Intranet
Acces
Contact
Accès direct
Unités de recherche
Bienvenue
ARN
Architecture et réactivité de l'ARN
Publications
1994
Felden B, Florentz C, Giege R, Westhof E
Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs Article de journal
Dans: J Mol Biol, vol. 235, no. 2, p. 508-531, 1994, ISBN: 8289279, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8289279},
isbn = {8289279},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {235},
number = {2},
pages = {508-531},
abstract = {The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Bromovirus/*genetics Computer Simulation Models, FLORENTZ, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry RNA, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.
Dumas P, Bergdoll M, Cagnon C, Masson J M
Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering Article de journal
Dans: EMBO J, vol. 13, no. 11, p. 2483-2492, 1994, ISBN: 7516875, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Acetyltransferases Amino Acid Sequence Bacterial Proteins/*chemistry/genetics/isolation & purification/metabolism Base Sequence Binding Sites Bleomycin/*metabolism/pharmacology Crystallization Crystallography, Bacterial/*genetics Models, Microbial/genetics Genes, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Secondary Recombinant Fusion Proteins/isolation & purification Structure-Activity Relationship Support, Site-Directed Protein Conformation Protein Structure, Structural, Unité ARN, X-Ray Drug Resistance
@article{,
title = {Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering},
author = {P Dumas and M Bergdoll and C Cagnon and J M Masson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7516875},
isbn = {7516875},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {11},
pages = {2483-2492},
abstract = {The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.},
note = {0261-4189
Journal Article},
keywords = {*Acetyltransferases Amino Acid Sequence Bacterial Proteins/*chemistry/genetics/isolation & purification/metabolism Base Sequence Binding Sites Bleomycin/*metabolism/pharmacology Crystallization Crystallography, Bacterial/*genetics Models, Microbial/genetics Genes, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Secondary Recombinant Fusion Proteins/isolation & purification Structure-Activity Relationship Support, Site-Directed Protein Conformation Protein Structure, Structural, Unité ARN, X-Ray Drug Resistance},
pubstate = {published},
tppubtype = {article}
}
The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.
Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry J C, Moras D
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction Article de journal
Dans: EMBO J, vol. 13, no. 2, p. 327-337, 1994, ISBN: 8313877, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Adenosine Triphosphate/metabolism Amino Acid Sequence Animals Aspartate-tRNA Ligase/chemistry/genetics/*metabolism Binding Sites Computer Graphics Human Molecular Sequence Data Mutagenesis, Amino Acid Structure-Activity Relationship Support, ERIANI, Non-U.S. Gov't, Site-Directed Saccharomyces cerevisiae/*enzymology Sequence Homology, Unité ARN
@article{,
title = {The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction},
author = {J Cavarelli and G Eriani and B Rees and M Ruff and M Boeglin and A Mitschler and F Martin and J Gangloff and J C Thierry and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8313877},
isbn = {8313877},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {2},
pages = {327-337},
abstract = {The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group and by amino acids conserved in the aspartyl synthetase family. The amino acids in contact with the substrates have been probed by site-directed mutagenesis for their functional implication.},
note = {0261-4189
Journal Article},
keywords = {Acylation Adenosine Triphosphate/metabolism Amino Acid Sequence Animals Aspartate-tRNA Ligase/chemistry/genetics/*metabolism Binding Sites Computer Graphics Human Molecular Sequence Data Mutagenesis, Amino Acid Structure-Activity Relationship Support, ERIANI, Non-U.S. Gov't, Site-Directed Saccharomyces cerevisiae/*enzymology Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group and by amino acids conserved in the aspartyl synthetase family. The amino acids in contact with the substrates have been probed by site-directed mutagenesis for their functional implication.
Buttcher V, Senger B, Schumacher S, Reinbolt J, Fasiolo F
Dans: Biochem Biophys Res Commun, vol. 200, no. 1, p. 370-377, 1994, ISBN: 8166708, (0006-291x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/metabolism Anticodon/*genetics Base Composition Base Sequence Chromosomes, Artificial, Bacterial Guanine Inversion (Genetics) Lysine-tRNA Ligase/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Plasmids RNA, Genetic Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation & purification Uracil, Gln/chemistry/genetics RNA, Ile/chemistry/*genetics RNA, Lys/chemistry/*genetics Saccharomyces cerevisiae/*genetics *Suppression, Structural, Transfer, Unité ARN, Yeast Escherichia coli/*genetics Genes
@article{,
title = {Modulation of the suppression efficiency and amino acid identity of an artificial yeast amber isoleucine transfer RNA in Escherichia coli by a G-U pair in the anticodon stem},
author = {V Buttcher and B Senger and S Schumacher and J Reinbolt and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8166708},
isbn = {8166708},
year = {1994},
date = {1994-01-01},
journal = {Biochem Biophys Res Commun},
volume = {200},
number = {1},
pages = {370-377},
abstract = {The artificial amber suppressor corresponding to the major isoleucine tRNA from yeast (pVBt5), when expressed in E. coli, is a poor suppressor of the amber mutation lacIam181-Z. By analysing mutant forms, we could show that this was due to the presence of a U30-G40 wobble pair in the anticodon stem of the yeast tRNA and not to the level of the heterologously expressed tRNA. Efficient suppressors were obtained by restoring a normal U30-A40 or G30-C40 Watson-Crick pair. In vivo the mutant forms are exclusively charged by the bacterial lysyl-tRNA synthetase (LysRS), whereas the original yeast amber tRNA is charged at a low level by E. coli glutaminyl-tRNA synthetase (GlnRS) and LysRS. The inversion of the U30-G40 pair also induces a loss of the Gln identity. We conclude from these experiments that the U30-G40 base pair constitutes a negative determinant for LysRS interaction which operates either at the level of complex formation or at the catalytic step. As no direct contacts are seen between GlnRS and positions 30-40 of the complexed homologous tRNA, the U30-G40 pair of pVBt5 is believed to influence aminoacylation by GlnRS indirectly, probably at the level of the anticodon loop conformation by favouring an optimal apposition of the anticodon nucleotides with the protein.},
note = {0006-291x
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/metabolism Anticodon/*genetics Base Composition Base Sequence Chromosomes, Artificial, Bacterial Guanine Inversion (Genetics) Lysine-tRNA Ligase/metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Plasmids RNA, Genetic Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation & purification Uracil, Gln/chemistry/genetics RNA, Ile/chemistry/*genetics RNA, Lys/chemistry/*genetics Saccharomyces cerevisiae/*genetics *Suppression, Structural, Transfer, Unité ARN, Yeast Escherichia coli/*genetics Genes},
pubstate = {published},
tppubtype = {article}
}
The artificial amber suppressor corresponding to the major isoleucine tRNA from yeast (pVBt5), when expressed in E. coli, is a poor suppressor of the amber mutation lacIam181-Z. By analysing mutant forms, we could show that this was due to the presence of a U30-G40 wobble pair in the anticodon stem of the yeast tRNA and not to the level of the heterologously expressed tRNA. Efficient suppressors were obtained by restoring a normal U30-A40 or G30-C40 Watson-Crick pair. In vivo the mutant forms are exclusively charged by the bacterial lysyl-tRNA synthetase (LysRS), whereas the original yeast amber tRNA is charged at a low level by E. coli glutaminyl-tRNA synthetase (GlnRS) and LysRS. The inversion of the U30-G40 pair also induces a loss of the Gln identity. We conclude from these experiments that the U30-G40 base pair constitutes a negative determinant for LysRS interaction which operates either at the level of complex formation or at the catalytic step. As no direct contacts are seen between GlnRS and positions 30-40 of the complexed homologous tRNA, the U30-G40 pair of pVBt5 is believed to influence aminoacylation by GlnRS indirectly, probably at the level of the anticodon loop conformation by favouring an optimal apposition of the anticodon nucleotides with the protein.
Blomberg P, Engdahl H M, Malmgren C, Romby P, Wagner E G
Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap-independent RepA synthesis Article de journal
Dans: Mol Microbiol, vol. 12, no. 1, p. 49-60, 1994, ISBN: 7520116, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN
@article{,
title = {Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap-independent RepA synthesis},
author = {P Blomberg and H M Engdahl and C Malmgren and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7520116},
isbn = {7520116},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {12},
number = {1},
pages = {49-60},
abstract = {The replication frequency of plasmid R1 is controlled by an antisense RNA, CopA, that inhibits the synthesis of the replication initiator protein, RepA, at the post-transcriptional level. This inhibition is indirect and affects translation of a leader peptide reading frame (tap). Translation of tap is required for repA translation (Blomberg et al., 1992). Here we asked whether an RNA stem-loop sequestering the repA ribosome-binding site blocks tap translation-independent repA expression. Destabilization of this structure resulted in tap-independent RepA synthesis, concomitant with a loss of CopA-mediated inhibition; thus, CopA acts at the level of tap translation. Structure probing of RepA mRNAs confirmed that the introduced mutations induced a local destabilization in the repA ribosome-binding site stem-loop. An increased spacing between the repA Shine-Dalgarno region and the start codon permitted even higher repA expression. In Incl alpha/IncB plasmids, an RNA pseudoknot acts as an activator for rep translation. We suggest that the regulatory pathway in plasmid R1 does not involve an activator RNA pseudoknot.},
note = {0950-382x
Journal Article},
keywords = {Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The replication frequency of plasmid R1 is controlled by an antisense RNA, CopA, that inhibits the synthesis of the replication initiator protein, RepA, at the post-transcriptional level. This inhibition is indirect and affects translation of a leader peptide reading frame (tap). Translation of tap is required for repA translation (Blomberg et al., 1992). Here we asked whether an RNA stem-loop sequestering the repA ribosome-binding site blocks tap translation-independent repA expression. Destabilization of this structure resulted in tap-independent RepA synthesis, concomitant with a loss of CopA-mediated inhibition; thus, CopA acts at the level of tap translation. Structure probing of RepA mRNAs confirmed that the introduced mutations induced a local destabilization in the repA ribosome-binding site stem-loop. An increased spacing between the repA Shine-Dalgarno region and the start codon permitted even higher repA expression. In Incl alpha/IncB plasmids, an RNA pseudoknot acts as an activator for rep translation. We suggest that the regulatory pathway in plasmid R1 does not involve an activator RNA pseudoknot.
