430-5441, 2004, ISBN: 15477393, (1362-4962 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: FLORENTZ, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/*genetics/*metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {Mitochondrial tRNA 3' end metabolism and human disease},
author = {L Levinger and M Mörl and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15477393},
isbn = {15477393},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {18},
pages = {5430-5441},
abstract = {Over 150 mutations in the mitochondrial genome have been shown to be associated with human disease. Remarkably, two-thirds of them are found in tRNA genes, which constitute only one-tenth of the mitochondrial genome. A total of 22 tRNAs punctuate the genome and are produced together with 11 mRNAs and 2 rRNAs from long polycistronic primary transcripts with almost no spacers. Pre-tRNAs thus require precise endonucleolytic excision. Furthermore, the CCA triplet which forms the 3' end of all tRNAs is not encoded, but must be synthesized by the CCA-adding enzyme after 3' end cleavage. Amino acid attachment to the CCA of mature tRNA is performed by aminoacyl-tRNA synthetases, which, like the preceding processing enzymes, are nuclear-encoded and imported into mitochondria. Here, we critically review the effectiveness and reliability of evidence obtained from reactions with in vitro transcripts that pathogenesis-associated mutant mitochondrial tRNAs can lead to deficiencies in tRNA 3' end metabolism (3' end cleavage, CCA addition and aminoacylation) toward an understanding of molecular mechanisms underlying human tRNA disorders. These defects probably contribute, individually and cumulatively, to the progression of human mitochondrial diseases.},
note = {1362-4962
Journal Article
Review
Review, Tutorial},
keywords = {FLORENTZ, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/*genetics/*metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E
Tools for the automatic identification and classification of RNA base pairs Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 13, p. 3450-3460, 2003, ISBN: 12824344, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Tools for the automatic identification and classification of RNA base pairs},
author = {H Yang and F Jossinet and N Leontis and L Chen and J Westbrook and H Berman and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824344},
isbn = {12824344},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {13},
pages = {3450-3460},
abstract = {Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.},
note = {1362-4962
Journal Article},
keywords = {Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Wilhelm F X, Wilhelm M, Gabriel A
Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase Article de journal
Dans: J Biol Chem, vol. 278, no. 48, p. 47678-47684, 2003, ISBN: 14500728, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA/chemistry DNA Primers DNA Replication Models, Calf Thymus/chemistry Support, Genetic, Genetic Molecular Sequence Data Purines/*chemistry RNA/chemistry RNA, Messenger/metabolism RNA, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN, Viral RNA-Directed DNA Polymerase/*chemistry Recombinant Proteins/chemistry Retroelements/*genetics Ribonuclease H
@article{,
title = {Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase},
author = {F X Wilhelm and M Wilhelm and A Gabriel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14500728},
isbn = {14500728},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {48},
pages = {47678-47684},
abstract = {Using hybrid RNA/DNA substrates containing the polypurine tract (PPT) plus-strand primer, we have examined the interaction between the Ty1 reverse transcriptase (RT) and the plus-strand initiation complex. We show here that, although the PPT sequence is relatively resistant to RNase H cleavage, it can be cleaved internally by the polymerase-independent RNase H activity of Ty1 RT. Alternatively, this PPT can be used to initiate plus-strand DNA synthesis. We demonstrate that cleavage at the PPT/DNA junction occurs only after at least 9 nucleotides are extended. Cleavage leaves a nick between the RNA primer and the nascent plus-strand DNA. We show that Ty1 RT has a strand displacement activity beyond a gap but that the PPT is not efficiently re-utilized in vitro for another round of DNA synthesis after a first plus-strand DNA has been synthesized and cleaved at the PPT/U3 junction.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA/chemistry DNA Primers DNA Replication Models, Calf Thymus/chemistry Support, Genetic, Genetic Molecular Sequence Data Purines/*chemistry RNA/chemistry RNA, Messenger/metabolism RNA, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN, Viral RNA-Directed DNA Polymerase/*chemistry Recombinant Proteins/chemistry Retroelements/*genetics Ribonuclease H},
pubstate = {published},
tppubtype = {article}
}
Thisse C, Degrave A, Kryukov G V, Gladyshev V N, Obrecht-Pflumio S, Krol A, Thisse B, Lescure A
Spatial and temporal expression patterns of selenoprotein genes during embryogenesis in zebrafish Article de journal
Dans: Gene Expr Patterns, vol. 3, no. 4, p. 525-532, 2003, ISBN: 12915322, (1567-133x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Gene Expression Regulation, Developmental In Situ Hybridization Molecular Sequence Data Proteins/*genetics/metabolism RNA Probes RNA, LESCURE, Messenger/metabolism Support, Non-U.S. Gov't Support, P.H.S. Tissue Distribution Zebrafish/*embryology, U.S. Gov't, Unité ARN
@article{,
title = {Spatial and temporal expression patterns of selenoprotein genes during embryogenesis in zebrafish},
author = {C Thisse and A Degrave and G V Kryukov and V N Gladyshev and S Obrecht-Pflumio and A Krol and B Thisse and A Lescure},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12915322},
isbn = {12915322},
year = {2003},
date = {2003-01-01},
journal = {Gene Expr Patterns},
volume = {3},
number = {4},
pages = {525-532},
abstract = {Selenium is important for embryogenesis in vertebrates but little is known about the expression patterns and biological functions of most selenoprotein genes. Taking advantage of the zebrafish model, systematic analysis of selenoprotein gene expression was performed by in situ hybridization on whole-mount embryos at different developmental stages. Twenty-one selenoprotein mRNAs were analyzed and all of them exhibited expression patterns restricted to specific tissues. Moreover, we demonstrated that highly similar selenoprotein paralogs were expressed within distinct territories. Therefore, tissue- and development-specific expression patterns provided new information for selenoproteins of unknown function.},
note = {1567-133x
Journal Article},