Benard L, Philippe C, Dondon L, Grunberg-Manago M, Ehresmann B, Ehresmann C, Portier C
Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli Article de journal
Dans: Mol Microbiol, vol. 14, no. 1, p. 31-40, 1994, ISBN: 7830558, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN
@article{,
title = {Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli},
author = {L Benard and C Philippe and L Dondon and M Grunberg-Manago and B Ehresmann and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7830558},
isbn = {7830558},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {14},
number = {1},
pages = {31-40},
abstract = {Expression of rpsO, the gene encoding the small ribosomal protein S15, is autoregulated at the translational level by S15, which binds to its mRNA in a region overlapping the ribosome-binding site. By measuring the effect of mutations on the expression of a translational rpsO-lacZ fusion and the S15 binding affinity for the translational operator, the formation of a pseudoknot in the operator site in vivo is fully demonstrated and appears to be a prerequisite for S15 binding. The mutational analysis suggests also that specific determinants for S15 binding are located in very limited regions of the structure formed by the pseudoknot. It is deduced that a specific pseudoknot conformation is a key element for autoregulation.},
note = {0950-382x
Journal Article},
keywords = {Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Expression of rpsO, the gene encoding the small ribosomal protein S15, is autoregulated at the translational level by S15, which binds to its mRNA in a region overlapping the ribosome-binding site. By measuring the effect of mutations on the expression of a translational rpsO-lacZ fusion and the S15 binding affinity for the translational operator, the formation of a pseudoknot in the operator site in vivo is fully demonstrated and appears to be a prerequisite for S15 binding. The mutational analysis suggests also that specific determinants for S15 binding are located in very limited regions of the structure formed by the pseudoknot. It is deduced that a specific pseudoknot conformation is a key element for autoregulation.
Baron C, Sturchler C, Wu X Q, Gross H J, Krol A, Bock A
Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 12, p. 2228-2233, 1994, ISBN: 8036149, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/chemistry/*genetics Selenocysteine/chemistry Serine-tRNA Ligase/metabolism Support, Animals Bacterial Proteins/metabolism Base Sequence Cloning, Molecular Escherichia coli/*genetics Genetic Complementation Test Human Nucleic Acid Conformation Peptide Elongation Factors/metabolism Proteins/*biosynthesis/genetics RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN
@article{,
title = {Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli},
author = {C Baron and C Sturchler and X Q Wu and H J Gross and A Krol and A Bock},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8036149},
isbn = {8036149},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {12},
pages = {2228-2233},
abstract = {Although the tRNA species directing selenocysteine insertion in prokaryotes differ greatly in their primary structure from that of their eukaryotic homologues they share very similar three-dimensional structures. To analyse whether this conservation of the overall shape of the molecules reflects a conservation of their functional interactions it was tested whether the selenocysteine inserting tRNA species from Homo sapiens supports selenoprotein synthesis in E. coli. It was found that the expression of the human tRNA(Sec) gene in E.coli can complement a lesion in the tRNA(Sec) gene of this organism. Transcripts of the Homo sapiens and Xenopus laevis tRNA(Sec) genes synthesised in vitro were amino-acylated by the E.coli seryl-tRNA ligase although at a very low rate and the resulting seryl-tRNA(Sec) was bound to and converted into selenocysteyl-tRNA(Sec) by the selenocysteine synthase of this organism. Selenocysteyl-tRNA(Sec) from both eukaryotes was able to form a complex with translation factor SELB from E.coli. Although the mechanism of selenocysteine incorporation into seleno-proteins appears to be rather different in E.coli and in vertebrates, we observe here a surprising conservation of functions over an enormous evolutionary distance.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/chemistry/*genetics Selenocysteine/chemistry Serine-tRNA Ligase/metabolism Support, Animals Bacterial Proteins/metabolism Base Sequence Cloning, Molecular Escherichia coli/*genetics Genetic Complementation Test Human Nucleic Acid Conformation Peptide Elongation Factors/metabolism Proteins/*biosynthesis/genetics RNA, Non-U.S. Gov't Xenopus laevis, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Although the tRNA species directing selenocysteine insertion in prokaryotes differ greatly in their primary structure from that of their eukaryotic homologues they share very similar three-dimensional structures. To analyse whether this conservation of the overall shape of the molecules reflects a conservation of their functional interactions it was tested whether the selenocysteine inserting tRNA species from Homo sapiens supports selenoprotein synthesis in E. coli. It was found that the expression of the human tRNA(Sec) gene in E.coli can complement a lesion in the tRNA(Sec) gene of this organism. Transcripts of the Homo sapiens and Xenopus laevis tRNA(Sec) genes synthesised in vitro were amino-acylated by the E.coli seryl-tRNA ligase although at a very low rate and the resulting seryl-tRNA(Sec) was bound to and converted into selenocysteyl-tRNA(Sec) by the selenocysteine synthase of this organism. Selenocysteyl-tRNA(Sec) from both eukaryotes was able to form a complex with translation factor SELB from E.coli. Although the mechanism of selenocysteine incorporation into seleno-proteins appears to be rather different in E.coli and in vertebrates, we observe here a surprising conservation of functions over an enormous evolutionary distance.
Baranowski W, Dirheimer G, Jakowicki J A, Keith G
Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women Article de journal
Dans: Cancer Res, vol. 54, no. 16, p. 4468-4471, 1994, ISBN: 8044797, (0008-5472 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adolescent Adult Female Guanine/*analogs & derivatives/analysis Human Middle Aged Ovarian Neoplasms/*chemistry/pathology RNA, Neoplasm/*chemistry RNA, Non-U.S. Gov't, Transfer/*chemistry Support, Unité ARN
@article{,
title = {Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women},
author = {W Baranowski and G Dirheimer and J A Jakowicki and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8044797},
isbn = {8044797},
year = {1994},
date = {1994-01-01},
journal = {Cancer Res},
volume = {54},
number = {16},
pages = {4468-4471},
abstract = {The tRNAs from rapidly growing tissues, particularly from neoplasia, often exhibit queuine deficiency. In order to check whether different kinds of ovarian tumors display queuine deficiencies we have analyzed tRNA samples from 16 ovarian malignancies. The tRNAs from histologically normal myometrium (4 samples) and myoma (6 samples) were taken as healthy tissue and benign tumor references. Queuine deficiency was determined by an exchange assay using [8-3H]guanine and tRNA:guanine transglycosylase from Escherichia coli. The mean values of queuine deficiencies in tRNAs were: 10.95 +/- 2.21 (SD) pmol/A260 in gonadal and germ cell tumors (5 cases); 23.75 +/- 7.89 pmol/A260 in primary epithelial tumors (9 cases); and 34.58 +/- 7.18 pmol/A260 in metastatic tumors (2 cases). These values displayed statistically significant differences (P = 0.0003, Kruskal-Wallis test). The queuine deficiencies in tRNAs significantly increased when moving from well-differentiated through moderately differentiated to poorly differentiated tumors, with the highest values found in poorly differentiated metastatic tumors (P = 0.0002, Kruskal-Wallis test). Queuine deficiency determination in tRNAs is proposed as a factor for clinical outcome prognosis of ovarian malignancies.},
note = {0008-5472
Journal Article},
keywords = {Adolescent Adult Female Guanine/*analogs & derivatives/analysis Human Middle Aged Ovarian Neoplasms/*chemistry/pathology RNA, Neoplasm/*chemistry RNA, Non-U.S. Gov't, Transfer/*chemistry Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The tRNAs from rapidly growing tissues, particularly from neoplasia, often exhibit queuine deficiency. In order to check whether different kinds of ovarian tumors display queuine deficiencies we have analyzed tRNA samples from 16 ovarian malignancies. The tRNAs from histologically normal myometrium (4 samples) and myoma (6 samples) were taken as healthy tissue and benign tumor references. Queuine deficiency was determined by an exchange assay using [8-3H]guanine and tRNA:guanine transglycosylase from Escherichia coli. The mean values of queuine deficiencies in tRNAs were: 10.95 +/- 2.21 (SD) pmol/A260 in gonadal and germ cell tumors (5 cases); 23.75 +/- 7.89 pmol/A260 in primary epithelial tumors (9 cases); and 34.58 +/- 7.18 pmol/A260 in metastatic tumors (2 cases). These values displayed statistically significant differences (P = 0.0003, Kruskal-Wallis test). The queuine deficiencies in tRNAs significantly increased when moving from well-differentiated through moderately differentiated to poorly differentiated tumors, with the highest values found in poorly differentiated metastatic tumors (P = 0.0002, Kruskal-Wallis test). Queuine deficiency determination in tRNAs is proposed as a factor for clinical outcome prognosis of ovarian malignancies.
Allmang C, Mougel M, Westhof E, Ehresmann B, Ehresmann C
Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8 Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 18, p. 3708-3714, 1994, ISBN: 7937081, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN
@article{,
title = {Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8},
author = {C Allmang and M Mougel and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7937081},
isbn = {7937081},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {18},
pages = {3708-3714},
abstract = {Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.},
note = {0305-1048
Journal Article},
keywords = {16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.