keywords = {Animals Gene Expression Regulation, Developmental In Situ Hybridization Molecular Sequence Data Proteins/*genetics/metabolism RNA Probes RNA, LESCURE, Messenger/metabolism Support, Non-U.S. Gov't Support, P.H.S. Tissue Distribution Zebrafish/*embryology, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rangan P, Masquida B, Westhof E, Woodson S A
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 100, no. 4, p. 1574-1579, 2003, ISBN: 12574513, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12574513},
isbn = {12574513},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {4},
pages = {1574-1579},
abstract = {Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.},
note = {0027-8424
Journal Article},
keywords = {Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Giege R, Florentz C
Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 7, p. 1904-1912, 2003, ISBN: 12655007, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, FLORENTZ, Ile/*genetics/metabolism Support, Mitochondrial/*genetics Endoribonucleases/metabolism Hela Cells Human Kinetics Molecular Sequence Data Mutation RNA Precursors/genetics/metabolism *RNA Processing, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro},
author = {L Levinger and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12655007},
isbn = {12655007},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {7},
pages = {1904-1912},
abstract = {The human mitochondrial genome encodes 22 tRNAs interspersed among the two rRNAs and 11 mRNAs, often without spacers, suggesting that tRNAs must be efficiently excised. Numerous maternally transmitted diseases and syndromes arise from mutations in mitochondrial tRNAs, likely due to defect(s) in tRNA metabolism. We have systematically explored the effect of pathogenic mutations on tRNA(Ile) precursor 3' end maturation in vitro by 3'-tRNase. Strikingly, four pathogenic tRNA(Ile) mutations reduce 3'-tRNase processing efficiency (V(max) / K(M)) to approximately 10-fold below that of wild-type, principally due to lower V(max). The structural impact of mutations was sought by secondary structure probing and wild-type tRNA(Ile) precursor was found to fold into a canonical cloverleaf. Among the mutant tRNA(Ile) precursors with the greatest 3' end processing deficiencies, only G4309A displays a secondary structure substantially different from wild-type, with changes in the T domain proximal to the substitution. Reduced efficiency of tRNA(Ile) precursor 3' end processing, in one case associated with structural perturbations, could thus contribute to human mitochondrial diseases caused by mutant tRNAs.},
note = {1362-4962
Journal Article},
keywords = {Base Sequence DNA, FLORENTZ, Ile/*genetics/metabolism Support, Mitochondrial/*genetics Endoribonucleases/metabolism Hela Cells Human Kinetics Molecular Sequence Data Mutation RNA Precursors/genetics/metabolism *RNA Processing, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Giege R, Schimmel P
RNA recognition by designed peptide fusion creates Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 100, no. 13, p. 7471-7475, 2003, ISBN: 12796515, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Motifs Amino Acid Sequence Amino Acyl-tRNA Ligases/*chemistry Base Sequence Binding Sites Catalytic Domain Escherichia coli/genetics/metabolism *Genetic Techniques Kinetics Models, FRUGIER, Genetic Molecular Sequence Data Mutation Nucleic Acid Conformation Peptides/*chemistry Protein Binding Protein Structure, Non-U.S. Gov't Support, P.H.S. Time Factors, Tertiary RNA/chemistry Recombinant Fusion Proteins/metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {RNA recognition by designed peptide fusion creates },
author = {M Frugier and R Giege and P Schimmel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12796515},
isbn = {12796515},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {13},
pages = {7471-7475},
abstract = {The genetic code was established through aminoacylations of RNA substrates that emerged as tRNAs. The 20 aminoacyl-tRNA synthetases (one for each amino acid) are ancient proteins, the active-site domain of which catalyzes formation of an aminoacyl adenylate that subsequently reacts with the 3' end of bound tRNA. Binding of tRNA depends on idiosyncratic (to the particular synthetase) domains and motifs that are fused to or inserted into the conserved active-site domain. Here we take the domain for synthesis of alanyl adenylate and fuse it to "artificial" peptide sequences (28 aa) that were shown previously to bind to the acceptor arm of tRNAAla. Certain fusions confer aminoacylation activity on tRNAAla and on hairpin microhelices modeled after its acceptor stem. Aminoacylation was sensitive to the presence of a specific G:U base pair known to be a major determinant of tRNAAla identity. Aminoacylation efficiency and specificity also depended on the specific peptide sequence. The results demonstrate that barriers to RNA-specific aminoacylations are low and can be achieved by relatively simple peptide fusions. They also suggest a paradigm for rationally designed specific aminoacylations based on peptide fusions.},
note = {0027-8424
Journal Article},
keywords = {Amino Acid Motifs Amino Acid Sequence Amino Acyl-tRNA Ligases/*chemistry Base Sequence Binding Sites Catalytic Domain Escherichia coli/genetics/metabolism *Genetic Techniques Kinetics Models, FRUGIER, Genetic Molecular Sequence Data Mutation Nucleic Acid Conformation Peptides/*chemistry Protein Binding Protein Structure, Non-U.S. Gov't Support, P.H.S. Time Factors, Tertiary RNA/chemistry Recombinant Fusion Proteins/metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Fishman J A, Pontikis R, Aubertin A M, Wilhelm F X
Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors Article de journal
Dans: Cell Mol Life Sci, vol. 59, no. 12, p. 2184-2190, 2002, ISBN: 12568344, (1420-682x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Animals Chlorides/metabolism Cloning, Calf Thymus/metabolism Sodium Chloride/metabolism Support, Non-U.S. Gov't Support, P.H.S. Swine, U.S. Gov't, Unité ARN
@article{,
title = {Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors},
author = {M Wilhelm and J A Fishman and R Pontikis and A M Aubertin and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12568344},
isbn = {12568344},
year = {2002},
date = {2002-01-01},
journal = {Cell Mol Life Sci},
volume = {59},
number = {12},
pages = {2184-2190},