Wilhelm M L, Reinbolt J, Gangloff J, Dirheimer G, Wilhelm F X
Transfer RNA binding protein in the nucleus of Saccharomyces cerevisiae Article de journal
Dans: FEBS Lett, vol. 349, no. 2, p. 260-264, 1994, ISBN: 8050578, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Cell Nucleus/*metabolism Chromatography, Fungal/*isolation & purification RNA, High Pressure Liquid DNA/metabolism DNA-Binding Proteins/genetics/*metabolism Fungal Proteins/genetics/*metabolism Molecular Sequence Data RNA, Transfer/*isolation & purification Saccharomyces cerevisiae/*metabolism *Saccharomyces cerevisiae Proteins, Unité ARN
@article{,
title = {Transfer RNA binding protein in the nucleus of Saccharomyces cerevisiae},
author = {M L Wilhelm and J Reinbolt and J Gangloff and G Dirheimer and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8050578},
isbn = {8050578},
year = {1994},
date = {1994-01-01},
journal = {FEBS Lett},
volume = {349},
number = {2},
pages = {260-264},
abstract = {A yeast nuclear protein that binds to tRNA was identified using a RNA mobility shift assay. Northwestern blotting and N-terminal sequencing experiments indicate that this tRNA-binding protein is identical to zuotin which has previously been shown to bind to Z-DNA [(1992) EMBO J. 11, 3787-3796]. Labeled tRNA and poly(dG-m5dC) stabilized in the Z-DNA form identify the same protein on a Northwestern blot. In a gel retardation assay poly(dG-m5dC) in the Z-form strongly diminishes the binding of tRNA to zuotin. These studies establish that zuotin is able to bind to both tRNA and Z-DNA. Zuotin may be transiently associated with tRNA in the nucleus of yeast cells and play a role in its processing or transport to the cytoplasm.},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Sequence Cell Nucleus/*metabolism Chromatography, Fungal/*isolation & purification RNA, High Pressure Liquid DNA/metabolism DNA-Binding Proteins/genetics/*metabolism Fungal Proteins/genetics/*metabolism Molecular Sequence Data RNA, Transfer/*isolation & purification Saccharomyces cerevisiae/*metabolism *Saccharomyces cerevisiae Proteins, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A yeast nuclear protein that binds to tRNA was identified using a RNA mobility shift assay. Northwestern blotting and N-terminal sequencing experiments indicate that this tRNA-binding protein is identical to zuotin which has previously been shown to bind to Z-DNA [(1992) EMBO J. 11, 3787-3796]. Labeled tRNA and poly(dG-m5dC) stabilized in the Z-DNA form identify the same protein on a Northwestern blot. In a gel retardation assay poly(dG-m5dC) in the Z-form strongly diminishes the binding of tRNA to zuotin. These studies establish that zuotin is able to bind to both tRNA and Z-DNA. Zuotin may be transiently associated with tRNA in the nucleus of yeast cells and play a role in its processing or transport to the cytoplasm.
Wilhelm M, Wilhelm F X, Keith G, Agoutin B, Heyman T
Dans: Nucleic Acids Res, vol. 22, no. 22, p. 4560-4565, 1994, ISBN: 7527135, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN
@article{,
title = {Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles},
author = {M Wilhelm and F X Wilhelm and G Keith and B Agoutin and T Heyman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7527135},
isbn = {7527135},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {22},
pages = {4560-4565},
abstract = {Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.
Santos M A, el-Adlouni C, Cox A D, Luz J M, Keith G, Tuite M F
Transfer RNA profiling: a new method for the identification of pathogenic Candida species Article de journal
Dans: Yeast, vol. 10, no. 5, p. 625-636, 1994, ISBN: 7941747, (0749-503x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Candida/classification/*genetics/pathogenicity Electrophoresis, Fungal RNA, Non-U.S. Gov't, Polyacrylamide Gel Genetic Markers RNA, Transfer/*analysis Support, Unité ARN
@article{,
title = {Transfer RNA profiling: a new method for the identification of pathogenic Candida species},
author = {M A Santos and C el-Adlouni and A D Cox and J M Luz and G Keith and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7941747},
isbn = {7941747},
year = {1994},
date = {1994-01-01},
journal = {Yeast},
volume = {10},
number = {5},
pages = {625-636},
abstract = {A new molecular taxonomic method applicable to the identification of medically important Candida species and other yeast species has been developed. It is based on the electrophoretic pattern of total tRNA samples (a 'tRNA profile') isolated from Candida species and generated using high-resolution semi-denaturing urea-polyacrylamide gel electrophoresis and methylene blue staining. Species-specific tRNA profiles for the species C. albicans, C. tropicalis, C. parapsilosis, C. guilliermondii, C. glabrata and Pichia guilliermondii were obtained. Detailed studies with the major human pathogen of the Candida genus, C. albicans, demonstrated that the tRNA profile for a given species was both reproducible and strain-independent; seven different C. albicans strains generated identical tRNA profiles. Minor strain-specific heterogeneities in the tRNA profiles of C. guilliermondii and C. parapsilosis were detected, but in neither case did they significantly alter the species-specific diagnostic tRNA profile. The potential of this method in clarifying taxonomic anomalies was demonstrated by the finding that Type I and Type II strains of C. stellatoidea generate very different tRNA profiles, with that of a Type II strain being identical to the C. albicans tRNA profile. This method offers a number of advantages over current electrophoretic karyotype methods for species identification, both within the Candida genus and with yeast species in general.},
note = {0749-503x
Journal Article},
keywords = {Candida/classification/*genetics/pathogenicity Electrophoresis, Fungal RNA, Non-U.S. Gov't, Polyacrylamide Gel Genetic Markers RNA, Transfer/*analysis Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A new molecular taxonomic method applicable to the identification of medically important Candida species and other yeast species has been developed. It is based on the electrophoretic pattern of total tRNA samples (a 'tRNA profile') isolated from Candida species and generated using high-resolution semi-denaturing urea-polyacrylamide gel electrophoresis and methylene blue staining. Species-specific tRNA profiles for the species C. albicans, C. tropicalis, C. parapsilosis, C. guilliermondii, C. glabrata and Pichia guilliermondii were obtained. Detailed studies with the major human pathogen of the Candida genus, C. albicans, demonstrated that the tRNA profile for a given species was both reproducible and strain-independent; seven different C. albicans strains generated identical tRNA profiles. Minor strain-specific heterogeneities in the tRNA profiles of C. guilliermondii and C. parapsilosis were detected, but in neither case did they significantly alter the species-specific diagnostic tRNA profile. The potential of this method in clarifying taxonomic anomalies was demonstrated by the finding that Type I and Type II strains of C. stellatoidea generate very different tRNA profiles, with that of a Type II strain being identical to the C. albicans tRNA profile. This method offers a number of advantages over current electrophoretic karyotype methods for species identification, both within the Candida genus and with yeast species in general.
Meissner W, Wanandi I, Carbon P, Krol A, Seifart K H
Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 4, p. 553-559, 1994, ISBN: 8127703, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics Support, Animals Base Sequence DNA-Binding Proteins/*physiology Human Molecular Sequence Data Oligonucleotide Probes RNA, Genetic Xenopus laevis, Non-U.S. Gov't TATA Box Transcription Factors/*genetics Transcription, Transfer, Unité ARN
@article{,
title = {Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro},
author = {W Meissner and I Wanandi and P Carbon and A Krol and K H Seifart},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8127703},
isbn = {8127703},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {4},
pages = {553-559},
abstract = {It has previously been reported that transcription in vivo of the tRNA(Sec) gene requires three promoter elements, a PSE and a TATA-box upstream of the coding region which are functionally interchangeable with the U6 snRNA gene counterparts and an internal B-block, resembling that of classical tRNA genes (1). We have established an in vitro transcription system from HeLa cells in which three factors, which are either essential for or stimulate transcription were identified. Apart from the TATA-binding protein TBP, the PSE-binding protein PBP was found to be essentially required for expression of the gene. Depletion of PBP from cell extracts by PSE-oligonucleotides abolished tRNA(Sec) transcription, which could be reconstituted by readdition of partially purified PBP. Addition of increasing amounts of recombinant human TBP to an S100 extract stimulated transcription of the tRNA(Sec), the mouse U6 snRNA and the human Y3 genes, an effect which was not observed in the case of a TATA-less tRNA gene. Purified human TFIIA strongly stimulated tRNA(Sec) transcription in a fashion depending on the concentration of TBP. Surprisingly, partially purified TFIIIC was shown to be dispensable for transcription in vitro and unable to bind the B-block of this gene in vitro, although its sequence matches the consensus for this element. Collectively, these data suggest that the mechanism by which transcription complexes are formed on the tRNA(Sec) gene is dramatically different from that observed for classical tRNA genes and much more resembles that observed for externally controlled pol III genes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*genetics Support, Animals Base Sequence DNA-Binding Proteins/*physiology Human Molecular Sequence Data Oligonucleotide Probes RNA, Genetic Xenopus laevis, Non-U.S. Gov't TATA Box Transcription Factors/*genetics Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
It has previously been reported that transcription in vivo of the tRNA(Sec) gene requires three promoter elements, a PSE and a TATA-box upstream of the coding region which are functionally interchangeable with the U6 snRNA gene counterparts and an internal B-block, resembling that of classical tRNA genes (1). We have established an in vitro transcription system from HeLa cells in which three factors, which are either essential for or stimulate transcription were identified. Apart from the TATA-binding protein TBP, the PSE-binding protein PBP was found to be essentially required for expression of the gene. Depletion of PBP from cell extracts by PSE-oligonucleotides abolished tRNA(Sec) transcription, which could be reconstituted by readdition of partially purified PBP. Addition of increasing amounts of recombinant human TBP to an S100 extract stimulated transcription of the tRNA(Sec), the mouse U6 snRNA and the human Y3 genes, an effect which was not observed in the case of a TATA-less tRNA gene. Purified human TFIIA strongly stimulated tRNA(Sec) transcription in a fashion depending on the concentration of TBP. Surprisingly, partially purified TFIIIC was shown to be dispensable for transcription in vitro and unable to bind the B-block of this gene in vitro, although its sequence matches the consensus for this element. Collectively, these data suggest that the mechanism by which transcription complexes are formed on the tRNA(Sec) gene is dramatically different from that observed for classical tRNA genes and much more resembles that observed for externally controlled pol III genes.
Heyman T, Agoutin B, Fix C, Dirheimer G, Keith G
Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU Article de journal
Dans: FEBS Lett, vol. 347, no. 2-3, p. 143-146, 1994, ISBN: 8033992, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU},
author = {T Heyman and B Agoutin and C Fix and G Dirheimer and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8033992},
isbn = {8033992},
year = {1994},
date = {1994-01-01},
journal = {FEBS Lett},
volume = {347},
number = {2-3},
pages = {143-146},
abstract = {The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.},
note = {0014-5793
Journal Article},
keywords = {Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.