abstract = {Transplantation of organs, tissues or cells from pigs to humans could be a potential solution to the shortage of human organs for transplantation. Porcine endogenous retroviruses (PERVs) remain a major safety concern for porcine xenotransplantation. Thus, finding drugs that could be used as virological prophylaxis (or therapy) against PERV replication would be desirable. One of the most effective ways to block retroviral multiplication is to inhibit the enzyme reverse transcriptase (RT) which catalyzes the reverse transcription of viral RNA to proviral double-stranded DNA. We report here the cloning and expression of PERV RT and its susceptibility to several inhibitors. Our data demonstrate PERV susceptibility in vitro to the triphosphorylated nucleoside analog of zidovudine (AZT) and to ddGTP and to a lesser extent to ddTTP but almost no susceptibility to the non-nucleoside RT inhibitors tested.},
note = {1420-682x
Journal Article},
keywords = {Amino Acid Sequence Animals Chlorides/metabolism Cloning, Calf Thymus/metabolism Sodium Chloride/metabolism Support, Non-U.S. Gov't Support, P.H.S. Swine, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Waugh A, Gendron P, Altman R, Brown J W, Case D, Gautheret D, Harvey S C, Leontis N, Westbrook J, Westhof E, Zuker M, Major F
RNAML: a standard syntax for exchanging RNA information Article de journal
Dans: RNA, vol. 8, no. 6, p. 707-717, 2002, ISBN: 12088144, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {RNAML: a standard syntax for exchanging RNA information},
author = {A Waugh and P Gendron and R Altman and J W Brown and D Case and D Gautheret and S C Harvey and N Leontis and J Westbrook and E Westhof and M Zuker and F Major},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12088144},
isbn = {12088144},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {6},
pages = {707-717},
abstract = {Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.},
note = {1355-8382
Journal Article},
keywords = {*Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Serra M J, Baird J D, Dale T, Fey B L, Retatagos K, Westhof E
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures Article de journal
Dans: RNA, vol. 8, no. 3, p. 307-323, 2002, ISBN: 12003491, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pairing Heat Hydrogen Bonding Magnesium/*pharmacology Models, Molecular Nucleic Acid Conformation RNA/*metabolism RNA Stability/*drug effects Support, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Effects of magnesium ions on the stabilization of RNA oligomers of defined structures},
author = {M J Serra and J D Baird and T Dale and B L Fey and K Retatagos and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12003491},
isbn = {12003491},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {3},
pages = {307-323},
abstract = {Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated.},
note = {1355-8382
Journal Article},
keywords = {Base Pairing Heat Hydrogen Bonding Magnesium/*pharmacology Models, Molecular Nucleic Acid Conformation RNA/*metabolism RNA Stability/*drug effects Support, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Uzun O, Mules E H, Gabriel A, Wilhelm F X
Polypurine tract formation by Ty1 RNase H Article de journal
Dans: J Biol Chem, vol. 276, no. 50, p. 47695-47701, 2001, ISBN: 11595735, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites DNA/metabolism DNA Primers/pharmacology Hydrolysis Molecular Sequence Data Mutation Protein Binding *Purines RNA/metabolism RNA-Directed DNA Polymerase/*chemistry/*metabolism Recombinant Proteins/metabolism *Retroelements Ribonuclease H, Calf Thymus/*chemistry/*genetics/metabolism Support, Non-U.S. Gov't Support, P.H.S. Time Factors, U.S. Gov't, Unité ARN
@article{,
title = {Polypurine tract formation by Ty1 RNase H},
author = {M Wilhelm and O Uzun and E H Mules and A Gabriel and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11595735},
isbn = {11595735},
year = {2001},
date = {2001-01-01},
journal = {J Biol Chem},
volume = {276},
number = {50},
pages = {47695-47701},
abstract = {To better understand the mechanism by which Ty1 RNase H creates the polypurine tract (PPT) primer, we have demonstrated the polymerase-dependent hydrolytic activity of Ty1 reverse transcriptase (RT) during minus-strand synthesis. Using RNase H and polymerase mutants of the recombinant Ty1 RT protein, we show that the two domains of Ty1 RT can act independently of one another. Our results indicate that RNA/DNA substrates containing a short RNA PPT, which serve as primers for plus-strand DNA synthesis, are relatively resistant to RNase H cleavage. RNA substrates with a correct 5' end but with 3' end extending beyond the plus-strand initiation site were cleaved specifically to generate the correct 3' end of the PPT. Using long RNA/DNA duplexes containing the PPT, we show that Ty1 RT is able to make specific internal cleavages that could generate the plus-strand primer with correct 5' and 3' ends. Long RNA/DNA duplexes with mutations in the PPT or in a U-rich region upstream of the PPT, which abolish plus-strand initiation in vivo, were not cleaved specifically at the 5' end of the PPT. Our work demonstrates that the in vitro enzyme can recapitulate key processes that control proper replication in vivo.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence Binding Sites DNA/metabolism DNA Primers/pharmacology Hydrolysis Molecular Sequence Data Mutation Protein Binding *Purines RNA/metabolism RNA-Directed DNA Polymerase/*chemistry/*metabolism Recombinant Proteins/metabolism *Retroelements Ribonuclease H, Calf Thymus/*chemistry/*genetics/metabolism Support, Non-U.S. Gov't Support, P.H.S. Time Factors, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Webb A E, Rose M A, Westhof E, Weeks K M
Protein-dependent transition states for ribonucleoprotein assembly Article de journal
Dans: J Mol Biol, vol. 309, no. 5, p. 1087-1100, 2001, ISBN: 11399081, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Allosteric Site Base Sequence Catalysis Catalytic Domain Fungal Proteins/*metabolism Hydroxyl Radical/metabolism Introns/genetics Iodine/metabolism Kinetics Models, Catalytic/chemistry/genetics/metabolism RNA-Binding Proteins/*metabolism Ribonucleoproteins/chemistry/*genetics/*metabolism Saccharomyces cerevisiae/enzymology/genetics *Saccharomyces cerevisiae Proteins Support, Molecular Neurospora crassa *Nucleic Acid Conformation Protein Binding RNA/chemistry/genetics/metabolism RNA Splicing/*genetics RNA Stability RNA, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN
@article{,
title = {Protein-dependent transition states for ribonucleoprotein assembly},
author = {A E Webb and M A Rose and E Westhof and K M Weeks},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11399081},
isbn = {11399081},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {309},
number = {5},
pages = {1087-1100},
abstract = {Native folding and splicing by the Saccharomyces cerevisiae mitochondrial bI5 group I intron RNA is facilitated by both the S. cerevisiae CBP2 and Neurospora crassa CYT-18 protein cofactors. Both protein-bI5 RNA complexes splice at similar rates, suggesting that the RNA active site structure is similar in both ribonucleoproteins. In contrast, the two proteins assemble with the bI5 RNA by distinct mechanisms and bind opposing, but partially overlapping, sides of the group I intron catalytic core. Assembly with CBP2 is limited by a slow, unimolecular RNA folding step characterized by a negligible activation enthalpy. We show that assembly with CYT-18 shows four distinctive features. (1) CYT-18 binds stably to the bI5 RNA at the diffusion controlled limit, but assembly to a catalytically active RNA structure is still limited by RNA folding, as visualized directly using time-resolved footprinting. (2) This mechanism of rapid stable protein binding followed by subsequent assembly steps has a distinctive kinetic signature: the apparent ratio of k(off) to k(on), determined in a partitioning experiment, differs from the equilibrium K(d) by a large factor. (3) Assembly with CYT-18 is characterized by a large activation enthalpy, consistent with a rate limiting conformational rearrangement. (4) Because assembly from the kinetically trapped state is faster at elevated temperature, we can identify conditions where CYT-18 accelerates (catalyzes) bI5 RNA folding relative to assembly with CBP2.},
note = {0022-2836
Journal Article},
keywords = {Allosteric Site Base Sequence Catalysis Catalytic Domain Fungal Proteins/*metabolism Hydroxyl Radical/metabolism Introns/genetics Iodine/metabolism Kinetics Models, Catalytic/chemistry/genetics/metabolism RNA-Binding Proteins/*metabolism Ribonucleoproteins/chemistry/*genetics/*metabolism Saccharomyces cerevisiae/enzymology/genetics *Saccharomyces cerevisiae Proteins Support, Molecular Neurospora crassa *Nucleic Acid Conformation Protein Binding RNA/chemistry/genetics/metabolism RNA Splicing/*genetics RNA Stability RNA, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Despons L, Walter P, Jakubowski H, Fasiolo F
Yeast cytoplasmic and mitochondrial methionyl-tRNA synthetases: two structural frameworks for identical functions Article de journal
Dans: J Mol Biol, vol. 311, no. 1, p. 205-216, 2001, ISBN: 11469869, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Amino Acid Sequence Binding Sites Coenzyme A/metabolism Comparative Study Cysteine/genetics/metabolism Cytoplasm/*enzymology Genes, Fungal/genetics Genetic Complementation Test Homocysteine/genetics/metabolism Kinetics Methionine/metabolism Methionine-tRNA Ligase/*chemistry/genetics/*metabolism Mitochondria/*enzymology Molecular Sequence Data Mutation/genetics Protein Transport RNA, Met/genetics/metabolism Saccharomyces cerevisiae/cytology/*enzymology/genetics Sequence Alignment Structure-Activity Relationship Support, Non-P.H.S. Zinc/metabolism Zinc Fingers/genetics/physiology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Yeast cytoplasmic and mitochondrial methionyl-tRNA synthetases: two structural frameworks for identical functions},
author = {B Senger and L Despons and P Walter and H Jakubowski and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11469869},
isbn = {11469869},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {311},
number = {1},
pages = {205-216},
abstract = {The yeast Saccharomyces cerevisiae possesses two methionyl-tRNA synthetases (MetRS), one in the cytoplasm and the other in mitochondria. The cytoplasmic MetRS has a zinc-finger motif of the type Cys-X(2)-Cys-X(9)-Cys-X(2)-Cys in an insertion domain that divides the nucleotide-binding fold into two halves, whereas no such motif is present in the mitochondrial MetRS. Here, we show that tightly bound zinc atom is present in the cytoplasmic MetRS but not in the mitochondrial MetRS. To test whether the presence of a zinc-binding site is required for cytoplasmic functions of MetRS, we constructed a yeast strain in which cytoplasmic MetRS gene was inactivated and the mitochondrial MetRS gene was expressed in the cytoplasm. Provided that methionine-accepting tRNA is overexpressed, this strain was viable, indicating that mitochondrial MetRS was able to aminoacylate tRNA(Met) in the cytoplasm. Site-directed mutagenesis demonstrated that the zinc domain was required for the stability and consequently for the activity of cytoplasmic MetRS. Mitochondrial MetRS, like cytoplasmic MetRS, supported homocysteine editing in vivo in the yeast cytoplasm. Both MetRSs catalyzed homocysteine editing and aminoacylation of coenzyme A in vitro. Thus, identical synthetic and editing functions can be carried out in different structural frameworks of cytoplasmic and mitochondrial MetRSs.},
note = {0022-2836
Journal Article},
keywords = {Acylation Amino Acid Sequence Binding Sites Coenzyme A/metabolism Comparative Study Cysteine/genetics/metabolism Cytoplasm/*enzymology Genes, Fungal/genetics Genetic Complementation Test Homocysteine/genetics/metabolism Kinetics Methionine/metabolism Methionine-tRNA Ligase/*chemistry/genetics/*metabolism Mitochondria/*enzymology Molecular Sequence Data Mutation/genetics Protein Transport RNA, Met/genetics/metabolism Saccharomyces cerevisiae/cytology/*enzymology/genetics Sequence Alignment Structure-Activity Relationship Support, Non-P.H.S. Zinc/metabolism Zinc Fingers/genetics/physiology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Libri D, Lescure A, Rosbash M
Splicing enhancement in the yeast rp51b intron Article de journal
Dans: RNA, vol. 6, no. 3, p. 352-368, 2000, ISBN: 10744020, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5' Untranslated Regions/genetics DNA Mutational Analysis Introns/*genetics Multigene Family Nucleic Acid Conformation RNA Splicing/*genetics *Regulatory Sequences, LESCURE, Non-U.S. Gov't Support, Nucleic Acid Ribonucleoprotein, P.H.S. Uridine/metabolism, U.S. Gov't, U1 Small Nuclear/chemistry/genetics Saccharomyces cerevisiae/*genetics Support, Unité ARN
@article{,
title = {Splicing enhancement in the yeast rp51b intron},
author = {D Libri and A Lescure and M Rosbash},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10744020},
isbn = {10744020},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {3},
pages = {352-368},
abstract = {Splicing enhancement in higher eukaryotes has been linked to SR proteins, to U1 snRNP, and to communication between splice sites across introns or exons mediated by protein-protein interactions. It has been previously shown that, in yeast, communication mediated by RNA-RNA interactions between the two ends of introns is a basis for splicing enhancement. We designed experiments of randomization-selection to isolate splicing enhancers that would work independently from RNA secondary structures. Surprisingly, one of the two families of sequences selected was essentially composed of 5' splice site variants. We show that this sequence enhances splicing independently of secondary structure, is exportable to heterologous contexts, and works in multiple copies with additive effects. The data argue in favor of an early role for splicing enhancement, possibly coincident with commitment complex formation. Genetic compensation experiments with U1 snRNA mutants suggest that U1 snRNP binding to noncanonical locations is required for splicing enhancement.},