1993
Zhang G Y, Beltchev B, Fournier A, Zhang Y H, Malassine A, Bisbal C, Ehresmann B, Ehresmann C, Darlix J L, Thang M N
High levels of 2',5'-oligoadenylate synthetase and 2',5'-oligoadenylate-dependent endonuclease in human trophoblast Article de journal
Dans: AIDS Res Hum Retroviruses, vol. 9, no. 2, p. 189-196, 1993, ISBN: 8457385, (0889-2229 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 2', 5'-Oligoadenylate Synthetase/*metabolism Endoribonucleases/*metabolism Enzyme Activation/drug effects Female HIV Infections/transmission HIV-1/*physiology Human In Vitro Maternal-Fetal Exchange Pregnancy RNA, Non-U.S. Gov't Trophoblasts/*enzymology/*microbiology Virus Replication, Unité ARN, Viral/pharmacology Support
@article{,
title = {High levels of 2',5'-oligoadenylate synthetase and 2',5'-oligoadenylate-dependent endonuclease in human trophoblast},
author = {G Y Zhang and B Beltchev and A Fournier and Y H Zhang and A Malassine and C Bisbal and B Ehresmann and C Ehresmann and J L Darlix and M N Thang},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8457385},
isbn = {8457385},
year = {1993},
date = {1993-01-01},
journal = {AIDS Res Hum Retroviruses},
volume = {9},
number = {2},
pages = {189-196},
abstract = {Human placenta contains a high level of 2',5'-oligoadenylate (2-5A) synthetase activity of the 100-kD form of the enzyme. About 20% of the placental 2-5A synthetase activity was found to be cytosolic, whereas the remaining 80% was released by 0.5 M KCl in the presence of detergent. Most of the enzyme activity was localized in trophoblast cells, which also contain a high level of 2-5A-dependent RNase L activity. The purified trophoblast 100-kD 2-5A synthetase was shown to be activated by human immunodeficiency virus type 1 (HIV-1) 5' RNA 1-311 and 1-707, which both contain the TAR and primer binding site (PBS) structured regions. These two HIV-1 RNAs activated human trophoblast 2-5A synthetase at the same level as poly(I).poly (C), a standard highly efficient activator of the enzyme, and at the same optimal concentration. On the contrary, HIV-1 RNA 311-618, a poorly structured region missing TAR and PBS, was shown to be a poor activator of the enzyme. The specific cellular location of the 2-5A synthetase and its efficient activation by HIV 5' RNA favors the idea that the trophoblast 2-5A system negatively controls HIV replication in trophoblasts.},
note = {0889-2229
Journal Article},
keywords = {2', 5'-Oligoadenylate Synthetase/*metabolism Endoribonucleases/*metabolism Enzyme Activation/drug effects Female HIV Infections/transmission HIV-1/*physiology Human In Vitro Maternal-Fetal Exchange Pregnancy RNA, Non-U.S. Gov't Trophoblasts/*enzymology/*microbiology Virus Replication, Unité ARN, Viral/pharmacology Support},
pubstate = {published},
tppubtype = {article}
}
Human placenta contains a high level of 2',5'-oligoadenylate (2-5A) synthetase activity of the 100-kD form of the enzyme. About 20% of the placental 2-5A synthetase activity was found to be cytosolic, whereas the remaining 80% was released by 0.5 M KCl in the presence of detergent. Most of the enzyme activity was localized in trophoblast cells, which also contain a high level of 2-5A-dependent RNase L activity. The purified trophoblast 100-kD 2-5A synthetase was shown to be activated by human immunodeficiency virus type 1 (HIV-1) 5' RNA 1-311 and 1-707, which both contain the TAR and primer binding site (PBS) structured regions. These two HIV-1 RNAs activated human trophoblast 2-5A synthetase at the same level as poly(I).poly (C), a standard highly efficient activator of the enzyme, and at the same optimal concentration. On the contrary, HIV-1 RNA 311-618, a poorly structured region missing TAR and PBS, was shown to be a poor activator of the enzyme. The specific cellular location of the 2-5A synthetase and its efficient activation by HIV 5' RNA favors the idea that the trophoblast 2-5A system negatively controls HIV replication in trophoblasts.
Xue H, Shen W, Giege R, Wong J T
Identity elements of tRNA(Trp). Identification and evolutionary conservation Article de journal
Dans: J Biol Chem, vol. 268, no. 13, p. 9316-9322, 1993, ISBN: 8486627, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN
@article{,
title = {Identity elements of tRNA(Trp). Identification and evolutionary conservation},
author = {H Xue and W Shen and R Giege and J T Wong},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8486627},
isbn = {8486627},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {13},
pages = {9316-9322},
abstract = {In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.},
note = {0021-9258
Journal Article},
keywords = {Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.
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}
}
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.
Sturchler C, Westhof E, Carbon P, Krol A
Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec) Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 5, p. 1073-1079, 1993, ISBN: 8464694, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN
@article{,
title = {Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec)},
author = {C Sturchler and E Westhof and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464694},
isbn = {8464694},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {5},
pages = {1073-1079},
abstract = {Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.
Skripkin E, Yusupova G, Yusupov M, Kessler P, Ehresmann C, Ehresmann B
Synthesis and ribosome binding properties of model mRNAs modified with undecagold cluster Article de journal
Dans: Bioconjug Chem, vol. 4, no. 6, p. 549-553, 1993, ISBN: 8305524, (1043-1802 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study Escherichia coli/metabolism Gold/metabolism Models, Genetic/drug effects/genetics, Messenger/*chemical synthesis/chemistry/*metabolism RNA, Met/metabolism Ribosomes/*metabolism Support, Molecular Molecular Sequence Data Organometallic Compounds/*chemical synthesis/chemistry/*metabolism RNA, Non-U.S. Gov't Translation, Transfer, Unité ARN
@article{,
title = {Synthesis and ribosome binding properties of model mRNAs modified with undecagold cluster},
author = {E Skripkin and G Yusupova and M Yusupov and P Kessler and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8305524},
isbn = {8305524},
year = {1993},
date = {1993-01-01},
journal = {Bioconjug Chem},
volume = {4},
number = {6},
pages = {549-553},
abstract = {The synthesis and purification of short model messenger RNAs modified with undecagold cluster are described. A monoamino undecagold cluster was introduced on the oxidized 3' cis-glycol group of the mRNA followed by reduction of the formed Schiff's base. The stability of the modified mRNA under the conditions used for in vitro messenger RNA translation is studied. The possibility of the formation of a specific translational initiation complex with bacterial ribosomes and modified mRNAs is shown. The results of these experiments indicate that the attachment of an undecagold cluster to a mRNA is a useful tool for electron microscopic and crystallographic studies.},
note = {1043-1802
Journal Article},
keywords = {Base Sequence Comparative Study Escherichia coli/metabolism Gold/metabolism Models, Genetic/drug effects/genetics, Messenger/*chemical synthesis/chemistry/*metabolism RNA, Met/metabolism Ribosomes/*metabolism Support, Molecular Molecular Sequence Data Organometallic Compounds/*chemical synthesis/chemistry/*metabolism RNA, Non-U.S. Gov't Translation, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The synthesis and purification of short model messenger RNAs modified with undecagold cluster are described. A monoamino undecagold cluster was introduced on the oxidized 3' cis-glycol group of the mRNA followed by reduction of the formed Schiff's base. The stability of the modified mRNA under the conditions used for in vitro messenger RNA translation is studied. The possibility of the formation of a specific translational initiation complex with bacterial ribosomes and modified mRNAs is shown. The results of these experiments indicate that the attachment of an undecagold cluster to a mRNA is a useful tool for electron microscopic and crystallographic studies.
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}
}
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.