note = {1355-8382
Journal Article},
keywords = {5' Untranslated Regions/genetics DNA Mutational Analysis Introns/*genetics Multigene Family Nucleic Acid Conformation RNA Splicing/*genetics *Regulatory Sequences, LESCURE, Non-U.S. Gov't Support, Nucleic Acid Ribonucleoprotein, P.H.S. Uridine/metabolism, U.S. Gov't, U1 Small Nuclear/chemistry/genetics Saccharomyces cerevisiae/*genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Costa M, Michel F, Westhof E
A three-dimensional perspective on exon binding by a group II self-splicing intron Article de journal
Dans: EMBO J, vol. 19, no. 18, p. 5007-5018, 2000, ISBN: 10990464, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Catalysis *Exons Hydroxyl Radical *Introns Kinetics *Models, Catalytic/metabolism Support, Genetic, Genetic Molecular Sequence Data Nucleic Acid Conformation *RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S. Temperature Transcription, U.S. Gov't, Unité ARN
@article{,
title = {A three-dimensional perspective on exon binding by a group II self-splicing intron},
author = {M Costa and F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10990464},
isbn = {10990464},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {18},
pages = {5007-5018},
abstract = {We have used chemical footprinting, kinetic dissection of reactions and comparative sequence analysis to show that in self-splicing introns belonging to subgroup IIB, the sites that bind the 5' and 3' exons are connected to one another by tertiary interactions. This unanticipated arrangement, which contrasts with the direct covalent linkage that prevails in the other major subdivision of group II (subgroup IIA), results in a unique three-dimensional architecture for the complex between the exons, their binding sites and intron domain V. A key feature of the modeled complex is the presence of several close contacts between domain V and one of the intron-exon pairings. These contacts, whose existence is supported by hydroxyl radical footprinting, provide a structural framework for the known role of domain V in catalysis and its recently demonstrated involvement in binding of the 5' exon.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Catalysis *Exons Hydroxyl Radical *Introns Kinetics *Models, Catalytic/metabolism Support, Genetic, Genetic Molecular Sequence Data Nucleic Acid Conformation *RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S. Temperature Transcription, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Becker H D, Roy H, Moulinier L, Mazauric M H, Keith G, Kern D
Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase Article de journal
Dans: Biochemistry, vol. 39, no. 12, p. 3216-3230, 2000, ISBN: 10727213, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase},
author = {H D Becker and H Roy and L Moulinier and M H Mazauric and G Keith and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10727213},
isbn = {10727213},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {12},
pages = {3216-3230},
abstract = {Thermus thermophilus possesses two aspartyl-tRNA synthetases (AspRSs), AspRS1 and AspRS2, encoded by distinct genes. Alignment of the protein sequences with AspRSs of other origins reveals that AspRS1 possesses the structural features of eubacterial AspRSs, whereas AspRS2 is structurally related to the archaebacterial AspRSs. The structural dissimilarity between the two thermophilic AspRSs is correlated with functional divergences. AspRS1 aspartylates tRNA(Asp) whereas AspRS2 aspartylates tRNA(Asp), and tRNA(Asn) with similar efficiencies. Since Asp bound on tRNA(Asn) is converted into Asn by a tRNA-dependent aspartate amidotransferase, AspRS2 is involved in Asn-tRNA(Asn) formation. These properties relate functionally AspRS2 to archaebacterial AspRSs. The structural basis of the dual specificity of T. thermophilus tRNA(Asn) was investigated by comparing its sequence with those of tRNA(Asp) and tRNA(Asn) of strict specificity. It is shown that the thermophilic tRNA(Asn) contains the elements defining asparagine identity in Escherichia coli, part of which being also the major elements of aspartate identity, whereas minor elements of this identity are missing. The structural context that permits expression of aspartate and asparagine identities by tRNA(Asn) and how AspRS2 accommodates tRNA(Asp) and tRNA(Asn) will be discussed. This work establishes a distinct structure-function relationship of eubacterial and archaebacterial AspRSs. The structural and functional properties of the two thermophilic AspRSs will be discussed in the context of the modern and primitive pathways of tRNA aspartylation and asparaginylation and related to the phylogenetic connexion of T. thermophilus to eubacteria and archaebacteria.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Perreau V M, Keith G, Holmes W M, Przykorska A, Santos M A, Tuite M F
The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal
Dans: J Mol Biol, vol. 293, no. 5, p. 1039-1053, 1999, ISBN: 10547284, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry/*genetics/metabolism Base Sequence Candida albicans/*genetics Evolution, Fungal/chemistry/genetics/metabolism RNA, Molecular Genetic Code/genetics Imidazoles/metabolism Lead/metabolism Methylation Mutation/genetics *Nucleic Acid Conformation Nucleosides/genetics/metabolism RNA, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. tRNA Methyltransferases/metabolism, Ser/*chemistry/*genetics/metabolism Ribonucleases/metabolism Saccharomyces cerevisiae/genetics Solutions Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure},
author = {V M Perreau and G Keith and W M Holmes and A Przykorska and M A Santos and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10547284},
isbn = {10547284},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {293},
number = {5},
pages = {1039-1053},
abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.},
note = {0022-2836
Journal Article},
keywords = {Anticodon/*chemistry/*genetics/metabolism Base Sequence Candida albicans/*genetics Evolution, Fungal/chemistry/genetics/metabolism RNA, Molecular Genetic Code/genetics Imidazoles/metabolism Lead/metabolism Methylation Mutation/genetics *Nucleic Acid Conformation Nucleosides/genetics/metabolism RNA, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. tRNA Methyltransferases/metabolism, Ser/*chemistry/*genetics/metabolism Ribonucleases/metabolism Saccharomyces cerevisiae/genetics Solutions Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Redlak M, Andraos-Selim C, Giege R, Florentz C, Holmes W M
Interaction of tRNA with tRNA (guanosine-1)methyltransferase: binding specificity determinants involve the dinucleotide G36pG37 and tertiary structure Article de journal
Dans: Biochemistry, vol. 36, no. 29, p. 8699-8709, 1997, ISBN: 9220956, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/metabolism Base Sequence Binding Sites Dinucleoside Phosphates/*metabolism Escherichia coli Kinetics Molecular Sequence Data *Nucleic Acid Conformation Poly G/*metabolism RNA, FLORENTZ, Non-P.H.S. tRNA Methyltransferases/isolation & purification/*metabolism, Non-U.S. Gov't Support, Transfer/chemistry/*metabolism Substrate Specificity Support, U.S. Gov't, Unité ARN
@article{,
title = {Interaction of tRNA with tRNA (guanosine-1)methyltransferase: binding specificity determinants involve the dinucleotide G36pG37 and tertiary structure},
author = {M Redlak and C Andraos-Selim and R Giege and C Florentz and W M Holmes},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9220956},
isbn = {9220956},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {29},
pages = {8699-8709},
abstract = {The sequence G37pG36 is present in all tRNA species recognized and methylated by the Escherichia coli modification enzyme tRNA (guanosine-1)methyltransferase. We have examined whether this dinucleotide sequence provides the base specific recognition signal for this enzyme and have assessed the role of the remaining tRNA in recognition. E. coli tRNAHis and yeast tRNAAsp were substituted with G at positions 36 and 37 and were found to be excellent substrates for methylation. This suggested that the general tRNA structure can be specifically bound by the enzyme. In addition, heterologous tRNA species including fully modified tRNA1Leu are excellent inhibitors of tRNA1Leu transcript methylation. Analyses of structural variants of yeast tRNAAsp and E. coli tRNA1Leu demonstrate clearly that the core tertiary structures of tRNA are required for recognition and that G37 must be in the correct position in space relative to important contacts elsewhere in the molecule. This latter conclusion was reached because the addition of one to three stacked base pairs in the anticodon stem of tRNA1Leu dramatically alters activity. In this case, the G37 base is rotated away from the correct position in space relative to other tRNA contact sites. The acceptor stem structure is required for optimal activity since deletion of three or five base pairs is detrimental to activity; however, specific base sequence may not be important because (i) the addition of three stacked base pairs of different sequence had little effect on activity and (ii) heterologous tRNAs with little or no sequence homology in the acceptor stem are excellent substrates. Both poly G and GpG are potent and specific inhibitors of enzyme activity and are minimal substrates which can be methylated, forming m1G. Taken together, these studies suggest that 1MGT can bind the general tRNA structure and that the crucial base-pair contacts are G37 and G36.},
note = {0006-2960
Journal Article},
keywords = {Anticodon/metabolism Base Sequence Binding Sites Dinucleoside Phosphates/*metabolism Escherichia coli Kinetics Molecular Sequence Data *Nucleic Acid Conformation Poly G/*metabolism RNA, FLORENTZ, Non-P.H.S. tRNA Methyltransferases/isolation & purification/*metabolism, Non-U.S. Gov't Support, Transfer/chemistry/*metabolism Substrate Specificity Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ng J D, Lorber B, Giege R, Koszelak S, Day J, Greenwood A, McPherson A
Comparative analysis of thaumatin crystals grown on earth and in microgravity Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 53, no. Pt 6, p. 724-733, 1997, ISBN: 11540583, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Comparative Study Crystallization Crystallography/instrumentation/methods Crystallography, Non-P.H.S. Sweetening Agents/*chemistry *Weightlessness, Non-U.S. Gov't Support, U.S. Gov't, Unité ARN, X-Ray Particle Size Plant Proteins/*chemistry Space Flight/*instrumentation Support
@article{,
title = {Comparative analysis of thaumatin crystals grown on earth and in microgravity},
author = {J D Ng and B Lorber and R Giege and S Koszelak and J Day and A Greenwood and A McPherson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11540583},
isbn = {11540583},
year = {1997},
date = {1997-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {53},
number = {Pt 6},
pages = {724-733},
abstract = {The protein thaumatin was studied as a model macro-molecule for crystallization in microgravity-environment experiments conducted on two US Space Shuttle missions (USML-2 and LMS). In this investigation, we have evaluated and compared the quality of space- and earth-grown thaumatin crystals using X-ray diffraction analyses, and characterized them according to crystal size, diffraction resolution limit and mosaicity. Two different approaches for growing thaumatin crystals in the microgravity environment, dialysis and liquid-liquid diffusion, were employed as a joint experiment by our two investigative teams. Thaumatin crystals grown in a microgravity environment were generally larger in volume and the total number of crystals was less, relative to crystals grown on earth. They diffracted to significantly higher resolution and with improved diffraction properties, as judged by relative plots of I/sigma versus resolution. The mosaicity of space-grown crystals was significantly less than that of crystals grown on earth. Increased concentrations of protein in the crystallization chambers in microgravity led to larger crystals. The data presented here lend further support to the idea that protein crystals of improved quality can be obtained in a microgravity environment.},
note = {0907-4449
Journal Article},
keywords = {Comparative Study Crystallization Crystallography/instrumentation/methods Crystallography, Non-P.H.S. Sweetening Agents/*chemistry *Weightlessness, Non-U.S. Gov't Support, U.S. Gov't, Unité ARN, X-Ray Particle Size Plant Proteins/*chemistry Space Flight/*instrumentation Support},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Lanchy J M, Yusupov M, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids Article de journal
Dans: J Mol Biol, vol. 261, no. 3, p. 315-321, 1996, ISBN: 8780773, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support
@article{,
title = {Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids},
author = {G Yusupova and J M Lanchy and M Yusupov and G Keith and S F Le Grice and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8780773},