Santos M A, Keith G, Tuite M F
Non-standard translational events in Candida albicans mediated by an unusual seryl-tRNA with a 5'-CAG-3' (leucine) anticodon Article de journal
Dans: EMBO J, vol. 12, no. 2, p. 607-616, 1993, ISBN: 8440250, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Base Sequence Candida albicans/*genetics Cloning, Fungal Genes, Fungal Leucine/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/isolation & purification RNA, Genetic, Molecular DNA, Non-U.S. Gov't *Translation, Ser/chemistry/*genetics/isolation & purification Support, Transfer, Unité ARN
@article{,
title = {Non-standard translational events in Candida albicans mediated by an unusual seryl-tRNA with a 5'-CAG-3' (leucine) anticodon},
author = {M A Santos and G Keith and M F Tuite},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8440250},
isbn = {8440250},
year = {1993},
date = {1993-01-01},
journal = {EMBO J},
volume = {12},
number = {2},
pages = {607-616},
abstract = {From in vitro translation studies we have previously demonstrated the existence of an apparent efficient UAG (amber) suppressor tRNA in the dimorphic fungus Candida albicans (Santos et al., 1990). Using an in vitro assay for termination codon readthrough the tRNA responsible was purified to homogeneity from C.albicans cells. The determined sequence of the purified tRNA predicts a 5'-CAG-3' anticodon that should decode the leucine codon CUG and not the UAG termination codon as originally hypothesized. However, the tRNA(CAG) sequence shows greater nucleotide homology with seryl-tRNAs from the closely related yeast Saccharomyces cerevisiae than with leucyl-tRNAs from the same species. In vitro tRNA-charging studies demonstrated that the purified tRNA(CAG) is charged with Ser. The gene encoding the tRNA was cloned from C.albicans by a PCR-based strategy and DNA sequence analysis confirmed both the structure of the tRNA(CAG) and the absence of any introns in the tRNA gene. The copy number of the tRNA(CAG) gene (1-2 genes per haploid genome) is in agreement with the relatively low abundance (< 0.5% total tRNA) of this tRNA. In vitro translation studies revealed that the purified tRNA(CAG) could induce apparent translational bypass of all three termination codons. However, peptide mapping of in vitro translation products demonstrated that the tRNA(CAG) induces translational misreading in the amino-terminal region of two RNA templates employed, namely the rabbit alpha- and beta-globin mRNAs. These results suggest that the C.albicans tRNA(CAG) is not an 'omnipotent' suppressor tRNA but rather may mediate a novel non-standard translational event in vitro during the translation of the CUG codon. The possible nature of this non-standard translation event is discussed in the context of both the unusual structural features of the tRNA(CAG) and its in vitro behaviour.},
note = {0261-4189
Journal Article},
keywords = {*Anticodon Base Sequence Candida albicans/*genetics Cloning, Fungal Genes, Fungal Leucine/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Fungal/chemistry/genetics/isolation & purification RNA, Genetic, Molecular DNA, Non-U.S. Gov't *Translation, Ser/chemistry/*genetics/isolation & purification Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
From in vitro translation studies we have previously demonstrated the existence of an apparent efficient UAG (amber) suppressor tRNA in the dimorphic fungus Candida albicans (Santos et al., 1990). Using an in vitro assay for termination codon readthrough the tRNA responsible was purified to homogeneity from C.albicans cells. The determined sequence of the purified tRNA predicts a 5'-CAG-3' anticodon that should decode the leucine codon CUG and not the UAG termination codon as originally hypothesized. However, the tRNA(CAG) sequence shows greater nucleotide homology with seryl-tRNAs from the closely related yeast Saccharomyces cerevisiae than with leucyl-tRNAs from the same species. In vitro tRNA-charging studies demonstrated that the purified tRNA(CAG) is charged with Ser. The gene encoding the tRNA was cloned from C.albicans by a PCR-based strategy and DNA sequence analysis confirmed both the structure of the tRNA(CAG) and the absence of any introns in the tRNA gene. The copy number of the tRNA(CAG) gene (1-2 genes per haploid genome) is in agreement with the relatively low abundance (< 0.5% total tRNA) of this tRNA. In vitro translation studies revealed that the purified tRNA(CAG) could induce apparent translational bypass of all three termination codons. However, peptide mapping of in vitro translation products demonstrated that the tRNA(CAG) induces translational misreading in the amino-terminal region of two RNA templates employed, namely the rabbit alpha- and beta-globin mRNAs. These results suggest that the C.albicans tRNA(CAG) is not an 'omnipotent' suppressor tRNA but rather may mediate a novel non-standard translational event in vitro during the translation of the CUG codon. The possible nature of this non-standard translation event is discussed in the context of both the unusual structural features of the tRNA(CAG) and its in vitro behaviour.
Roth A, Eriani G, Dirheimer G, Gangloff J
Kinetic properties of pure overproduced Bacillus subtilis phenylalanyl-tRNA synthetase do not favour its in vivo inhibition by ochratoxin A Article de journal
Dans: FEBS Lett, vol. 326, no. 1-3, p. 87-91, 1993, ISBN: 8325392, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacillus subtilis/drug effects/*enzymology Binding, Bacterial, Competitive Escherichia coli/enzymology/genetics Kinetics Macromolecular Systems Ochratoxins/*pharmacology Phenylalanine/metabolism Phenylalanine-tRNA Ligase/antagonists & inhibitors/*metabolism Support, ERIANI, Non-U.S. Gov't Transformation, Unité ARN
@article{,
title = {Kinetic properties of pure overproduced Bacillus subtilis phenylalanyl-tRNA synthetase do not favour its in vivo inhibition by ochratoxin A},
author = {A Roth and G Eriani and G Dirheimer and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8325392},
isbn = {8325392},
year = {1993},
date = {1993-01-01},
journal = {FEBS Lett},
volume = {326},
number = {1-3},
pages = {87-91},
abstract = {Ochratoxine A (OTA) inhibits growth of Bacillus subtilis at pHs below 7. Since OTA is a phenylalanine analogue, this effect could be due to inhibition of phenylalanine-tRNA synthetase (PheRS) by competition of this mycotoxin with the amino acid. Homogeneous PheRS was purified from Bacillus subtilis and from E. coli transformed with the PheRS gene. The latter produced about 40 times more PheRS than B. subtilis. The Km and Ki values of PheRS, respectively, for phenylalanine and OTA were measured and their concentrations within the cell determined. It appears that the concentration of OTA in the cell, in spite of a 25-fold accumulation, remained too low to significantly compete with phenylalanine. This does not suggest PheRS to be the target of OTA in cell growth and protein synthesis inhibition in Bacillus subtilis. It was also shown that the 2-3-fold increase of PheRS in OTA-treated cells is not due to phenylalanine-controlled attenuation regulation.},
note = {0014-5793
Journal Article},
keywords = {Bacillus subtilis/drug effects/*enzymology Binding, Bacterial, Competitive Escherichia coli/enzymology/genetics Kinetics Macromolecular Systems Ochratoxins/*pharmacology Phenylalanine/metabolism Phenylalanine-tRNA Ligase/antagonists & inhibitors/*metabolism Support, ERIANI, Non-U.S. Gov't Transformation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ochratoxine A (OTA) inhibits growth of Bacillus subtilis at pHs below 7. Since OTA is a phenylalanine analogue, this effect could be due to inhibition of phenylalanine-tRNA synthetase (PheRS) by competition of this mycotoxin with the amino acid. Homogeneous PheRS was purified from Bacillus subtilis and from E. coli transformed with the PheRS gene. The latter produced about 40 times more PheRS than B. subtilis. The Km and Ki values of PheRS, respectively, for phenylalanine and OTA were measured and their concentrations within the cell determined. It appears that the concentration of OTA in the cell, in spite of a 25-fold accumulation, remained too low to significantly compete with phenylalanine. This does not suggest PheRS to be the target of OTA in cell growth and protein synthesis inhibition in Bacillus subtilis. It was also shown that the 2-3-fold increase of PheRS in OTA-treated cells is not due to phenylalanine-controlled attenuation regulation.
Reinbolt J, Eliseikina I, Sedelnilkova S, Garber M, Ehresmann C, Ehresmann B
The complete amino acid sequence of ribosomal protein S8 from Thermus thermophilus Article de journal
Dans: J Protein Chem, vol. 12, no. 1, p. 79-83, 1993, ISBN: 8427638, (0277-8033 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Serine Endopeptidases/chemistry Thermus/chemistry Thermus thermophilus/*chemistry, Amino Acid Sequence Hydrolysis Metalloendopeptidases/chemistry Molecular Sequence Data Ribosomal Proteins/*chemistry Sequence Homology, Unité ARN
@article{,
title = {The complete amino acid sequence of ribosomal protein S8 from Thermus thermophilus},
author = {J Reinbolt and I Eliseikina and S Sedelnilkova and M Garber and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8427638},
isbn = {8427638},
year = {1993},
date = {1993-01-01},
journal = {J Protein Chem},
volume = {12},
number = {1},
pages = {79-83},
abstract = {Protein S8 from Thermus thermophilus consists of 138 amino acids of M(r) 15,840. Its primary structure was established using peptide sequences from two different digests. Protein S8 from T. thermophilus shares a high percentage of identity with protein S8 from Thermus aquaticus. There are some consensus sequences between proteins S8 from eubacteria, archebacteria, chloroplasts, and cyanelles.},
note = {0277-8033
Journal Article},
keywords = {Amino Acid Serine Endopeptidases/chemistry Thermus/chemistry Thermus thermophilus/*chemistry, Amino Acid Sequence Hydrolysis Metalloendopeptidases/chemistry Molecular Sequence Data Ribosomal Proteins/*chemistry Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Protein S8 from Thermus thermophilus consists of 138 amino acids of M(r) 15,840. Its primary structure was established using peptide sequences from two different digests. Protein S8 from T. thermophilus shares a high percentage of identity with protein S8 from Thermus aquaticus. There are some consensus sequences between proteins S8 from eubacteria, archebacteria, chloroplasts, and cyanelles.
Putz J, Puglisi J D, Florentz C, Giege R
Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA Article de journal
Dans: EMBO J, vol. 12, no. 7, p. 2949-2957, 1993, ISBN: 8335008, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA},
author = {J Putz and J D Puglisi and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8335008},
isbn = {8335008},
year = {1993},
date = {1993-01-01},
journal = {EMBO J},
volume = {12},
number = {7},
pages = {2949-2957},
abstract = {We have investigated the functional relationship between nucleotides in yeast tRNAAsp that are important for aspartylation by yeast aspartyl-tRNA synthetase. Transcripts of tRNAAsp with two or more mutations at identity positions G73, G34, U35, C36 and base pair G10-U25 have been prepared and the steady-state kinetics of their aspartylation were measured. Multiple mutations affect the catalytic activities of the synthetase mainly at the level of the catalytic constant, kcat. Kinetic data were expressed as free energy variation at transition state of these multiple mutants and comparison of experimental values with those calculated from results on single mutants defined three types of relationships between the identity nucleotides of this tRNA. Nucleotides located far apart in the three-dimensional structure of the tRNA act cooperatively whereas nucleotides of the anticodon triplet act either additively or anti-cooperatively. These results are related to the specific interactions of functional groups on identity nucleotides with amino acids in the protein as revealed by the crystal structure of the tRNAAsp/aspartyl-tRNA synthetase complex. These relationships between identity nucleotides may play an important role in the biological function of tRNAs.},
note = {0261-4189
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/metabolism Aspartic Acid/chemistry/genetics Base Sequence Catalysis Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Nucleotides/*metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/enzymology Support, FLORENTZ, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We have investigated the functional relationship between nucleotides in yeast tRNAAsp that are important for aspartylation by yeast aspartyl-tRNA synthetase. Transcripts of tRNAAsp with two or more mutations at identity positions G73, G34, U35, C36 and base pair G10-U25 have been prepared and the steady-state kinetics of their aspartylation were measured. Multiple mutations affect the catalytic activities of the synthetase mainly at the level of the catalytic constant, kcat. Kinetic data were expressed as free energy variation at transition state of these multiple mutants and comparison of experimental values with those calculated from results on single mutants defined three types of relationships between the identity nucleotides of this tRNA. Nucleotides located far apart in the three-dimensional structure of the tRNA act cooperatively whereas nucleotides of the anticodon triplet act either additively or anti-cooperatively. These results are related to the specific interactions of functional groups on identity nucleotides with amino acids in the protein as revealed by the crystal structure of the tRNAAsp/aspartyl-tRNA synthetase complex. These relationships between identity nucleotides may play an important role in the biological function of tRNAs.
Puglisi J D, Putz J, Florentz C, Giege R
Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 1, p. 41-49, 1993, ISBN: 8441619, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN
@article{,
title = {Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase},
author = {J D Puglisi and J Putz and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8441619},
isbn = {8441619},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {1},
pages = {41-49},
abstract = {Mutations have been designed that disrupt the tertiary structure of yeast tRNA(Asp). The effects of these mutations on both tRNA structure and specific aspartylation by yeast aspartyl-tRNA synthetase were assayed. Mutations that disrupt tertiary interactions involving the D-stem or D-loop result in destabilization of the base-pairing in the D-stem, as monitored by nuclease digestion and chemical modification studies. These mutations also decrease the specificity constant (kcat/Km) for aspartylation by aspartyl-tRNA synthetase up to 10(3)-10(4) fold. The size of the T-loop also influences tRNA(Asp) structure and function; change of its T-loop to a tetraloop (-UUCG-) sequence results in a denatured D-stem and an almost 10(4) fold decrease of kcat/Km for aspartylation. The negative effects of these mutations on aspartylation activity are significantly alleviated by additional mutations that stabilize the D-stem. These results indicate that a critical role of tertiary structure in tRNA(Asp) for aspartylation is the maintenance of a base-paired D-stem.},
note = {0305-1048
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mutations have been designed that disrupt the tertiary structure of yeast tRNA(Asp). The effects of these mutations on both tRNA structure and specific aspartylation by yeast aspartyl-tRNA synthetase were assayed. Mutations that disrupt tertiary interactions involving the D-stem or D-loop result in destabilization of the base-pairing in the D-stem, as monitored by nuclease digestion and chemical modification studies. These mutations also decrease the specificity constant (kcat/Km) for aspartylation by aspartyl-tRNA synthetase up to 10(3)-10(4) fold. The size of the T-loop also influences tRNA(Asp) structure and function; change of its T-loop to a tetraloop (-UUCG-) sequence results in a denatured D-stem and an almost 10(4) fold decrease of kcat/Km for aspartylation. The negative effects of these mutations on aspartylation activity are significantly alleviated by additional mutations that stabilize the D-stem. These results indicate that a critical role of tertiary structure in tRNA(Asp) for aspartylation is the maintenance of a base-paired D-stem.
Poterszman A, Plateau P, Moras D, Blanquet S, Mazauric M H, Kreutzer R, Kern D
Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus. Implications for the structure of prokaryotic aspartyl-tRNA synthetases Article de journal
Dans: FEBS Lett, vol. 325, no. 3, p. 183-186, 1993, ISBN: 8319804, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN
@article{,
title = {Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus. Implications for the structure of prokaryotic aspartyl-tRNA synthetases},
author = {A Poterszman and P Plateau and D Moras and S Blanquet and M H Mazauric and R Kreutzer and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8319804},
isbn = {8319804},
year = {1993},
date = {1993-01-01},
journal = {FEBS Lett},
volume = {325},
number = {3},
pages = {183-186},
abstract = {The genes of aspartyl-tRNA synthetase (AspRS) from two Thermus thermophilus strain VK-1 and HB8, have been cloned and sequenced. Their nucleotidic sequences code for the same protein which displays the three characteristic motifs of class II aminoacyl-tRNA synthetases. This enzyme shows 50% identity with Escherichia coli AspRS, over the totality of the chain (580 amino acids). A comparison with the eukaryotic yeast cytoplasmic AspRS indicates the presence in the prokaryotic AspRS of an extra domain between motifs 2 and 3 much larger than in the eukaryotic ones. When its gene is under the control of the tac promoter of the expression vector pKK223-3, the protein is efficiently overexpressed as a thermostable protein in E. coli. It can be further purified to homogeneity using a heat treatment followed by a single anion exchange chromatography. Single crystals of the pure protein, diffracting at least to 2.2 A resolution (space group P2(1)2(1)2(1)},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The genes of aspartyl-tRNA synthetase (AspRS) from two Thermus thermophilus strain VK-1 and HB8, have been cloned and sequenced. Their nucleotidic sequences code for the same protein which displays the three characteristic motifs of class II aminoacyl-tRNA synthetases. This enzyme shows 50% identity with Escherichia coli AspRS, over the totality of the chain (580 amino acids). A comparison with the eukaryotic yeast cytoplasmic AspRS indicates the presence in the prokaryotic AspRS of an extra domain between motifs 2 and 3 much larger than in the eukaryotic ones. When its gene is under the control of the tac promoter of the expression vector pKK223-3, the protein is efficiently overexpressed as a thermostable protein in E. coli. It can be further purified to homogeneity using a heat treatment followed by a single anion exchange chromatography. Single crystals of the pure protein, diffracting at least to 2.2 A resolution (space group P2(1)2(1)2(1)
Podyminogin M A, Vlassov V V, Giege R
Synthetic RNA-cleaving molecules mimicking ribonuclease A active center. Design and cleavage of tRNA transcripts Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 25, p. 5950-5956, 1993, ISBN: 7507235, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/*metabolism Ribonuclease, Base Sequence Binding Sites Hydrogen-Ion Concentration Molecular Sequence Data Nucleic Acid Conformation RNA/metabolism RNA, Genetic, Non-U.S. Gov't Temperature Transcription, Pancreatic/antagonists & inhibitors/chemical synthesis/*metabolism Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Synthetic RNA-cleaving molecules mimicking ribonuclease A active center. Design and cleavage of tRNA transcripts},
author = {M A Podyminogin and V V Vlassov and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507235},
isbn = {7507235},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {25},
pages = {5950-5956},
abstract = {RNA cleaving molecules were synthesized by conjugating imidazole residues imitating the essential imidazoles in the active center of pancreatic ribonuclease to an intercalating compound, derivative of phenazine capable of binding to the double stranded regions of polynucleotides. Action of the molecules on tRNA was investigated. It was found, that some of the compounds bearing two imidazole residues cleave tRNA under physiological conditions. The cleavage reaction shows a bell-shaped pH dependence with a maximum at pH 7.0 indicating participation of protonated and non-protonated imidazole residues in the process. Under the conditions stabilizing the tRNA structure, a tRNAAsp transcript was cleaved preferentially at the junctions of the stem and loop regions of the cloverleaf tRNA fold, at the five positions C56, C43, C20.1, U13, and U8, with a marked preference for C56. This cleavage pattern is consistent with a hydrolysis mechanism involving non-covalent binding of the compounds to the double-stranded regions of tRNA followed by an attack of the imidazole residues at the juxtaposed flexible single-stranded regions of the molecule. The compounds provide new probes for the investigation of RNA structure in solution and potential reactive groups for antisense oligonucleotide derivatives.},
note = {0305-1048
Journal Article},
keywords = {Asp/*metabolism Ribonuclease, Base Sequence Binding Sites Hydrogen-Ion Concentration Molecular Sequence Data Nucleic Acid Conformation RNA/metabolism RNA, Genetic, Non-U.S. Gov't Temperature Transcription, Pancreatic/antagonists & inhibitors/chemical synthesis/*metabolism Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA cleaving molecules were synthesized by conjugating imidazole residues imitating the essential imidazoles in the active center of pancreatic ribonuclease to an intercalating compound, derivative of phenazine capable of binding to the double stranded regions of polynucleotides. Action of the molecules on tRNA was investigated. It was found, that some of the compounds bearing two imidazole residues cleave tRNA under physiological conditions. The cleavage reaction shows a bell-shaped pH dependence with a maximum at pH 7.0 indicating participation of protonated and non-protonated imidazole residues in the process. Under the conditions stabilizing the tRNA structure, a tRNAAsp transcript was cleaved preferentially at the junctions of the stem and loop regions of the cloverleaf tRNA fold, at the five positions C56, C43, C20.1, U13, and U8, with a marked preference for C56. This cleavage pattern is consistent with a hydrolysis mechanism involving non-covalent binding of the compounds to the double-stranded regions of tRNA followed by an attack of the imidazole residues at the juxtaposed flexible single-stranded regions of the molecule. The compounds provide new probes for the investigation of RNA structure in solution and potential reactive groups for antisense oligonucleotide derivatives.
Pochart P, Agoutin B, Fix C, Keith G, Heyman T
A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 7, p. 1517-1521, 1993, ISBN: 8386834, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Transposable Elements/*physiology Electrophoresis, Gel, Met/metabolism RNA, Ser/*metabolism RNA, Transfer, Two-Dimensional Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*metabolism Retroviridae/*growth & development Saccharomyces cerevisiae/metabolism
@article{,
title = {A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles},
author = {P Pochart and B Agoutin and C Fix and G Keith and T Heyman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8386834},
isbn = {8386834},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {7},
pages = {1517-1521},
abstract = {The analysis of the tRNAs associated to the virus-like particles produced by the Ty1 element revealed the specific packaging of three major tRNA species, in about equal amounts: the replication primer initiator tRNA(Met), the tRNA(Ser)AGA and a tRNA undetected until now as an expressed species in yeast. The latter tRNA is coded by the already described tDNA(Ser)GCT. This tRNA is enriched more than 150 fold in the particles as compared to its content in total cellular tRNA where it represents less than 0.1% (initiator tRNA(Met) and tRNA(Ser)AGA being 11 and 4 fold enriched respectively). This tRNA is the only species coded by the tDNA(Ser)GCT gene which is found in three copies per genome since no other corresponding expressed tRNA could be detected. This gene is thus very poorly expressed. The high concentration of tRNA(Ser)GCU in the particles compared to its very low cellular content led us to consider its possible implication in Ty specific processes.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence DNA Transposable Elements/*physiology Electrophoresis, Gel, Met/metabolism RNA, Ser/*metabolism RNA, Transfer, Two-Dimensional Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*metabolism Retroviridae/*growth & development Saccharomyces cerevisiae/metabolism},
pubstate = {published},
tppubtype = {article}
}
The analysis of the tRNAs associated to the virus-like particles produced by the Ty1 element revealed the specific packaging of three major tRNA species, in about equal amounts: the replication primer initiator tRNA(Met), the tRNA(Ser)AGA and a tRNA undetected until now as an expressed species in yeast. The latter tRNA is coded by the already described tDNA(Ser)GCT. This tRNA is enriched more than 150 fold in the particles as compared to its content in total cellular tRNA where it represents less than 0.1% (initiator tRNA(Met) and tRNA(Ser)AGA being 11 and 4 fold enriched respectively). This tRNA is the only species coded by the tDNA(Ser)GCT gene which is found in three copies per genome since no other corresponding expressed tRNA could be detected. This gene is thus very poorly expressed. The high concentration of tRNA(Ser)GCU in the particles compared to its very low cellular content led us to consider its possible implication in Ty specific processes.