isbn = {8780773},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {261},
number = {3},
pages = {315-321},
abstract = {During reverse transcription of the genomic RNA of human immunodeficiency virus type 1 (HIV-1) into double-stranded DNA, reverse transcriptase (RT) must accommodate RNA-RNA, DNA-RNA, RNA-DNA and DNA-DNA hybrids as primer-template. In this study, we examined extension of RNA-tRNA3Lys, and DNA-tRNA3Lys complexes by HIV-1 RT. When the 3' end of tRNA3Lys is annealed to oligoribonucleotides, tRNA3Lys, but not the complementary RNAs, is extended by HIV-1 RT, indicating that tRNA3Lys is efficiently used as primer and RNA as template. An opposite primer usage is observed when tRNA3Lys is annealed to complementary oligodeoxyribonucleotides. In this case, the oligodeoxyribonucleotides are efficiently used as primer and tRNA3Lys as template. This result indicates that the nature of nucleic acid bound to tRNA3Lys determines which strand of the RNA-tRNA3Lys and DNA-tRNA3Lys hybrids is extended by HIV-1 RT. When an oligoribonucleotide is annealed to an unmodified transcript of tRNA3Lys, both nucleic acids are extended by HIV-1 RT, indicating that specific selection of tRNA3Lys as primer requires the post-transcriptional modifications of tRNA3Lys.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Wesolowski D, Altman S
Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent Article de journal
Dans: J Mol Biol, vol. 258, no. 4, p. 600-613, 1996, ISBN: 8636995, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Proteins/chemistry/metabolism Base Sequence Coenzymes/*chemistry/drug effects Computer Simulation Edetic Acid/*pharmacology Endoribonucleases/*chemistry/drug effects Escherichia coli/chemistry Ferrous Compounds/*pharmacology Magnesium/pharmacology Models, Bacterial/*chemistry/drug effects RNA, Catalytic/*chemistry/drug effects RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/metabolism Ribonuclease P Support, U.S. Gov't, Unité ARN
@article{,
title = {Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent},
author = {E Westhof and D Wesolowski and S Altman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8636995},
isbn = {8636995},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {258},
number = {4},
pages = {600-613},
abstract = {The accessibility of the ribose groups in the phosphodiester chain of M1 RNA, the catalytic subunit of ribonuclease P from Escherichia coli, has been probed with an Fe(II)-EDTA reagent when the RNA is alone in solution, when it is in a complex with a tRNA precursor substrate, and when it is in the holoenzyme complex with its cofactor, C5 protein. The regions found to be protected under these various conditions, as well as those previously identified in other chemical probing experiments, have been mapped on a three-dimensional working model of M1 RNA and are generally compatible with the previously proposed placement of the substrate on the enzyme and with previous data and inferences regarding the interactions of C5 protein with M1 RNA. On the basis of the accessibilities of the C(4') atoms, refinements have been introduced in the model to accommodate the Fe(II)-EDTA protection data. The protein cofactor makes contact with several helical regions of the catalytic RNA on the opposite side of the surface to which substrates bind.},
note = {0022-2836
Journal Article},
keywords = {Bacterial Proteins/chemistry/metabolism Base Sequence Coenzymes/*chemistry/drug effects Computer Simulation Edetic Acid/*pharmacology Endoribonucleases/*chemistry/drug effects Escherichia coli/chemistry Ferrous Compounds/*pharmacology Magnesium/pharmacology Models, Bacterial/*chemistry/drug effects RNA, Catalytic/*chemistry/drug effects RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/metabolism Ribonuclease P Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Ehresmann C, Grice S F Le, Ehresmann B, Marquet R
Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription Article de journal
Dans: EMBO J, vol. 15, no. 24, p. 7178-7187, 1996, ISBN: 9003793, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN
@article{,
title = {Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription},
author = {J M Lanchy and C Ehresmann and S F Le Grice and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9003793},
isbn = {9003793},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {24},
pages = {7178-7187},
abstract = {We recently showed that primer tRNA3Lys, human immunodeficiency virus type 1 (HIV-1) RNA and HIV-1 reverse transcriptase (RT) form a specific complex of initiation of reverse transcription that can be functionally distinguished from the elongation complex, which can be obtained by substituting an 18mer oligodeoxyribonucleotide (ODN) for the natural primer (Isel et al., 1996). Here, we compared the binding properties and the single and multiple turnover kinetics of HIV-1 RT in the initiation and elongation complexes. Even though the equilibrium dissociation constants of HIV-1 RT are not very different for the two complexes, RT dissociates approximately 200-fold faster from the initiation complex. Furthermore, nucleotide incorporation by the pre-formed primer-template-RT complexes is reduced by a approximately 50-fold factor during initiation of reverse transcription, compared with elongation. As a consequence, processivity of HIV-1 RT in the initiation complex is close to unity, while it increases by four orders of magnitude during elongation, as expected for a replication enzyme. This processivity change is reminiscent of the transition from initiation to elongation of transcription. Furthermore, our results indicate that the post-transcriptional modifications of tRNA3Lys play a role similar to that of the sigma factor in transcription by the Escherichia coli RNA polymerase: they favour the formation of the specific initiation complex but do not affect the polymerization rate of the bound enzyme.},
note = {0261-4189
Journal Article},
keywords = {DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Caprara M G, Lehnert V, Lambowitz A M, Westhof E
A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core Article de journal
Dans: Cell, vol. 87, no. 6, p. 1135-1145, 1996, ISBN: 8978617, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN
@article{,
title = {A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core},
author = {M G Caprara and V Lehnert and A M Lambowitz and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8978617},
isbn = {8978617},
year = {1996},
date = {1996-01-01},
journal = {Cell},
volume = {87},
number = {6},
pages = {1135-1145},