Philippe C, Eyermann F, Benard L, Portier C, Ehresmann B, Ehresmann C
Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 10, p. 4394-4398, 1993, ISBN: 7685101, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site},
author = {C Philippe and F Eyermann and L Benard and C Portier and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685101},
isbn = {7685101},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {10},
pages = {4394-4398},
abstract = {From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use "toeprint" experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(fMet) complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3' terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(fMet) complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(fMet) complex.},
note = {0027-8424
Journal Article},
keywords = {Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use "toeprint" experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(fMet) complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3' terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(fMet) complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(fMet) complex.
Pellequer J L, Westhof E, Regenmortel M H Van
Correlation between the location of antigenic sites and the prediction of turns in proteins Article de journal
Dans: Immunol Lett, vol. 36, no. 1, p. 83-99, 1993, ISBN: 7688347, (0165-2478 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Databases, Factual Epitopes/*chemistry Molecular Sequence Data Protein Conformation Protein Folding *Protein Structure, Secondary Proteins/*chemistry, Unité ARN
@article{,
title = {Correlation between the location of antigenic sites and the prediction of turns in proteins},
author = {J L Pellequer and E Westhof and M H Van Regenmortel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7688347},
isbn = {7688347},
year = {1993},
date = {1993-01-01},
journal = {Immunol Lett},
volume = {36},
number = {1},
pages = {83-99},
abstract = {In the present study, we developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. We found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. We used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein (two or three). We found that it leads to a high level of accurate prediction (70% of correct prediction of known epitopes). Our method should be useful for selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein.},
note = {0165-2478
Journal Article},
keywords = {Amino Acid Sequence Databases, Factual Epitopes/*chemistry Molecular Sequence Data Protein Conformation Protein Folding *Protein Structure, Secondary Proteins/*chemistry, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In the present study, we developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. We found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. We used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein (two or three). We found that it leads to a high level of accurate prediction (70% of correct prediction of known epitopes). Our method should be useful for selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein.
Pellequer J L, Westhof E
PREDITOP: a program for antigenicity prediction Article de journal
Dans: J Mol Graph, vol. 11, no. 3, p. 204-210, 191-202, 1993, ISBN: 7509182, (0263-7855 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antigens/*chemistry Computer Graphics Epitopes/chemistry Proteins/*chemistry/*immunology *Software Software Design, Unité ARN
@article{,
title = {PREDITOP: a program for antigenicity prediction},
author = {J L Pellequer and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7509182},
isbn = {7509182},
year = {1993},
date = {1993-01-01},
journal = {J Mol Graph},
volume = {11},
number = {3},
pages = {204-210, 191-202},
abstract = {A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on proteins is described. This program and the associated ones are written in Turbo Pascal and run on IBM-PC compatibles. The program contains 22 normalized scales, corresponding to hydrophilicity, accessibility, flexibility, or secondary structure propensities. New scales are easily implemented. An hydrophobic moment procedure has also been implemented in order to determine amphiphilic helices. The program generates a result file where the values represent a particular physicochemical aspect of the studied protein. PREDITOP can display one or several result files by simple graphical super-imposition. Curve combinations can be done by the ADDITIO or MULTIPLI routines which create a new result file by adding or multiplying previously calculated files representing several propensities. The program is useful and efficient for identifying potential antigenic regions in a protein with the aim of raising antibodies against synthesized peptides which cross-react with the native protein.},
note = {0263-7855
Journal Article},
keywords = {Antigens/*chemistry Computer Graphics Epitopes/chemistry Proteins/*chemistry/*immunology *Software Software Design, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on proteins is described. This program and the associated ones are written in Turbo Pascal and run on IBM-PC compatibles. The program contains 22 normalized scales, corresponding to hydrophilicity, accessibility, flexibility, or secondary structure propensities. New scales are easily implemented. An hydrophobic moment procedure has also been implemented in order to determine amphiphilic helices. The program generates a result file where the values represent a particular physicochemical aspect of the studied protein. PREDITOP can display one or several result files by simple graphical super-imposition. Curve combinations can be done by the ADDITIO or MULTIPLI routines which create a new result file by adding or multiplying previously calculated files representing several propensities. The program is useful and efficient for identifying potential antigenic regions in a protein with the aim of raising antibodies against synthesized peptides which cross-react with the native protein.
Paoletti J, Mougel M, Tounekti N, Girard P M, Ehresmann C, Ehresmann B
Spontaneous dimerization of retroviral MoMuLV RNA Article de journal
Dans: Biochimie, vol. 75, no. 8, p. 681-686, 1993, ISBN: 8286441, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Biopolymers Molecular Sequence Data Moloney murine leukemia virus/*genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry Support
@article{,
title = {Spontaneous dimerization of retroviral MoMuLV RNA},
author = {J Paoletti and M Mougel and N Tounekti and P M Girard and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8286441},
isbn = {8286441},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {8},
pages = {681-686},
abstract = {The genome of the Moloney murine leukemia virus (MoMuLV) is composed of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Dimerization sequences are located within the PSI encapsidation domain. We present here an overview of the work we have performed on spontaneous dimerization of a MoMuLV RNA fragment encompassing the PSI domain in order to understand the mechanism by which retroviral RNA dimerization takes place. We present kinetical, thermodynamical and conformational evidence which leads to the conclusion that the PSI domain is a structurally independent domain and that conformational changes are triggered by the dimerization process. We conclude that at least one particular region (nucleotides 278-309) of the RNA is directly involved in the process while the conformation of some other regions is changed probably because of a long-range effect.},
note = {0300-9084
Journal Article},
keywords = {Base Sequence Biopolymers Molecular Sequence Data Moloney murine leukemia virus/*genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
The genome of the Moloney murine leukemia virus (MoMuLV) is composed of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Dimerization sequences are located within the PSI encapsidation domain. We present here an overview of the work we have performed on spontaneous dimerization of a MoMuLV RNA fragment encompassing the PSI domain in order to understand the mechanism by which retroviral RNA dimerization takes place. We present kinetical, thermodynamical and conformational evidence which leads to the conclusion that the PSI domain is a structurally independent domain and that conformational changes are triggered by the dimerization process. We conclude that at least one particular region (nucleotides 278-309) of the RNA is directly involved in the process while the conformation of some other regions is changed probably because of a long-range effect.
Oguiza J A, Malumbres M, Eriani G, Pisabarro A, Mateos L M, Martin F, Martin J F
Dans: J Bacteriol, vol. 175, no. 22, p. 7356-7362, 1993, ISBN: 8226683, (0021-9193 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN
@article{,
title = {A gene encoding arginyl-tRNA synthetase is located in the upstream region of the lysA gene in Brevibacterium lactofermentum: regulation of argS-lysA cluster expression by arginine},
author = {J A Oguiza and M Malumbres and G Eriani and A Pisabarro and L M Mateos and F Martin and J F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8226683},
isbn = {8226683},
year = {1993},
date = {1993-01-01},
journal = {J Bacteriol},
volume = {175},
number = {22},
pages = {7356-7362},
abstract = {The Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an M(r) of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria.},
note = {0021-9193
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an M(r) of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria.
Myslinski E, Schuster C, Krol A, Carbon P
Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements Article de journal
Dans: J Mol Biol, vol. 234, no. 2, p. 311-318, 1993, ISBN: 7693950, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN
@article{,
title = {Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements},
author = {E Myslinski and C Schuster and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7693950},
isbn = {7693950},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {2},
pages = {311-318},
abstract = {RNA polymerase III transcription of genes with external promoters only (e.g. U6 snRNA) or containing in addition an internal B box (selenocysteine tRNA(Sec)) is stimulated by upstream elements; a distal sequence element (DSE) for U6 or an activator element in the tRNA(Sec) gene. In contrast to the composite structure of the DSE which requires an octamer motif, the Xenopus tRNA(Sec) activator element contains an SPH motif only. In vivo transcription is optimally stimulated by SPH in an absolute octamer-independent manner since adding octamer does not induce superstimulation. Experiments performed in the work presented here led to the following observations. Co-operation between SPH and octamer motifs can be detected in two distinct cases: first when these motifs are placed in front of B box-less tRNA(Sec) or U6 external promoters and second, if either element of the external promoter (proximal sequence element or TATA element), or the SPH motif itself, are altered. Altogether, our data provide evidence that an SPH motif can function alone in an optimized promoter only. In contrast, an octamer becomes indispensable when the basal promoter is weak or disabled. It follows that module composition of Pol III transcriptional activator elements is dependent on the structure and strength of the promoter. This reveals the existence of cross-talk between activator and promoter elements, mediated by the bound transcription factors, which are thus able to compensate for each other in order to allow successful assembly of the transcription complex.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA polymerase III transcription of genes with external promoters only (e.g. U6 snRNA) or containing in addition an internal B box (selenocysteine tRNA(Sec)) is stimulated by upstream elements; a distal sequence element (DSE) for U6 or an activator element in the tRNA(Sec) gene. In contrast to the composite structure of the DSE which requires an octamer motif, the Xenopus tRNA(Sec) activator element contains an SPH motif only. In vivo transcription is optimally stimulated by SPH in an absolute octamer-independent manner since adding octamer does not induce superstimulation. Experiments performed in the work presented here led to the following observations. Co-operation between SPH and octamer motifs can be detected in two distinct cases: first when these motifs are placed in front of B box-less tRNA(Sec) or U6 external promoters and second, if either element of the external promoter (proximal sequence element or TATA element), or the SPH motif itself, are altered. Altogether, our data provide evidence that an SPH motif can function alone in an optimized promoter only. In contrast, an octamer becomes indispensable when the basal promoter is weak or disabled. It follows that module composition of Pol III transcriptional activator elements is dependent on the structure and strength of the promoter. This reveals the existence of cross-talk between activator and promoter elements, mediated by the bound transcription factors, which are thus able to compensate for each other in order to allow successful assembly of the transcription complex.
Myslinski E, Schuster C, Huet J, Sentenac A, Krol A, Carbon P
Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 25, p. 5852-5858, 1993, ISBN: 8290344, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics/metabolism Recombinant Proteins/metabolism Support, Animals Base Sequence DNA/metabolism DNA-Binding Proteins/*metabolism Molecular Sequence Data *Point Mutation Protein Binding RNA Polymerase III/*metabolism RNA, Genetic Xenopus laevis, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factors/*metabolism *Transcription, Transfer, Unité ARN
@article{,
title = {Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP},
author = {E Myslinski and C Schuster and J Huet and A Sentenac and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8290344},
isbn = {8290344},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {25},
pages = {5852-5858},
abstract = {The selenocysteine tRNA(Sec) gene possesses two external promoter elements, one of which is constituted by a strong TATA box. Point mutant analysis performed in this study led to the conclusion that the functional TATA promoter actually encompasses the sequence -34 GGGTATAAAAGG-23. Individual changes at T-31 do not affect transcription much. Position T-29 is less permissive to mutation since transversion to a G, for example, is less well tolerated than at T-31. Interestingly, a double point mutation, converting GG(-33/-32) to TT, causes abrogation of transcription in vivo and severe reduction of transcription in vitro with human TBP. Therefore, data obtained underscore the fact that, in the Xenopus tRNA(Sec), these two Gs are an integral part of the TATA promoter. Gel retardation experiments indicate that the GG to TT substitution, which led human TBP to lose its ability to support efficient transcription in vitro, correlates with the appearance of an altered pattern of retarded complexes. Altogether, the data presented in this report support a model in which TBP interacts directly with the TATA element of the tRNA(Sec) gene, in contrast to the type of interaction proposed for classical TATA-less tRNA genes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*genetics/metabolism Recombinant Proteins/metabolism Support, Animals Base Sequence DNA/metabolism DNA-Binding Proteins/*metabolism Molecular Sequence Data *Point Mutation Protein Binding RNA Polymerase III/*metabolism RNA, Genetic Xenopus laevis, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factors/*metabolism *Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The selenocysteine tRNA(Sec) gene possesses two external promoter elements, one of which is constituted by a strong TATA box. Point mutant analysis performed in this study led to the conclusion that the functional TATA promoter actually encompasses the sequence -34 GGGTATAAAAGG-23. Individual changes at T-31 do not affect transcription much. Position T-29 is less permissive to mutation since transversion to a G, for example, is less well tolerated than at T-31. Interestingly, a double point mutation, converting GG(-33/-32) to TT, causes abrogation of transcription in vivo and severe reduction of transcription in vitro with human TBP. Therefore, data obtained underscore the fact that, in the Xenopus tRNA(Sec), these two Gs are an integral part of the TATA promoter. Gel retardation experiments indicate that the GG to TT substitution, which led human TBP to lose its ability to support efficient transcription in vitro, correlates with the appearance of an altered pattern of retarded complexes. Altogether, the data presented in this report support a model in which TBP interacts directly with the TATA element of the tRNA(Sec) gene, in contrast to the type of interaction proposed for classical TATA-less tRNA genes.
Muller G, Gaspin C, Etienne A, Westhof E
Automatic display of RNA secondary structures Article de journal
Dans: Comput Appl Biosci, vol. 9, no. 5, p. 551-561, 1993, ISBN: 7507400, (0266-7061 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN
@article{,
title = {Automatic display of RNA secondary structures},
author = {G Muller and C Gaspin and A Etienne and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507400},
isbn = {7507400},
year = {1993},
date = {1993-01-01},
journal = {Comput Appl Biosci},
volume = {9},
number = {5},
pages = {551-561},
abstract = {A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.},
note = {0266-7061
Journal Article},
keywords = {16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.
Mougel M, Tounekti N, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C
Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 20, p. 4677-4684, 1993, ISBN: 8233816, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology
@article{,
title = {Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization},
author = {M Mougel and N Tounekti and J L Darlix and J Paoletti and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8233816},
isbn = {8233816},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {20},
pages = {4677-4684},
abstract = {Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region.},
note = {0305-1048
Journal Article},
keywords = {Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology},
pubstate = {published},
tppubtype = {article}
}
Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region.
Mougel M, Allmang C, Eyermann F, Cachia C, Ehresmann B, Ehresmann C
Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition Article de journal
Dans: Eur J Biochem, vol. 215, no. 3, p. 787-792, 1993, ISBN: 7689052, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN
@article{,
title = {Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition},
author = {M Mougel and C Allmang and F Eyermann and C Cachia and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7689052},
isbn = {7689052},
year = {1993},
date = {1993-01-01},
journal = {Eur J Biochem},
volume = {215},
number = {3},
pages = {787-792},
abstract = {Escherichia coli ribosomal protein S8 was previously shown to bind a 16S rRNA fragment (nucleotides 584-756) with the same affinity as the complete 16S rRNA, and to shield an irregular helical region (region C) [Mougel, M., Eyermann, F., Westhof, E., Romby, P., Expert-Bezancon, Ebel, J. P., Ehresmann, B. & Ehresmann, C. (1987). J. Mol. Biol. 198, 91-107]. Region C was postulated to display characteristic features: three bulged adenines (A595, A640 and A642), a non-canonical U598-U641 pair surrounded by two G.C pairs. In order to delineate the minimal RNA binding site, deletions were introduced by site-directed mutagenesis and short RNA fragments were synthesized. Their ability to bind S8 was assayed by filter binding. Our results show that the RNA binding site can be restricted to a short helical stem (588-605/633-651) containing region C. The second part of the work focused on region C and on the role of conserved nucleotides as potential determinants of S8 recognition. Single and double mutations were introduced by site-directed mutagenesis in fragment 584-756, and their effect on S8 binding was measured. It was found that the three bulged positions are essential and that adenines are required at positions 640 and 642. U598 is also crucial and the highly conserved G597.C643 pair cannot be inverted. These conserved nucleotides are either directly involved in the recognition process as direct contacts or required to maintain a specific conformation. The strong evolutionary pressure and the small number of positive mutants stress the high stringency of the recognition process.},
note = {0014-2956
Journal Article},
keywords = {16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Escherichia coli ribosomal protein S8 was previously shown to bind a 16S rRNA fragment (nucleotides 584-756) with the same affinity as the complete 16S rRNA, and to shield an irregular helical region (region C) [Mougel, M., Eyermann, F., Westhof, E., Romby, P., Expert-Bezancon, Ebel, J. P., Ehresmann, B. & Ehresmann, C. (1987). J. Mol. Biol. 198, 91-107]. Region C was postulated to display characteristic features: three bulged adenines (A595, A640 and A642), a non-canonical U598-U641 pair surrounded by two G.C pairs. In order to delineate the minimal RNA binding site, deletions were introduced by site-directed mutagenesis and short RNA fragments were synthesized. Their ability to bind S8 was assayed by filter binding. Our results show that the RNA binding site can be restricted to a short helical stem (588-605/633-651) containing region C. The second part of the work focused on region C and on the role of conserved nucleotides as potential determinants of S8 recognition. Single and double mutations were introduced by site-directed mutagenesis in fragment 584-756, and their effect on S8 binding was measured. It was found that the three bulged positions are essential and that adenines are required at positions 640 and 642. U598 is also crucial and the highly conserved G597.C643 pair cannot be inverted. These conserved nucleotides are either directly involved in the recognition process as direct contacts or required to maintain a specific conformation. The strong evolutionary pressure and the small number of positive mutants stress the high stringency of the recognition process.
Martin F, Eriani G, Eiler S, Moras D, Dirheimer G, Gangloff J
Overproduction and purification of native and queuine-lacking Escherichia coli tRNA(Asp). Role of the wobble base in tRNA(Asp) acylation Article de journal
Dans: J Mol Biol, vol. 234, no. 4, p. 965-974, 1993, ISBN: 8263943, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Activation Anticodon Aspartate-tRNA Ligase/metabolism Base Composition Base Sequence Cloning, Asp/chemistry/*metabolism Saccharomyces cerevisiae/metabolism Structure-Activity Relationship Support, ERIANI, Molecular Comparative Study Crystallography, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray Escherichia coli/*metabolism Guanine/*analogs & derivatives/chemistry Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Overproduction and purification of native and queuine-lacking Escherichia coli tRNA(Asp). Role of the wobble base in tRNA(Asp) acylation},
author = {F Martin and G Eriani and S Eiler and D Moras and G Dirheimer and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8263943},
isbn = {8263943},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {4},
pages = {965-974},
abstract = {Escherichia coli tRNA(Asp) was overproduced in E. coli up to 15-fold from a synthetic tRNA(Asp) gene placed in a plasmid under the dependence of an isopropyl-beta,D-thiogalactopyranoside-inducible promoter. Purification to nearly homogeneity (95%) was achieved after two HPLC DEAE-cellulose columns. E. coli tRNA(Asp)[G34] (having guanine instead of queuine at p