abstract = {The Neurospora crassa mitochondrial (mt) tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns, in addition to aminoacylating tRNA(Tyr). Here, we compared the CYT-18 binding sites in the N. crassa mt LSU and ND1 introns with that in N. crassa mt tRNA(Tyr) by constructing three-dimensional models based on chemical modification and RNA footprinting data. Remarkably, superimposition of the CYT-18 binding sites in the model structures revealed an extended three-dimensional overlap between the tRNA and the group I intron catalytic core. Our results provide insight into how an RNA-splicing factor can evolve from a cellular RNA-binding protein. Further, the structural similarities between group I introns and tRNAs are consistent with an evolutionary relationship and suggest a general mechanism for the evolution of complex catalytic RNAs.},
note = {0092-8674
Journal Article},
keywords = {Base Sequence Binding Sites/genetics Conserved Sequence Evolution *Introns Molecular Sequence Data Neurospora crassa Nucleic Acid Conformation Protein Conformation Protein Structure, Fungal/chemistry/metabolism/physiology RNA, Non-U.S. Gov't Support, P.H.S. Tyrosine-tRNA Ligase/*chemistry/*genetics/metabolism, Tertiary RNA Splicing/physiology RNA, Transfer, Tyr/chemistry Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Stetor S R, Li X, Rausch J W, Howard K J, Ehresmann B, North T W, Wohrl B M, Goody R S, Wainberg M A, Grice S F
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 19, p. 10063-10068, 1996, ISBN: 8816751, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support
@article{,
title = {Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases},
author = {E J Arts and S R Stetor and X Li and J W Rausch and K J Howard and B Ehresmann and T W North and B M Wohrl and R S Goody and M A Wainberg and S F Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8816751},
isbn = {8816751},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {19},
pages = {10063-10068},
abstract = {Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Ghosh M, Jacques P S, Ehresmann B, Grice S F Le
Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication Article de journal
Dans: J Biol Chem, vol. 271, no. 15, p. 9054-9061, 1996, ISBN: 8621554, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication},
author = {E J Arts and M Ghosh and P S Jacques and B Ehresmann and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621554},
isbn = {8621554},
year = {1996},
date = {1996-01-01},
journal = {J Biol Chem},
volume = {271},
number = {15},
pages = {9054-9061},
abstract = {The mechanism for the initiation of reverse transcription in human immunodeficiency virus type 1 (HIV-1) was studied utilizing a unique reverse transcriptase (RT) mutant altered in its noncatalytic p51 subunit. This mutant (p66/p51Delta13) retains full DNA- and RNA-dependent DNA polymerase activity but has reduced affinity for tRNA3Lys, the cognate HIV primer. When the ability to support(-)-strand DNA synthesis on a viral RNA template was evaluated, this mutant initiated from an 18-nucleotide (nt) oligoribo- or oligodeoxyribonucleotide primer complementary to the primer binding site (pbs). However, it failed to do so from natural and synthetic versions of tRNA3Lys. tRNA-primed(-)-strand synthesis could, however, be rescued by substituting the 76-nt tRNA3Lys with 81- and 107-nt tRNA-DNA chimeras, i.e. tRNA3Lys extended by 5 and 31 deoxyribonucleotides complementary to the viral genome upstream of the pbs. These findings imply that through interactions involving its p51 subunit, RT may be required to disrupt additional tRNA-viral RNA duplexes outside the pbs to proceed into productive(-)-strand DNA synthesis. Alternatively, specific interactions between tRNA3Lys and HIV-1 RT may be necessary for efficient initiation of(-)-strand DNA synthesis.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA},
pubstate = {published},
tppubtype = {article}
}
O'Connor M, Brunelli C A, Firpo M A, Gregory S T, Lieberman K R, Lodmell J S, Moine H, Ryk D I Van, Dahlberg A E
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-868, 1995, ISBN: 8722001, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: 16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN
@article{,
title = {Genetic probes of ribosomal RNA function},
author = {M O'Connor and C A Brunelli and M A Firpo and S T Gregory and K R Lieberman and J S Lodmell and H Moine and D I Van Ryk and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722001},
isbn = {8722001},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-868},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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}
}
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}
}
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}
}
Frugier M, Florentz C, Schimmel P, Giege R
Triple aminoacylation specificity of a chimerized transfer RNA Article de journal
Dans: Biochemistry, vol. 32, no. 50, p. 14053-14061, 1993, ISBN: 8268184, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Triple aminoacylation specificity of a chimerized transfer RNA},
author = {M Frugier and C Florentz and P Schimmel and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268184},
isbn = {8268184},
year = {1993},
date = {1993-01-01},
journal = {Biochemistry},
volume = {32},
number = {50},
pages = {14053-14061},
abstract = {We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.},
note = {0006-2960
Journal Article},
keywords = {Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Florentz C, Dreher T, Giege R
Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 8, p. 1865-1870, 1992, ISBN: 1579487, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support
@article{,
title = {Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA},
author = {J Rudinger and C Florentz and T Dreher and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579487},
isbn = {1579487},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {8},
pages = {1865-1870},
abstract = {Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Dreher T W, Tsai C H, Florentz C, Giege R
Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides Article de journal
Dans: Biochemistry, vol. 31, no. 38, p. 9183-9189, 1992, ISBN: 1390705, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support
@article{,
title = {Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides},
author = {T W Dreher and C H Tsai and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1390705},
isbn = {1390705},
year = {1992},
date = {1992-01-01},
journal = {Biochemistry},
volume = {31},
number = {38},
pages = {9183-9189},
abstract = {The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].},
note = {0006-2960
Journal Article},
keywords = {Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support},
pubstate = {published},
tppubtype = {article}
}